==> Synchronizing chroot copy [/home/leming/armv7/root] -> [leming]...done
==> Making package: r 4.5.1-1 (Fri Jun 13 09:24:35 2025)
==> Retrieving sources...
-> Found R-4.5.1.tar.gz
-> Found r.desktop
-> Found r.png
-> Found R.conf
==> WARNING: Skipping verification of source file PGP signatures.
==> Validating source files with sha256sums...
R-4.5.1.tar.gz ... Passed
r.desktop ... Passed
r.png ... Passed
R.conf ... Passed
==> Making package: r 4.5.1-1 (Fri Jun 13 09:24:55 2025)
==> Checking runtime dependencies...
==> Installing missing dependencies...
[?25lresolving dependencies...
looking for conflicting packages...
warning: dependency cycle detected:
warning: harfbuzz will be installed before its freetype2 dependency
Packages (35) fontconfig-2:2.16.2-1 freetype2-2.13.3-3 fribidi-1.0.16-2
graphite-1:1.3.14-4 harfbuzz-11.2.1-1 jbigkit-2.1-8
libdatrie-0.2.13-4 libice-1.1.2-1 libsm-1.2.6-1
libthai-0.1.29-3 libxau-1.0.12-1 libxcb-1.17.0-1
libxdmcp-1.1.5-1.1 libxext-1.3.6-1 libxft-2.3.9-1
libxrender-0.9.12-1 libxss-1.2.4-2 lzo-2.10-5 pixman-0.46.2-1
tcl-8.6.16-1 xcb-proto-1.17.0-3 xorgproto-2024.1-2
blas-3.12.1-2 cairo-1.18.4-1 lapack-3.12.1-2
libjpeg-turbo-3.1.0-1 libpng-1.6.48-1 libtiff-4.7.0-1
libx11-1.8.12-1 libxmu-1.2.1-1 libxt-1.3.1-1 pango-1:1.56.3-1
tk-8.6.16-1 unzip-6.0-22 zip-3.0-11
Total Download Size: 16.53 MiB
Total Installed Size: 62.53 MiB
:: Proceed with installation? [Y/n]
:: Retrieving packages...
lapack-3.12.1-2-armv7h downloading...
tcl-8.6.16-1-armv7h downloading...
libx11-1.8.12-1-armv7h downloading...
tk-8.6.16-1-armv7h downloading...
libxcb-1.17.0-1-armv7h downloading...
harfbuzz-11.2.1-1-armv7h downloading...
cairo-1.18.4-1-armv7h downloading...
libxt-1.3.1-1-armv7h downloading...
libtiff-4.7.0-1-armv7h downloading...
freetype2-2.13.3-3-armv7h downloading...
libjpeg-turbo-3.1.0-1-armv7h downloading...
pango-1:1.56.3-1-armv7h downloading...
fontconfig-2:2.16.2-1-armv7h downloading...
libthai-0.1.29-3-armv7h downloading...
xorgproto-2024.1-2-any downloading...
libpng-1.6.48-1-armv7h downloading...
blas-3.12.1-2-armv7h downloading...
pixman-0.46.2-1-armv7h downloading...
zip-3.0-11-armv7h downloading...
xcb-proto-1.17.0-3-any downloading...
unzip-6.0-22-armv7h downloading...
libdatrie-0.2.13-4-armv7h downloading...
libxext-1.3.6-1-armv7h downloading...
lzo-2.10-5-armv7h downloading...
libice-1.1.2-1-armv7h downloading...
graphite-1:1.3.14-4-armv7h downloading...
fribidi-1.0.16-2-armv7h downloading...
libxmu-1.2.1-1-armv7h downloading...
libxft-2.3.9-1-armv7h downloading...
jbigkit-2.1-8-armv7h downloading...
libsm-1.2.6-1-armv7h downloading...
libxrender-0.9.12-1-armv7h downloading...
libxdmcp-1.1.5-1.1-armv7h downloading...
libxss-1.2.4-2-armv7h downloading...
libxau-1.0.12-1-armv7h downloading...
checking keyring...
checking package integrity...
loading package files...
checking for file conflicts...
checking available disk space...
:: Processing package changes...
installing blas...
installing libpng...
installing graphite...
Optional dependencies for graphite
graphite-docs: Documentation
installing harfbuzz...
Optional dependencies for harfbuzz
harfbuzz-utils: utilities
installing freetype2...
installing fontconfig...
Creating fontconfig configuration...
Rebuilding fontconfig cache...
installing xcb-proto...
installing xorgproto...
installing libxdmcp...
installing libxau...
installing libxcb...
installing libx11...
installing libxext...
installing libxrender...
installing lzo...
installing pixman...
installing cairo...
installing lapack...
installing libjpeg-turbo...
installing jbigkit...
installing libtiff...
Optional dependencies for libtiff
freeglut: for using tiffgt
installing libice...
installing libsm...
installing libxt...
installing libxmu...
installing fribidi...
installing libdatrie...
installing libthai...
installing libxft...
installing pango...
installing tcl...
installing libxss...
installing tk...
installing unzip...
installing zip...
:: Running post-transaction hooks...
(1/3) Arming ConditionNeedsUpdate...
(2/3) Updating fontconfig configuration...
(3/3) Updating fontconfig cache...
[?25h==> Checking buildtime dependencies...
==> Installing missing dependencies...
[?25lresolving dependencies...
looking for conflicting packages...
Packages (45) aom-3.12.1-1 avahi-1:0.8+r194+g3f79789-3 dav1d-1.5.1-1
dvisvgm-3.3-1 gd-2.3.3-8 gdk-pixbuf2-2.42.12-2
ghostscript-10.05.1-2 giflib-5.2.2-2 hicolor-icon-theme-0.18-1
ijs-0.35-6 java-environment-common-3-6 java-runtime-common-3-6
jbig2dec-0.20-1 lcms2-2.17-1 libavif-1.3.0-1
libcups-2:2.4.12-2 libdaemon-0.14-6 libde265-1.0.16-1
libheif-1.19.8-3 libidn-1.43-1 libnet-2:1.3-1 libpaper-2.2.6-1
libsigsegv-2.15-1 libsynctex-2025.2-1 libwebp-1.5.0-1
libxaw-1.0.16-1 libxpm-3.5.17-2 libyuv-r2426+464c51a03-1
nspr-4.36-1 nss-3.112-1 openjpeg2-2.5.3-1
poppler-data-0.4.12-2 potrace-1.16-3 rav1e-0.7.1-1
shared-mime-info-2.4-2 texlive-basic-2025.2-1
texlive-bin-2025.2-1 texlive-latex-2025.2-1 woff2-1.0.2-6
x265-4.1-1 zziplib-0.13.80-1
gcc-fortran-14.2.1+r753+g1cd744a6828f-1 jdk-openjdk-24.0.1.u9-1
texlive-fontsrecommended-2025.2-1
texlive-latexrecommended-2025.2-1
Total Download Size: 269.77 MiB
Total Installed Size: 660.03 MiB
:: Proceed with installation? [Y/n]
:: Retrieving packages...
jdk-openjdk-24.0.1.u9-1-armv7h downloading...
texlive-fontsrecommended-2025.2-1-any downloading...
ghostscript-10.05.1-2-armv7h downloading...
texlive-bin-2025.2-1-armv7h downloading...
gcc-fortran-14.2.1+r753+g1cd744a6828f-1-armv7h downloading...
texlive-basic-2025.2-1-any downloading...
texlive-latexrecommended-2025.2-1-any downloading...
aom-3.12.1-1-armv7h downloading...
poppler-data-0.4.12-2-any downloading...
nss-3.112-1-armv7h downloading...
texlive-latex-2025.2-1-any downloading...
rav1e-0.7.1-1-armv7h downloading...
dvisvgm-3.3-1-armv7h downloading...
openjpeg2-2.5.3-1-armv7h downloading...
x265-4.1-1-armv7h downloading...
shared-mime-info-2.4-2-armv7h downloading...
libheif-1.19.8-3-armv7h downloading...
gdk-pixbuf2-2.42.12-2-armv7h downloading...
avahi-1:0.8+r194+g3f79789-3-armv7h downloading...
dav1d-1.5.1-1-armv7h downloading...
libxaw-1.0.16-1-armv7h downloading...
libidn-1.43-1-armv7h downloading...
libnet-2:1.3-1-armv7h downloading...
libwebp-1.5.0-1-armv7h downloading...
libavif-1.3.0-1-armv7h downloading...
libcups-2:2.4.12-2-armv7h downloading...
libde265-1.0.16-1-armv7h downloading...
lcms2-2.17-1-armv7h downloading...
nspr-4.36-1-armv7h downloading...
libyuv-r2426+464c51a03-1-armv7h downloading...
gd-2.3.3-8-armv7h downloading...
potrace-1.16-3-armv7h downloading...
libxpm-3.5.17-2-armv7h downloading...
zziplib-0.13.80-1-armv7h downloading...
giflib-5.2.2-2-armv7h downloading...
jbig2dec-0.20-1-armv7h downloading...
ijs-0.35-6-armv7h downloading...
woff2-1.0.2-6-armv7h downloading...
libpaper-2.2.6-1-armv7h downloading...
libsynctex-2025.2-1-armv7h downloading...
libdaemon-0.14-6-armv7h downloading...
hicolor-icon-theme-0.18-1-any downloading...
libsigsegv-2.15-1-armv7h downloading...
java-runtime-common-3-6-any downloading...
java-environment-common-3-6-any downloading...
checking keyring...
checking package integrity...
loading package files...
checking for file conflicts...
checking available disk space...
:: Processing package changes...
installing gcc-fortran...
installing java-runtime-common...
For the complete set of Java binaries to be available in your PATH,
you need to re-login or source /etc/profile
Please note that this package does not support forcing JAVA_HOME as former package java-common did
installing nspr...
installing nss...
installing lcms2...
installing libnet...
installing java-environment-common...
installing hicolor-icon-theme...
installing giflib...
installing jdk-openjdk...
Optional dependencies for jdk-openjdk
java-rhino: for some JavaScript support
alsa-lib: for basic sound support
gtk3: for the Gtk+ 3 look and feel - desktop usage
installing libxpm...
installing libwebp...
installing aom...
installing dav1d...
Optional dependencies for dav1d
dav1d-doc: HTML documentation
installing libyuv...
installing rav1e...
installing libavif...
installing libde265...
Optional dependencies for libde265
ffmpeg: for sherlock265
qt5-base: for sherlock265
sdl: dec265 YUV overlay output
installing x265...
installing libheif...
Optional dependencies for libheif
libjpeg-turbo: for heif-convert and heif-enc [installed]
libpng: for heif-convert and heif-enc [installed]
dav1d: dav1d encoder [installed]
ffmpeg: hardware decode
rav1e: rav1e encoder [installed]
installing gd...
Optional dependencies for gd
perl: bdftogd script [installed]
installing libpaper...
installing libsigsegv...
installing libsynctex...
installing libxaw...
installing potrace...
installing zziplib...
installing texlive-bin...
Optional dependencies for texlive-bin
psutils: to manipulate the output of dvips
installing texlive-basic...
Optional dependencies for texlive-basic
perl-tk: for the tlmgr GUI
biber: for bibliography processing
installing texlive-fontsrecommended...
installing libdaemon...
installing avahi...
Optional dependencies for avahi
gtk3: avahi-discover, avahi-discover-standalone, bshell, bssh, bvnc
libevent: libevent bindings [installed]
nss-mdns: NSS support for mDNS
python-dbus: avahi-bookmarks, avahi-discover
python-gobject: avahi-bookmarks, avahi-discover
python-twisted: avahi-bookmarks
qt5-base: qt5 bindings
installing libcups...
installing jbig2dec...
installing ijs...
installing openjpeg2...
installing libidn...
installing poppler-data...
installing shared-mime-info...
installing gdk-pixbuf2...
Optional dependencies for gdk-pixbuf2
libwmf: Load .wmf and .apm
libopenraw: Load .dng, .cr2, .crw, .nef, .orf, .pef, .arw, .erf, .mrw, and
.raf
libavif: Load .avif [installed]
libheif: Load .heif, .heic, and .avif [installed]
libjxl: Load .jxl
librsvg: Load .svg, .svgz, and .svg.gz
webp-pixbuf-loader: Load .webp
installing ghostscript...
Optional dependencies for ghostscript
gtk3: needed for gsx
installing woff2...
installing dvisvgm...
Optional dependencies for dvisvgm
mupdf-tools: to process PDF files
installing texlive-latex...
installing texlive-latexrecommended...
:: Running post-transaction hooks...
( 1/11) Creating system user accounts...
Creating group 'avahi' with GID 971.
Creating user 'avahi' (Avahi mDNS/DNS-SD daemon) with UID 971 and GID 971.
( 2/11) Reloading system manager configuration...
Skipped: Current root is not booted.
( 3/11) Arming ConditionNeedsUpdate...
( 4/11) Updating the MIME type database...
( 5/11) Updating TeXLive filename database...
mktexlsr: Updating /etc/texmf/ls-R...
mktexlsr: Updating /usr/share/texmf-dist/ls-R...
mktexlsr: Updating /var/lib/texmf/ls-R...
mktexlsr: Done.
( 6/11) Updating TeXLive format files...
( 7/11) Updating TeXLive font maps...
mktexlsr: Updating /etc/texmf/ls-R...
mktexlsr: Updating /usr/share/texmf-dist/ls-R...
mktexlsr: Updating /var/lib/texmf/ls-R...
mktexlsr: Done.
( 8/11) Reloading system bus configuration...
Skipped: Current root is not booted.
( 9/11) Updating fontconfig cache...
(10/11) Probing GDK-Pixbuf loader modules...
(11/11) Updating the info directory file...
[?25h==> Retrieving sources...
-> Found R-4.5.1.tar.gz
-> Found r.desktop
-> Found r.png
-> Found R.conf
==> WARNING: Skipping all source file integrity checks.
==> Extracting sources...
-> Extracting R-4.5.1.tar.gz with bsdtar
==> Starting prepare()...
==> Starting build()...
checking build system type... armv7l-unknown-linux-gnueabihf
checking host system type... armv7l-unknown-linux-gnueabihf
loading site script './config.site'
loading build-specific script './config.site'
checking for pwd... /usr/bin/pwd
checking whether builddir is srcdir... yes
checking whether ln -s works... yes
checking for ar... ar
checking for a BSD-compatible install... /usr/bin/install -c
checking for sed... /usr/bin/sed
checking for which... /usr/bin/which
checking for less... /usr/bin/less
checking for gtar... no
checking for gnutar... no
checking for tar... /usr/bin/tar
checking for tex... /usr/bin/tex
checking for pdftex... /usr/bin/pdftex
checking for pdflatex... /usr/bin/pdflatex
checking for makeindex... /usr/bin/makeindex
checking for texi2any... /usr/bin/texi2any
checking whether texi2any version is at least 6.1... yes
checking for ginstall-info... no
checking for install-info... /usr/bin/install-info
checking for texi2dvi... /usr/bin/texi2dvi
checking for kpsewhich... /usr/bin/kpsewhich
checking for latex inconsolata package... missing
configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes and package manuals will not be rendered optimally
checking for unzip... /usr/bin/unzip
checking for zip... /usr/bin/zip
checking for gzip... /usr/bin/gzip
checking for bzip2... /usr/bin/bzip2
checking for xdg-open... no
checking for firefox... no
checking for mozilla... no
checking for epiphany... no
checking for galeon... no
checking for opera... no
checking for kfmclient... no
checking for gnome-moz-remote... no
checking for open... no
checking for lynx... no
checking for links... no
configure: WARNING: I could not determine a browser
checking for xdg-open... no
checking for acroread... no
checking for acroread4... no
checking for evince... no
checking for atril... no
checking for xpdf... no
checking for gv... no
checking for gnome-gv... no
checking for ggv... no
checking for okular... no
checking for kpdf... no
checking for open... no
checking for gpdf... no
checking for kghostview... no
configure: WARNING: I could not determine a PDF viewer
checking for working aclocal... found
checking for working autoconf... found
checking for working autoheader... found
checking for bison... bison -y
checking for notangle... false
checking for realpath... /usr/bin/realpath
checking for pkg-config... /usr/bin/pkg-config
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for wchar.h... yes
checking for minix/config.h... no
checking for sys/time.h... yes
checking for sys/param.h... yes
checking whether it is safe to define __EXTENSIONS__... yes
checking whether _XOPEN_SOURCE should be defined... no
checking whether gcc is a C23 compiler... no
checking whether gcc -std=gnu23 is a C23 compiler... yes
checking how to run the C preprocessor... gcc -std=gnu23 -E
looking for a modern Fortran compiler
checking for gfortran... gfortran
checking whether the compiler supports GNU Fortran... yes
checking whether gfortran accepts -g... yes
checking for g++... g++
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking whether g++ -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -Wp,-D_GLIBCXX_ASSERTIONS -ffat-lto-objects can compile C++ code... yes
checking how to run the C++ preprocessor... g++ -E
checking whether __attribute__((visibility())) is supported... yes
checking whether gcc -std=gnu23 accepts -fvisibility... yes
checking whether g++ accepts -fvisibility... yes
checking whether gfortran accepts -fvisibility... yes
checking for gcc... gcc
checking whether the compiler supports GNU Objective C... no
checking whether gcc accepts -g... no
checking whether gcc -std=gnu17 is a C17 compiler... yes
checking whether gcc -std=gnu90 is a C90 compiler... yes
checking whether gcc -std=gnu99 is a C99 compiler... yes
checking how to print strings... printf
checking for a sed that does not truncate output... (cached) /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc -std=gnu23... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking how to convert armv7l-unknown-linux-gnueabihf file names to armv7l-unknown-linux-gnueabihf format... func_convert_file_noop
checking how to convert armv7l-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking for gawk... gawk
checking command to parse /usr/bin/nm -B output from gcc -std=gnu23 object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc -std=gnu23 supports -fno-rtti -fno-exceptions... no
checking for gcc -std=gnu23 option to produce PIC... -fPIC -DPIC
checking if gcc -std=gnu23 PIC flag -fPIC -DPIC works... yes
checking if gcc -std=gnu23 static flag -static works... yes
checking if gcc -std=gnu23 supports -c -o file.o... yes
checking if gcc -std=gnu23 supports -c -o file.o... (cached) yes
checking whether the gcc -std=gnu23 linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for gfortran option to produce PIC... -fPIC
checking if gfortran PIC flag -fPIC works... yes
checking if gfortran static flag -static works... no
checking if gfortran supports -c -o file.o... yes
checking if gfortran supports -c -o file.o... (cached) yes
checking whether the gfortran linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for cos in -lm... yes
checking for sin in -lm... yes
checking for dlopen in -ldl... yes
checking for readline/history.h... yes
checking for readline/readline.h... yes
checking for rl_callback_read_char in -lreadline... yes
checking for history_truncate_file... yes
checking for tilde_expand_word... yes
checking whether rl_completion_matches exists and is declared... yes
checking whether rl_resize_terminal exists and is declared... yes
checking whether rl_sort_completion_matches exists and is declared... yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for dlfcn.h... (cached) yes
checking for fcntl.h... yes
checking for glob.h... yes
checking for grp.h... yes
checking for pwd.h... yes
checking for sched.h... yes
checking for strings.h... (cached) yes
checking for sys/resource.h... yes
checking for sys/select.h... yes
checking for sys/socket.h... yes
checking for sys/stat.h... (cached) yes
checking for sys/time.h... (cached) yes
checking for sys/times.h... yes
checking for sys/utsname.h... yes
checking for unistd.h... (cached) yes
checking for utime.h... yes
checking for arpa/inet.h... yes
checking for elf.h... yes
checking for features.h... yes
checking for floatingpoint.h... no
checking for langinfo.h... yes
checking for netdb.h... yes
checking for netinet/in.h... yes
checking for sys/param.h... (cached) yes
checking for stdalign.h... yes
checking for errno.h... yes
checking for inttypes.h... (cached) yes
checking for limits.h... yes
checking for locale.h... yes
checking for stdarg.h... yes
checking for stdbool.h... yes
checking for stdint.h... (cached) yes
checking for string.h... (cached) yes
checking for gcc -std=gnu23 options needed to detect all undeclared functions... none needed
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking for egrep -e... (cached) /usr/bin/grep -E
checking for GNU C library with version >= 2... yes
checking for uint64_t... yes
checking for int64_t... yes
checking for int_fast64_t... yes
checking for pid_t... yes
checking for size_t... yes
checking whether SIZE_MAX is declared... yes
checking for blkcnt_t... yes
checking for type of socket length... socklen_t *
checking for stack_t... yes
checking for intptr_t... yes
checking for uintptr_t... yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking size of int... 4
checking size of long... 4
checking size of long long... 8
checking size of double... 8
checking size of size_t... 4
checking for C stack direction... down
checking size of long double... 8
checking whether we can compute C Make dependencies... yes, using $(CC) -MM
checking whether gcc -std=gnu23 supports -c -o FILE.lo... yes
checking for gcc -std=gnu23 option to support OpenMP... -fopenmp
checking how to get verbose linking output from gfortran... -v
checking for Fortran libraries of gfortran... -L/usr/lib/gcc/armv7l-unknown-linux-gnueabihf/14.2.1 -L/usr/lib/gcc/armv7l-unknown-linux-gnueabihf/14.2.1/../../.. -lgfortran -lm
checking how to get verbose linking output from gcc -std=gnu23... -v
checking for C libraries of gcc -std=gnu23... -L/usr/lib/gcc/armv7l-unknown-linux-gnueabihf/14.2.1 -L/usr/lib/gcc/armv7l-unknown-linux-gnueabihf/14.2.1/../../.. -lgcc_s
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore
checking whether gfortran appends underscores to external names... yes
checking whether gfortran appends extra underscores to external names... no
checking whether mixed C/Fortran code can be run... yes
checking whether gfortran and gcc -std=gnu23 agree on int and double... yes
checking whether gfortran and gcc -std=gnu23 agree on double complex... yes
checking for gfortran option to support OpenMP... -fopenmp
checking whether g++ accepts -M for generating dependencies... yes
checking whether we can compute ObjC Make dependencies... no
checking for type of 'hidden' Fortran character lengths... size_t
checking for xmkmf... no
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checking whether g++ supports C++14 features with -std=gnu++14... yes
checking whether g++ supports C++17 features with -std=gnu++17... yes
checking whether g++ supports C++20 features with -std=gnu++20... yes
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checking whether g++ -std=gnu++17 can compile ObjC++... no
checking whether can compile ObjC++... no
checking for Objective C++ compiler... no working ObjC++ compiler found
checking for g++ -std=gnu++17 option to support OpenMP... -fopenmp
checking for option providing pthread_kill... none required
checking whether POSIX threads are supported... yes
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checking for tanpi... yes
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checking whether unsetenv exists and is declared... yes
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checking whether access exists and is declared... yes
checking whether chdir exists and is declared... yes
checking whether execv exists and is declared... yes
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checking whether readlink exists and is declared... yes
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checking whether sysconf exists and is declared... yes
checking whether sched_setaffinity exists and is declared... yes
checking whether sched_getaffinity exists and is declared... yes
checking whether utime exists and is declared... yes
checking whether utimensat exists and is declared... yes
checking for clock_gettime in -lrt... yes
checking whether clock_gettime exists and is declared... yes
checking whether timespec_get exists and is declared... yes
checking for putenv... yes
checking whether putenv is declared... yes
checking for vasprintf... yes
checking whether vasprintf is declared... yes
checking for mempcpy... yes
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checking whether realpath is declared... yes
checking whether glob exists and is declared... yes
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checking for dlsym... yes
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checking whether RTLD_NEXT is declared... yes
checking for thread.h... no
checking whether thr_stksegment exists and is declared... no
checking for stpcpy... yes
checking for isnan... yes
checking whether isfinite is declared... yes
checking whether isnan is declared... yes
checking whether you have IEEE 754 floating-point arithmetic... yes
checking whether putenv("FOO") can unset an environment variable... yes
checking whether putenv("FOO=") can unset an environment variable... no
checking for nl_langinfo and CODESET... yes
checking for mkdtemp... yes
checking for strdup... yes
checking for strncasecmp... yes
checking whether mkdtemp is declared... yes
checking whether strdup is declared... yes
checking whether strncasecmp is declared... yes
checking for library containing connect... none required
checking for library containing gethostbyname... none required
checking for working calloc... yes
checking for working isfinite... yes
checking for working log1p... yes
checking whether ftell works correctly on files opened for append... yes
checking for working sigaction... yes
checking whether the base type of an enum can be specified... yes
checking whether mktime, gmtime, localtime work correctly in 2020... yes
checking whether mktime sets errno... yes
checking whether mktime works correctly after 2037... no
checking whether mktime works correctly before 1902... no
checking whether mktime works correctly in 1969... yes
checking for complex.h... yes
checking for double complex... yes
checking whether C99 double complex is supported... yes
checking whether cabs exists and is declared... yes
checking whether carg exists and is declared... yes
checking whether cexp exists and is declared... yes
checking whether clog exists and is declared... yes
checking whether csqrt exists and is declared... yes
checking whether cpow exists and is declared... yes
checking whether ccos exists and is declared... yes
checking whether csin exists and is declared... yes
checking whether ctan exists and is declared... yes
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checking whether casin exists and is declared... yes
checking whether catan exists and is declared... yes
checking whether ccosh exists and is declared... yes
checking whether csinh exists and is declared... yes
checking whether ctanh exists and is declared... yes
checking for working ctanh... yes
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checking whether 'struct tm' includes tm_gmtoff... yes
configure: searching for an external BLAS
configure: searching for BLAS in default libraries
checking for dgemm_... no
configure: searching for OpenBLAS
checking for sgemm_ in -lopenblas... no
configure: searching for BLIS
checking for sgemm_ in -lblis... no
configure: searching for ATLAS
checking for ATL_xerbla in -latlas... no
configure: searching for PhiPACK
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configure: searching for IBM ESSL
checking for dgemm_ in -lblas... (cached) yes
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configure: searching for generic BLAS library
checking for dgemm_ in -lblas... (cached) yes
checking whether double complex BLAS can be used... yes
checking whether the BLAS is complete... yes
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checking whether iconv accepts "CP1252"... yes
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checking for iconv declaration...
extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft);
checking for wchar.h... (cached) yes
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checking for X... libraries , headers
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking for X11/Intrinsic.h... yes
checking for XtToolkitInitialize in -lXt... yes
using X11 ... yes
checking for KeySym... yes
checking for X11/Xmu/Atoms.h... yes
checking for XmuInternAtom in -lXmu... yes
checking whether pkg-config knows about cairo and pango... yes
checking whether cairo including pango is >= 1.2 and works... yes
checking for tclConfig.sh... no
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checking for tkConfig.sh... no
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checking for tcl.h... yes
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checking whether compiling/linking Tcl/Tk code works... yes
checking for BSD networking... yes
checking for rpc/types.h... no
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checking for tirpc/rpc/xdr.h... yes
checking for XDR library... -ltirpc
checking for XDR support... yes
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checking for zlib.h... yes
checking if zlib version >= 1.2.5... yes
checking whether zlib support suffices... yes
checking for BZ2_bzlibVersion in -lbz2... yes
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checking for lzma_version_number in -llzma... yes
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checking for zstd.h... yes
checking if zstd version >= 1.3.3... yes
checking for ZSTD_decompressBound... yes
checking for libdeflate.h... no
checking for pcre2.h... yes
checking for pcre2_compile_8 in -lpcre2-8... yes
checking if PCRE2 has Unicode support... yes
checking whether PCRE support suffices... yes
checking for curl-config... /usr/bin/curl-config
checking libcurl version ... 8.14.1
checking for curl/curl.h... yes
checking if libcurl is >= 7.28.0... yes
checking if libcurl supports https... yes
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checking if jpeglib version >= 6b... yes
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checking if libpng version >= 1.2.7... yes
checking for png_create_write_struct in -lpng... yes
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checking for tiffio.h... yes
checking for TIFFOpen in -ltiff... yes
checking whether leap seconds are treated according to POSIX... yes
checking for inline... inline
checking for struct stat.st_atim.tv_nsec... yes
checking whether struct stat.st_atim is of type struct timespec... yes
checking for setitimer... yes
checking for gcc -std=gnu23 option to enable large file support... -D_FILE_OFFSET_BITS=64
checking for declarations of fseeko and ftello... yes
checking whether KERN_USRSTACK sysctl is supported... no
checking for visible __lib_stack_end... yes
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checking for lp... no
checking for paperconf... /usr/bin/paperconf
checking for Fortran flag to compile .f90 files... none
checking for Fortran flag to compile .f95 files... none
checking for gfortran option to support OpenMP... (cached) -fopenmp
checking for recommended packages... yes
checking whether NLS is requested... yes
Configuring src/extra/intl directory
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking whether we are using the GNU C Library 2 or newer... yes
checking for ranlib... (cached) ranlib
checking for simple visibility declarations... yes
checking for stdint.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking whether integer division by zero raises SIGFPE... no
checking for inttypes.h... yes
checking for unsigned long long int... yes
checking for inttypes.h... (cached) yes
checking whether the inttypes.h PRIxNN macros are broken... no
checking for ld used by gcc -std=gnu23... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for shared library run path origin... done
checking whether imported symbols can be declared weak... yes
checking for multithread API to use... none
checking for argz.h... yes
checking for inttypes.h... (cached) yes
checking for limits.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... (cached) yes
checking for getcwd... yes
checking for getegid... yes
checking for geteuid... yes
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checking for getuid... yes
checking for mempcpy... (cached) yes
checking for munmap... yes
checking for stpcpy... (cached) yes
checking for strcasecmp... yes
checking for strdup... (cached) yes
checking for strtoul... yes
checking for tsearch... yes
checking for argz_count... yes
checking for argz_stringify... yes
checking for argz_next... yes
checking for __fsetlocking... yes
checking whether feof_unlocked is declared... yes
checking whether fgets_unlocked is declared... yes
checking for iconv... (cached) yes
checking for iconv declaration... (cached)
extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft);
checking for NL_LOCALE_NAME macro... yes
checking for bison... bison
checking version of bison... 3.8.2, ok
checking for long long int... yes
checking for long double... yes
checking for wchar_t... yes
checking for wint_t... yes
checking for intmax_t... yes
checking whether printf() supports POSIX/XSI format strings... yes
checking whether we are using the GNU C Library 2.1 or newer... yes
checking for stdint.h... (cached) yes
checking for SIZE_MAX... yes
checking for stdint.h... (cached) yes
checking for CFPreferencesCopyAppValue... no
checking for CFLocaleCopyCurrent... no
checking for ptrdiff_t... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for asprintf... yes
checking for fwprintf... yes
checking for putenv... (cached) yes
checking for setenv... yes
checking for setlocale... yes
checking for snprintf... yes
checking for wcslen... yes
checking whether _snprintf is declared... no
checking whether _snwprintf is declared... no
checking whether getc_unlocked is declared... yes
checking for nl_langinfo and CODESET... (cached) yes
checking for LC_MESSAGES... yes
checking for CFPreferencesCopyAppValue... (cached) no
checking for CFLocaleCopyCurrent... (cached) no
checking whether included gettext is requested... no
checking for GNU gettext in libc... yes
checking whether to use NLS... yes
checking where the gettext function comes from... libc
Finished configuring src/extra/intl directory
checking whether OpenMP SIMD reduction is supported... yes
using as R_SHELL for scripts ... /bin/sh
configure: creating ./config.status
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configure: WARNING: --with-libdeflate-compression requires libdeflate
R is now configured for armv7l-unknown-linux-gnueabihf
Source directory: .
Installation directory: /usr
C compiler: gcc -std=gnu23 -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects
Fortran fixed-form compiler: gfortran -g -O2
Default C++ compiler: g++ -std=gnu++17 -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -Wp,-D_GLIBCXX_ASSERTIONS -ffat-lto-objects
Fortran free-form compiler: gfortran -g -O2
Obj-C compiler:
Interfaces supported: X11, tcltk
External libraries: pcre2, readline, BLAS(generic), LAPACK(generic), curl
Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU
Options enabled: shared R library, R profiling, memory profiling
Capabilities skipped:
Options not enabled: shared BLAS
Recommended packages: yes
configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes and package manuals will not be rendered optimally
configure: WARNING: I could not determine a browser
configure: WARNING: I could not determine a PDF viewer
configure: WARNING: 32-bit build -- this is little tested
make[1]: Entering directory '/build/r/src/R-4.5.1/m4'
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creating src/scripts/R.fe
make[3]: Entering directory '/build/r/src/R-4.5.1/src/scripts'
mkdir -p -- ../../bin
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make[2]: Entering directory '/build/r/src/R-4.5.1/src/include'
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make[3]: Leaving directory '/build/r/src/R-4.5.1/src/include/R_ext'
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make[2]: Entering directory '/build/r/src/R-4.5.1/src/extra'
make[3]: Entering directory '/build/r/src/R-4.5.1/src/extra/tre'
make[4]: Entering directory '/build/r/src/R-4.5.1/src/extra/tre'
making regcomp.d from regcomp.c
making regerror.d from regerror.c
making regexec.d from regexec.c
making tre-ast.d from tre-ast.c
making tre-compile.d from tre-compile.c
making tre-match-approx.d from tre-match-approx.c
making tre-match-backtrack.d from tre-match-backtrack.c
making tre-match-parallel.d from tre-match-parallel.c
making tre-mem.d from tre-mem.c
making tre-parse.d from tre-parse.c
making tre-stack.d from tre-stack.c
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/extra/tre'
make[4]: Entering directory '/build/r/src/R-4.5.1/src/extra/tre'
gcc -std=gnu23 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fvisibility=hidden -c regcomp.c -o regcomp.o
gcc -std=gnu23 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fvisibility=hidden -c regerror.c -o regerror.o
gcc -std=gnu23 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fvisibility=hidden -c regexec.c -o regexec.o
gcc -std=gnu23 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fvisibility=hidden -c tre-ast.c -o tre-ast.o
gcc -std=gnu23 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fvisibility=hidden -c tre-compile.c -o tre-compile.o
gcc -std=gnu23 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fvisibility=hidden -c tre-match-approx.c -o tre-match-approx.o
gcc -std=gnu23 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fvisibility=hidden -c tre-match-backtrack.c -o tre-match-backtrack.o
gcc -std=gnu23 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fvisibility=hidden -c tre-match-parallel.c -o tre-match-parallel.o
gcc -std=gnu23 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fvisibility=hidden -c tre-mem.c -o tre-mem.o
gcc -std=gnu23 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fvisibility=hidden -c tre-parse.c -o tre-parse.o
gcc -std=gnu23 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fvisibility=hidden -c tre-stack.c -o tre-stack.o
ar -cr libtre.a regcomp.o regerror.o regexec.o tre-ast.o tre-compile.o tre-match-approx.o tre-match-backtrack.o tre-match-parallel.o tre-mem.o tre-parse.o tre-stack.o
ranlib libtre.a
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/extra/tre'
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/extra/tre'
make[2]: Leaving directory '/build/r/src/R-4.5.1/src/extra'
make[2]: Entering directory '/build/r/src/R-4.5.1/src/appl'
making interv.d from interv.c
making integrate.d from integrate.c
making maxcol.d from maxcol.c
making optim.d from optim.c
making pretty.d from pretty.c
making uncmin.d from uncmin.c
make[3]: Entering directory '/build/r/src/R-4.5.1/src/appl'
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c integrate.c -o integrate.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c interv.c -o interv.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c maxcol.c -o maxcol.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c optim.c -o optim.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pretty.c -o pretty.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c uncmin.c -o uncmin.o
gfortran -fpic -g -O2 -c dchdc.f -o dchdc.o
gfortran -fpic -g -O2 -c dpbfa.f -o dpbfa.o
gfortran -fpic -g -O2 -c dpbsl.f -o dpbsl.o
gfortran -fpic -g -O2 -c dpoco.f -o dpoco.o
gfortran -fpic -g -O2 -c dpodi.f -o dpodi.o
gfortran -fpic -g -O2 -c dpofa.f -o dpofa.o
gfortran -fpic -g -O2 -c dposl.f -o dposl.o
gfortran -fpic -g -O2 -c dqrdc.f -o dqrdc.o
gfortran -fpic -g -O2 -c dqrdc2.f -o dqrdc2.o
gfortran -fpic -g -O2 -c dqrls.f -o dqrls.o
gfortran -fpic -g -O2 -c dqrsl.f -o dqrsl.o
gfortran -fpic -g -O2 -c dqrutl.f -o dqrutl.o
gfortran -fpic -g -O2 -c dsvdc.f -o dsvdc.o
gfortran -fpic -g -O2 -c dtrco.f -o dtrco.o
gfortran -fpic -g -O2 -c dtrsl.f -o dtrsl.o
ar -cr libappl.a integrate.o interv.o maxcol.o optim.o pretty.o uncmin.o dchdc.o dpbfa.o dpbsl.o dpoco.o dpodi.o dpofa.o dposl.o dqrdc.o dqrdc2.o dqrls.o dqrsl.o dqrutl.o dsvdc.o dtrco.o dtrsl.o
ranlib libappl.a
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/appl'
make[2]: Leaving directory '/build/r/src/R-4.5.1/src/appl'
make[2]: Entering directory '/build/r/src/R-4.5.1/src/nmath'
making mlutils.d from mlutils.c
making d1mach.d from d1mach.c
making i1mach.d from i1mach.c
making fmax2.d from fmax2.c
making fmin2.d from fmin2.c
making fprec.d from fprec.c
making fround.d from fround.c
making ftrunc.d from ftrunc.c
making sign.d from sign.c
making fsign.d from fsign.c
making imax2.d from imax2.c
making imin2.d from imin2.c
making chebyshev.d from chebyshev.c
making log1p.d from log1p.c
making lgammacor.d from lgammacor.c
making gammalims.d from gammalims.c
making stirlerr.d from stirlerr.c
making bd0.d from bd0.c
making gamma.d from gamma.c
making lgamma.d from lgamma.c
making beta.d from beta.c
making gamma_cody.d from gamma_cody.c
making lbeta.d from lbeta.c
making polygamma.d from polygamma.c
making cospi.d from cospi.c
making bessel_i.d from bessel_i.c
making bessel_j.d from bessel_j.c
making bessel_k.d from bessel_k.c
making bessel_y.d from bessel_y.c
making choose.d from choose.c
making snorm.d from snorm.c
making sexp.d from sexp.c
making dgamma.d from dgamma.c
making pgamma.d from pgamma.c
making qgamma.d from qgamma.c
making rgamma.d from rgamma.c
making dbeta.d from dbeta.c
making pbeta.d from pbeta.c
making qbeta.d from qbeta.c
making rbeta.d from rbeta.c
making dunif.d from dunif.c
making punif.d from punif.c
making qunif.d from qunif.c
making runif.d from runif.c
making dnorm.d from dnorm.c
making pnorm.d from pnorm.c
making qnorm.d from qnorm.c
making rnorm.d from rnorm.c
making dlnorm.d from dlnorm.c
making plnorm.d from plnorm.c
making qlnorm.d from qlnorm.c
making rlnorm.d from rlnorm.c
making df.d from df.c
making pf.d from pf.c
making qf.d from qf.c
making rf.d from rf.c
making dnf.d from dnf.c
making dt.d from dt.c
making pt.d from pt.c
making qt.d from qt.c
making rt.d from rt.c
making dnt.d from dnt.c
making dchisq.d from dchisq.c
making pchisq.d from pchisq.c
making qchisq.d from qchisq.c
making rchisq.d from rchisq.c
making rnchisq.d from rnchisq.c
making dbinom.d from dbinom.c
making pbinom.d from pbinom.c
making qbinom.d from qbinom.c
making rbinom.d from rbinom.c
making rmultinom.d from rmultinom.c
making dcauchy.d from dcauchy.c
making pcauchy.d from pcauchy.c
making qcauchy.d from qcauchy.c
making rcauchy.d from rcauchy.c
making dexp.d from dexp.c
making pexp.d from pexp.c
making qexp.d from qexp.c
making rexp.d from rexp.c
making dgeom.d from dgeom.c
making pgeom.d from pgeom.c
making qgeom.d from qgeom.c
making rgeom.d from rgeom.c
making dhyper.d from dhyper.c
making phyper.d from phyper.c
making qhyper.d from qhyper.c
making rhyper.d from rhyper.c
making dnbinom.d from dnbinom.c
making pnbinom.d from pnbinom.c
making qnbinom.d from qnbinom.c
making qnbinom_mu.d from qnbinom_mu.c
making rnbinom.d from rnbinom.c
making dpois.d from dpois.c
making ppois.d from ppois.c
making qpois.d from qpois.c
making rpois.d from rpois.c
making dweibull.d from dweibull.c
making pweibull.d from pweibull.c
making qweibull.d from qweibull.c
making rweibull.d from rweibull.c
making dlogis.d from dlogis.c
making plogis.d from plogis.c
making qlogis.d from qlogis.c
making rlogis.d from rlogis.c
making dnchisq.d from dnchisq.c
making pnchisq.d from pnchisq.c
making qnchisq.d from qnchisq.c
making dnbeta.d from dnbeta.c
making pnbeta.d from pnbeta.c
making qnbeta.d from qnbeta.c
making pnf.d from pnf.c
making pnt.d from pnt.c
making qnf.d from qnf.c
making qnt.d from qnt.c
making ptukey.d from ptukey.c
making qtukey.d from qtukey.c
making toms708.d from toms708.c
making wilcox.d from wilcox.c
making signrank.d from signrank.c
make[3]: Entering directory '/build/r/src/R-4.5.1/src/nmath'
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c mlutils.c -o mlutils.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c d1mach.c -o d1mach.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c i1mach.c -o i1mach.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c fmax2.c -o fmax2.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c fmin2.c -o fmin2.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c fprec.c -o fprec.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c fround.c -o fround.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c ftrunc.c -o ftrunc.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c sign.c -o sign.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c fsign.c -o fsign.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c imax2.c -o imax2.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c imin2.c -o imin2.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c chebyshev.c -o chebyshev.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c log1p.c -o log1p.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c lgammacor.c -o lgammacor.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c gammalims.c -o gammalims.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c stirlerr.c -o stirlerr.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c bd0.c -o bd0.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c gamma.c -o gamma.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c lgamma.c -o lgamma.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c gamma_cody.c -o gamma_cody.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c beta.c -o beta.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c lbeta.c -o lbeta.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c polygamma.c -o polygamma.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c cospi.c -o cospi.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c bessel_i.c -o bessel_i.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c bessel_j.c -o bessel_j.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c bessel_k.c -o bessel_k.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c bessel_y.c -o bessel_y.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c choose.c -o choose.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c snorm.c -o snorm.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c sexp.c -o sexp.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dgamma.c -o dgamma.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pgamma.c -o pgamma.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qgamma.c -o qgamma.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rgamma.c -o rgamma.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dbeta.c -o dbeta.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pbeta.c -o pbeta.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qbeta.c -o qbeta.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rbeta.c -o rbeta.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dunif.c -o dunif.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c punif.c -o punif.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qunif.c -o qunif.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c runif.c -o runif.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dnorm.c -o dnorm.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pnorm.c -o pnorm.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qnorm.c -o qnorm.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rnorm.c -o rnorm.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dlnorm.c -o dlnorm.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c plnorm.c -o plnorm.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qlnorm.c -o qlnorm.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rlnorm.c -o rlnorm.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c df.c -o df.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pf.c -o pf.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qf.c -o qf.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rf.c -o rf.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dnf.c -o dnf.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dt.c -o dt.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pt.c -o pt.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qt.c -o qt.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rt.c -o rt.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dnt.c -o dnt.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dchisq.c -o dchisq.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pchisq.c -o pchisq.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qchisq.c -o qchisq.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rchisq.c -o rchisq.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rnchisq.c -o rnchisq.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dbinom.c -o dbinom.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pbinom.c -o pbinom.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qbinom.c -o qbinom.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rbinom.c -o rbinom.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rmultinom.c -o rmultinom.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dcauchy.c -o dcauchy.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pcauchy.c -o pcauchy.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qcauchy.c -o qcauchy.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rcauchy.c -o rcauchy.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dexp.c -o dexp.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pexp.c -o pexp.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qexp.c -o qexp.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rexp.c -o rexp.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dgeom.c -o dgeom.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pgeom.c -o pgeom.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qgeom.c -o qgeom.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rgeom.c -o rgeom.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dhyper.c -o dhyper.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c phyper.c -o phyper.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qhyper.c -o qhyper.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rhyper.c -o rhyper.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dnbinom.c -o dnbinom.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pnbinom.c -o pnbinom.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qnbinom.c -o qnbinom.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qnbinom_mu.c -o qnbinom_mu.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rnbinom.c -o rnbinom.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dpois.c -o dpois.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c ppois.c -o ppois.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qpois.c -o qpois.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rpois.c -o rpois.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dweibull.c -o dweibull.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pweibull.c -o pweibull.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qweibull.c -o qweibull.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rweibull.c -o rweibull.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dlogis.c -o dlogis.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c plogis.c -o plogis.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qlogis.c -o qlogis.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rlogis.c -o rlogis.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dnchisq.c -o dnchisq.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pnchisq.c -o pnchisq.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qnchisq.c -o qnchisq.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dnbeta.c -o dnbeta.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pnbeta.c -o pnbeta.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qnbeta.c -o qnbeta.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pnf.c -o pnf.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pnt.c -o pnt.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qnf.c -o qnf.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qnt.c -o qnt.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c ptukey.c -o ptukey.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qtukey.c -o qtukey.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c toms708.c -o toms708.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c wilcox.c -o wilcox.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c signrank.c -o signrank.o
ar -cr libnmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o qnbinom_mu.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o
ranlib libnmath.a
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/nmath'
make[2]: Leaving directory '/build/r/src/R-4.5.1/src/nmath'
make[2]: Entering directory '/build/r/src/R-4.5.1/src/unix'
config.status: creating src/unix/Makefile
making Rembedded.d from Rembedded.c
making dynload.d from dynload.c
making system.d from system.c
making sys-unix.d from sys-unix.c
making sys-std.d from sys-std.c
making X11.d from X11.c
make[3]: Entering directory '/build/r/src/R-4.5.1/src/unix'
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c Rembedded.c -o Rembedded.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dynload.c -o dynload.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c system.c -o system.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c sys-unix.c -o sys-unix.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c sys-std.c -o sys-std.o
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c X11.c -o X11.o
ar -cr libunix.a Rembedded.o dynload.o system.o sys-unix.o sys-std.o X11.o
ranlib libunix.a
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/unix'
make[3]: Entering directory '/build/r/src/R-4.5.1/src/unix'
gcc -std=gnu23 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -DR_HOME='"/build/r/src/R-4.5.1"' \
-o Rscript ./Rscript.c
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/unix'
make[2]: Leaving directory '/build/r/src/R-4.5.1/src/unix'
make[2]: Entering directory '/build/r/src/R-4.5.1/src/main'
config.status: creating src/main/Makefile
making CommandLineArgs.d from CommandLineArgs.c
making Rdynload.d from Rdynload.c
making Renviron.d from Renviron.c
making RNG.d from RNG.c
making agrep.d from agrep.c
making altclasses.d from altclasses.c
making altrep.d from altrep.c
making apply.d from apply.c
making arithmetic.d from arithmetic.c
making array.d from array.c
making attrib.d from attrib.c
making bind.d from bind.c
making builtin.d from builtin.c
making character.d from character.c
making clippath.d from clippath.c
making coerce.d from coerce.c
making colors.d from colors.c
making complex.d from complex.c
making connections.d from connections.c
making context.d from context.c
making cum.d from cum.c
making dcf.d from dcf.c
making datetime.d from datetime.c
making debug.d from debug.c
making deparse.d from deparse.c
making devices.d from devices.c
making dotcode.d from dotcode.c
making dounzip.d from dounzip.c
making dstruct.d from dstruct.c
making duplicate.d from duplicate.c
making edit.d from edit.c
making engine.d from engine.c
making envir.d from envir.c
making errors.d from errors.c
making eval.d from eval.c
making flexiblas.d from flexiblas.c
making format.d from format.c
making gevents.d from gevents.c
making gram.d from gram.c
making gram-ex.d from gram-ex.c
making graphics.d from graphics.c
making grep.d from grep.c
making identical.d from identical.c
making inlined.d from inlined.c
making inspect.d from inspect.c
making internet.d from internet.c
making iosupport.d from iosupport.c
making lapack.d from lapack.c
making list.d from list.c
making localecharset.d from localecharset.c
making logic.d from logic.c
making machine.d from machine.c
making main.d from main.c
making mapply.d from mapply.c
making mask.d from mask.c
making match.d from match.c
making memory.d from memory.c
making names.d from names.c
making objects.d from objects.c
making options.d from options.c
making paste.d from paste.c
making patterns.d from patterns.c
making platform.d from platform.c
making plot.d from plot.c
making plot3d.d from plot3d.c
making plotmath.d from plotmath.c
making print.d from print.c
making printarray.d from printarray.c
making printvector.d from printvector.c
making printutils.d from printutils.c
making qsort.d from qsort.c
making radixsort.d from radixsort.c
making random.d from random.c
making raw.d from raw.c
making registration.d from registration.c
making relop.d from relop.c
making rlocale.d from rlocale.c
making saveload.d from saveload.c
making scan.d from scan.c
making seq.d from seq.c
making serialize.d from serialize.c
making sort.d from sort.c
making source.d from source.c
making split.d from split.c
making sprintf.d from sprintf.c
making startup.d from startup.c
making subassign.d from subassign.c
making subscript.d from subscript.c
making subset.d from subset.c
making summary.d from summary.c
making sysutils.d from sysutils.c
making times.d from times.c
making unique.d from unique.c
making util.d from util.c
making version.d from version.c
making g_alab_her.d from g_alab_her.c
making g_cntrlify.d from g_cntrlify.c
making g_fontdb.d from g_fontdb.c
making g_her_glyph.d from g_her_glyph.c
making Rmain.d from Rmain.c
making alloca.d from alloca.c
making mkdtemp.d from mkdtemp.c
making strdup.d from strdup.c
making strncasecmp.d from strncasecmp.c
make[3]: Entering directory '/build/r/src/R-4.5.1/src/main'
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c CommandLineArgs.c -o CommandLineArgs.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c Rdynload.c -o Rdynload.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c Renviron.c -o Renviron.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c RNG.c -o RNG.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c agrep.c -o agrep.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c altclasses.c -o altclasses.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c altrep.c -o altrep.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c apply.c -o apply.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c arithmetic.c -o arithmetic.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c array.c -o array.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c attrib.c -o attrib.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c bind.c -o bind.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c builtin.c -o builtin.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c character.c -o character.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c clippath.c -o clippath.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c coerce.c -o coerce.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c colors.c -o colors.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c complex.c -o complex.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c connections.c -o connections.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c context.c -o context.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c cum.c -o cum.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dcf.c -o dcf.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c datetime.c -o datetime.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c debug.c -o debug.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c deparse.c -o deparse.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c devices.c -o devices.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dotcode.c -o dotcode.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dounzip.c -o dounzip.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dstruct.c -o dstruct.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c duplicate.c -o duplicate.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c edit.c -o edit.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c engine.c -o engine.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c envir.c -o envir.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c errors.c -o errors.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c eval.c -o eval.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c flexiblas.c -o flexiblas.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c format.c -o format.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c gevents.c -o gevents.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c gram.c -o gram.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c gram-ex.c -o gram-ex.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c graphics.c -o graphics.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c grep.c -o grep.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c identical.c -o identical.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c inlined.c -o inlined.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c inspect.c -o inspect.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c internet.c -o internet.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c iosupport.c -o iosupport.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c lapack.c -o lapack.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c list.c -o list.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c localecharset.c -o localecharset.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c logic.c -o logic.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c machine.c -o machine.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c main.c -o main.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c mapply.c -o mapply.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c mask.c -o mask.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c match.c -o match.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c memory.c -o memory.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c names.c -o names.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c objects.c -o objects.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c options.c -o options.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c paste.c -o paste.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c patterns.c -o patterns.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c platform.c -o platform.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c plot.c -o plot.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c plot3d.c -o plot3d.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c plotmath.c -o plotmath.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c print.c -o print.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c printarray.c -o printarray.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c printvector.c -o printvector.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c printutils.c -o printutils.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qsort.c -o qsort.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c radixsort.c -o radixsort.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c random.c -o random.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c raw.c -o raw.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c registration.c -o registration.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c relop.c -o relop.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rlocale.c -o rlocale.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c saveload.c -o saveload.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c scan.c -o scan.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c seq.c -o seq.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c serialize.c -o serialize.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c sort.c -o sort.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c source.c -o source.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c split.c -o split.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c sprintf.c -o sprintf.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c startup.c -o startup.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c subassign.c -o subassign.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c subscript.c -o subscript.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c subset.c -o subset.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c summary.c -o summary.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c sysutils.c -o sysutils.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c times.c -o times.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c unique.c -o unique.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c util.c -o util.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c version.c -o version.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c g_alab_her.c -o g_alab_her.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c g_cntrlify.c -o g_cntrlify.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c g_fontdb.c -o g_fontdb.o
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c g_her_glyph.c -o g_her_glyph.o
gfortran -fpic -g -O2 -c xxxpr.f -o xxxpr.o
gcc -std=gnu23 -shared -fopenmp -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o altclasses.o altrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o clippath.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o flexiblas.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o machine.o main.o mapply.o mask.o match.o memory.o names.o objects.o options.o paste.o patterns.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o radixsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o times.o unique.o util.o version.o g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o xxxpr.o `ls ../unix/*.o ../appl/*.o ../nmath/*.o` ../extra/tre/libtre.a -lblas -lgfortran -lm -lreadline -lpcre2-8 -lzstd -llzma -lbz2 -lz -ltirpc -lrt -ldl -lm -licuuc -licui18n
make[4]: Entering directory '/build/r/src/R-4.5.1/src/main'
mkdir -p -- /build/r/src/R-4.5.1/bin/exec
mkdir -p -- /build/r/src/R-4.5.1/lib
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/main'
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/main'
make[3]: Entering directory '/build/r/src/R-4.5.1/src/main'
gcc -std=gnu23 -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c Rmain.c -o Rmain.o
gcc -std=gnu23 -Wl,--export-dynamic -fopenmp -L"../../lib" -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o R.bin Rmain.o -lR
make[4]: Entering directory '/build/r/src/R-4.5.1/src/main'
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/main'
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/main'
make[2]: Leaving directory '/build/r/src/R-4.5.1/src/main'
make[2]: Entering directory '/build/r/src/R-4.5.1/src/modules'
make[3]: Entering directory '/build/r/src/R-4.5.1/src/modules/X11'
make[3]: Entering directory '/build/r/src/R-4.5.1/src/modules/lapack'
make[3]: Entering directory '/build/r/src/R-4.5.1/src/modules/internet'
making Rhttpd.d from Rhttpd.c
making devX11.d from devX11.c
making Lapack.d from Lapack.c
making Rsock.d from Rsock.c
making rotated.d from rotated.c
making internet.d from internet.c
making rbitmap.d from rbitmap.c
making libcurl.d from libcurl.c
making sock.d from sock.c
making sockconn.d from sockconn.c
make[4]: Entering directory '/build/r/src/R-4.5.1/src/modules/lapack'
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c Lapack.c -o Lapack.o
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c ../../main/flexiblas.c -o flexiblas.o
make[4]: Entering directory '/build/r/src/R-4.5.1/src/modules/internet'
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fvisibility=hidden -c Rhttpd.c -o Rhttpd.o
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fvisibility=hidden -c Rsock.c -o Rsock.o
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fvisibility=hidden -c internet.c -o internet.o
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fvisibility=hidden -c libcurl.c -o libcurl.o
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fvisibility=hidden -c sock.c -o sock.o
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fvisibility=hidden -c sockconn.c -o sockconn.o
gcc -std=gnu23 -shared -L"../../../lib" -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o lapack.so Lapack.o flexiblas.o -lR -llapack -lblas -lgfortran -lm
make[4]: Entering directory '/build/r/src/R-4.5.1/src/modules/X11'
gcc -std=gnu23 -I/usr/include/libpng16 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/fribidi -I/usr/include/harfbuzz -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/usr/include/pixman-1 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c devX11.c -o devX11.o
gcc -std=gnu23 -I/usr/include/libpng16 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/fribidi -I/usr/include/harfbuzz -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/usr/include/pixman-1 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rotated.c -o rotated.o
gcc -std=gnu23 -I/usr/include/libpng16 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/fribidi -I/usr/include/harfbuzz -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/usr/include/pixman-1 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rbitmap.c -o rbitmap.o
gcc -std=gnu23 -I/usr/include/libpng16 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/fribidi -I/usr/include/harfbuzz -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/usr/include/pixman-1 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dataentry.c -o dataentry.o
gcc -std=gnu23 -shared -L"../../../lib" -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o internet.so Rhttpd.o Rsock.o internet.o libcurl.o sock.o sockconn.o -lcurl -lR
make[5]: Entering directory '/build/r/src/R-4.5.1/src/modules/lapack'
mkdir -p -- /build/r/src/R-4.5.1/modules
make[5]: Leaving directory '/build/r/src/R-4.5.1/src/modules/lapack'
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/modules/lapack'
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/modules/lapack'
make[5]: Entering directory '/build/r/src/R-4.5.1/src/modules/internet'
make[5]: Leaving directory '/build/r/src/R-4.5.1/src/modules/internet'
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/modules/internet'
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/modules/internet'
gcc -std=gnu23 -shared -L"../../../lib" -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o R_de.so dataentry.o -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lcairo -lpng16 -lz -lharfbuzz -lglib-2.0 -lXext -lX11 -lX11 -lXt -lXmu -lR -lm
gcc -std=gnu23 -shared -L"../../../lib" -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o R_X11.so devX11.o rotated.o rbitmap.o -ltiff -ljpeg -lpng16 -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lcairo -lpng16 -lz -lharfbuzz -lglib-2.0 -lXext -lX11 -lX11 -lXt -lXmu -lR -lm
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/modules/X11'
make[4]: Entering directory '/build/r/src/R-4.5.1/src/modules/X11'
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/modules/X11'
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/modules/X11'
make[2]: Leaving directory '/build/r/src/R-4.5.1/src/modules'
make[2]: Entering directory '/build/r/src/R-4.5.1/src/library'
mkdir -p -- ../../library
make[3]: Entering directory '/build/r/src/R-4.5.1/src/library/profile'
building system startup profile
mkdir -p -- ../../../library/base/R
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/library/profile'
make[3]: Entering directory '/build/r/src/R-4.5.1/src/library/translations'
building package 'translations'
mkdir -p -- ../../../library/translations
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/translations'
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/translations'
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/library/translations'
make[3]: Entering directory '/build/r/src/R-4.5.1/src/library/base'
building package 'base'
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/base'
mkdir -p -- ../../../library/base/demo
mv: setting attribute 'security.SMACK64' for 'security.SMACK64': Operation not permitted
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/base'
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/library/base'
make[3]: Entering directory '/build/r/src/R-4.5.1/src/library/tools'
building package 'tools'
mkdir -p -- ../../../library/tools
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/tools'
mkdir -p -- ../../../library/tools/R
mv: setting attribute 'security.SMACK64' for 'security.SMACK64': Operation not permitted
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/tools'
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/tools'
make[5]: Entering directory '/build/r/src/R-4.5.1/src/library/tools/src'
making text.d from text.c
making init.d from init.c
making Rmd5.d from Rmd5.c
making md5.d from md5.c
making signals.d from signals.c
making install.d from install.c
making getfmts.d from getfmts.c
making http.d from http.c
making gramLatex.d from gramLatex.c
making gramRd.d from gramRd.c
making pdscan.d from pdscan.c
making Rsha256.d from Rsha256.c
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c text.c -o text.o
making sha256.d from sha256.c
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c init.c -o init.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c Rmd5.c -o Rmd5.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c md5.c -o md5.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c signals.c -o signals.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c install.c -o install.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c getfmts.c -o getfmts.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c http.c -o http.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c gramLatex.c -o gramLatex.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c gramRd.c -o gramRd.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pdscan.c -o pdscan.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c Rsha256.c -o Rsha256.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c sha256.c -o sha256.o
gcc -std=gnu23 -shared -L../../../../lib -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o tools.so text.o init.o Rmd5.o md5.o signals.o install.o getfmts.o http.o gramLatex.o gramRd.o pdscan.o Rsha256.o sha256.o -L../../../../lib -lR
make[6]: Entering directory '/build/r/src/R-4.5.1/src/library/tools/src'
mkdir -p -- ../../../../library/tools/libs
make[6]: Leaving directory '/build/r/src/R-4.5.1/src/library/tools/src'
make[5]: Leaving directory '/build/r/src/R-4.5.1/src/library/tools/src'
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/tools'
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/tools'
installing 'sysdata.rda'
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/tools'
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/library/tools'
make[3]: Entering directory '/build/r/src/R-4.5.1/src/library/compiler'
building package 'compiler'
mkdir -p -- ../../../library/compiler
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/compiler'
mkdir -p -- ../../../library/compiler/R
mv: setting attribute 'security.SMACK64' for 'security.SMACK64': Operation not permitted
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/compiler'
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/compiler'
byte-compiling package 'compiler'
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/compiler'
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/library/compiler'
make[3]: Entering directory '/build/r/src/R-4.5.1/src/library/base'
byte-compiling package 'base'
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/library/base'
make[3]: Entering directory '/build/r/src/R-4.5.1/src/library/tools'
byte-compiling package 'tools'
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/library/tools'
make[3]: Entering directory '/build/r/src/R-4.5.1/src/library/utils'
building package 'utils'
mkdir -p -- ../../../library/utils
mkdir -p -- ../../../library/utils/doc
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/utils'
mkdir -p -- ../../../library/utils/R
mkdir -p -- ../../../library/utils/Sweave
mv: setting attribute 'security.SMACK64' for 'security.SMACK64': Operation not permitted
mkdir -p -- ../../../library/utils/misc
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/utils'
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/utils'
make[5]: Entering directory '/build/r/src/R-4.5.1/src/library/utils/src'
making init.d from init.c
making io.d from io.c
making size.d from size.c
making sock.d from sock.c
making stubs.d from stubs.c
making utils.d from utils.c
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c init.c -o init.o
making hashtab.d from hashtab.c
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c io.c -o io.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c size.c -o size.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c sock.c -o sock.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c stubs.c -o stubs.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c utils.c -o utils.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c hashtab.c -o hashtab.o
gcc -std=gnu23 -shared -L../../../../lib -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o utils.so init.o io.o size.o sock.o stubs.o utils.o hashtab.o -L../../../../lib -lR
make[6]: Entering directory '/build/r/src/R-4.5.1/src/library/utils/src'
mkdir -p -- ../../../../library/utils/libs
make[6]: Leaving directory '/build/r/src/R-4.5.1/src/library/utils/src'
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make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/utils'
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/utils'
installing 'sysdata.rda'
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/utils'
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/utils'
byte-compiling package 'utils'
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/utils'
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/library/utils'
make[3]: Entering directory '/build/r/src/R-4.5.1/src/library/grDevices'
building package 'grDevices'
mkdir -p -- ../../../library/grDevices
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/grDevices'
mkdir -p -- ../../../library/grDevices/R
mkdir -p -- ../../../library/grDevices/afm
mv: setting attribute 'security.SMACK64' for 'security.SMACK64': Operation not permitted
mkdir -p -- ../../../library/grDevices/enc
mkdir -p -- ../../../library/grDevices/fonts/Roboto
mkdir -p -- ../../../library/grDevices/fonts/Montserrat/static
mkdir -p -- ../../../library/grDevices/icc
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/grDevices'
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/grDevices'
make[5]: Entering directory '/build/r/src/R-4.5.1/src/library/grDevices/src'
making axis_scales.d from axis_scales.c
making chull.d from chull.c
making devices.d from devices.c
making init.d from init.c
making stubs.d from stubs.c
making colors.d from colors.c
making clippath.d from clippath.c
making patterns.d from patterns.c
making mask.d from mask.c
making group.d from group.c
making devCairo.d from devCairo.c
making devPicTeX.d from devPicTeX.c
making devPS.d from devPS.c
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c axis_scales.c -o axis_scales.o
making devQuartz.d from devQuartz.c
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c chull.c -o chull.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c devices.c -o devices.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c init.c -o init.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c stubs.c -o stubs.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c colors.c -o colors.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c clippath.c -o clippath.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c patterns.c -o patterns.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c mask.c -o mask.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c group.c -o group.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c devCairo.c -o devCairo.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c devPicTeX.c -o devPicTeX.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c devPS.c -o devPS.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c devQuartz.c -o devQuartz.o
gcc -std=gnu23 -shared -L../../../../lib -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o grDevices.so axis_scales.o chull.o devices.o init.o stubs.o colors.o clippath.o patterns.o mask.o group.o devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR
make[6]: Entering directory '/build/r/src/R-4.5.1/src/library/grDevices/src'
mkdir -p -- ../../../../library/grDevices/libs
make[7]: Entering directory '/build/r/src/R-4.5.1/src/library/grDevices/src/cairo'
making cairoBM.d from cairoBM.c
make[8]: Entering directory '/build/r/src/R-4.5.1/src/library/grDevices/src/cairo'
make[9]: Entering directory '/build/r/src/R-4.5.1/src/library/grDevices/src/cairo'
gcc -std=gnu23 -I. -I../../../../../src/include -I../../../../../src/include -I/usr/include/pango-1.0 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/fribidi -I/usr/include/harfbuzz -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/usr/include/pixman-1 -I/usr/include/libpng16 -I../../../../../src/modules/X11 -DHAVE_CONFIG_H -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c cairoBM.c -o cairoBM.o
gcc -std=gnu23 -shared -L"../../../../../lib" -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o cairo.so cairoBM.o ../../../../../src/modules/X11/rbitmap.o -ltiff -ljpeg -lpng16 -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lcairo -lharfbuzz -lglib-2.0 -lpng16 -lz -L"../../../../../lib" -lR -lm
make[9]: Leaving directory '/build/r/src/R-4.5.1/src/library/grDevices/src/cairo'
make[8]: Leaving directory '/build/r/src/R-4.5.1/src/library/grDevices/src/cairo'
make[7]: Leaving directory '/build/r/src/R-4.5.1/src/library/grDevices/src/cairo'
make[6]: Leaving directory '/build/r/src/R-4.5.1/src/library/grDevices/src'
make[5]: Leaving directory '/build/r/src/R-4.5.1/src/library/grDevices/src'
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/grDevices'
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/grDevices'
byte-compiling package 'grDevices'
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/grDevices'
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/library/grDevices'
make[3]: Entering directory '/build/r/src/R-4.5.1/src/library/graphics'
building package 'graphics'
mkdir -p -- ../../../library/graphics
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/graphics'
mkdir -p -- ../../../library/graphics/R
mv: setting attribute 'security.SMACK64' for 'security.SMACK64': Operation not permitted
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/graphics'
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/graphics'
make[5]: Entering directory '/build/r/src/R-4.5.1/src/library/graphics/src'
making init.d from init.c
making base.d from base.c
making graphics.d from graphics.c
making par.d from par.c
making plot.d from plot.c
making plot3d.d from plot3d.c
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c init.c -o init.o
making stem.d from stem.c
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c base.c -o base.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c graphics.c -o graphics.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c par.c -o par.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c plot.c -o plot.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c plot3d.c -o plot3d.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c stem.c -o stem.o
gcc -std=gnu23 -shared -L../../../../lib -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o graphics.so init.o base.o graphics.o par.o plot.o plot3d.o stem.o -L../../../../lib -lR
make[6]: Entering directory '/build/r/src/R-4.5.1/src/library/graphics/src'
mkdir -p -- ../../../../library/graphics/libs
make[6]: Leaving directory '/build/r/src/R-4.5.1/src/library/graphics/src'
make[5]: Leaving directory '/build/r/src/R-4.5.1/src/library/graphics/src'
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/graphics'
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/graphics'
byte-compiling package 'graphics'
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/graphics'
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/library/graphics'
make[3]: Entering directory '/build/r/src/R-4.5.1/src/library/stats'
building package 'stats'
mkdir -p -- ../../../library/stats
mkdir -p -- ../../../library/stats/doc
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/stats'
mkdir -p -- ../../../library/stats/R
mv: setting attribute 'security.SMACK64' for 'security.SMACK64': Operation not permitted
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/stats'
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/stats'
make[5]: Entering directory '/build/r/src/R-4.5.1/src/library/stats/src'
making init.d from init.c
making kmeans.d from kmeans.c
making ansari.d from ansari.c
making bandwidths.d from bandwidths.c
making chisqsim.d from chisqsim.c
making d2x2xk.d from d2x2xk.c
making fexact.d from fexact.c
making kendall.d from kendall.c
making ks.d from ks.c
making line.d from line.c
making smooth.d from smooth.c
making prho.d from prho.c
making swilk.d from swilk.c
making ksmooth.d from ksmooth.c
making loessc.d from loessc.c
making monoSpl.d from monoSpl.c
making isoreg.d from isoreg.c
making Srunmed.d from Srunmed.c
making dblcen.d from dblcen.c
making distance.d from distance.c
making hclust-utils.d from hclust-utils.c
making nls.d from nls.c
making rWishart.d from rWishart.c
making HoltWinters.d from HoltWinters.c
making PPsum.d from PPsum.c
making arima.d from arima.c
making burg.d from burg.c
making filter.d from filter.c
making mAR.d from mAR.c
making pacf.d from pacf.c
making starma.d from starma.c
making port.d from port.c
making family.d from family.c
making sbart.d from sbart.c
making approx.d from approx.c
making loglin.d from loglin.c
making lowess.d from lowess.c
making massdist.d from massdist.c
making splines.d from splines.c
making lm.d from lm.c
making complete_cases.d from complete_cases.c
making cov.d from cov.c
making deriv.d from deriv.c
making fft.d from fft.c
making fourier.d from fourier.c
making model.d from model.c
making optim.d from optim.c
making optimize.d from optimize.c
making integrate.d from integrate.c
making random.d from random.c
making distn.d from distn.c
making zeroin.d from zeroin.c
making rcont.d from rcont.c
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c init.c -o init.o
making influence.d from influence.c
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c kmeans.c -o kmeans.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c ansari.c -o ansari.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c bandwidths.c -o bandwidths.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c chisqsim.c -o chisqsim.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c d2x2xk.c -o d2x2xk.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c fexact.c -o fexact.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c kendall.c -o kendall.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c ks.c -o ks.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c line.c -o line.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c smooth.c -o smooth.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c prho.c -o prho.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c swilk.c -o swilk.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c ksmooth.c -o ksmooth.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c loessc.c -o loessc.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c monoSpl.c -o monoSpl.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c isoreg.c -o isoreg.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c Srunmed.c -o Srunmed.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dblcen.c -o dblcen.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c distance.c -o distance.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c hclust-utils.c -o hclust-utils.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c nls.c -o nls.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rWishart.c -o rWishart.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c HoltWinters.c -o HoltWinters.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c PPsum.c -o PPsum.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c arima.c -o arima.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c burg.c -o burg.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c filter.c -o filter.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c mAR.c -o mAR.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pacf.c -o pacf.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c starma.c -o starma.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c port.c -o port.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c family.c -o family.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c sbart.c -o sbart.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c approx.c -o approx.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c loglin.c -o loglin.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c lowess.c -o lowess.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c massdist.c -o massdist.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c splines.c -o splines.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c lm.c -o lm.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c complete_cases.c -o complete_cases.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c cov.c -o cov.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c deriv.c -o deriv.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c fft.c -o fft.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c fourier.c -o fourier.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c model.c -o model.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c optim.c -o optim.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c optimize.c -o optimize.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c integrate.c -o integrate.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c random.c -o random.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c distn.c -o distn.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c zeroin.c -o zeroin.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rcont.c -o rcont.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c influence.c -o influence.o
gfortran -fvisibility=hidden -fpic -g -O2 -c bsplvd.f -o bsplvd.o
gfortran -fvisibility=hidden -fpic -g -O2 -c bvalue.f -o bvalue.o
gfortran -fvisibility=hidden -fpic -g -O2 -c bvalus.f -o bvalus.o
gfortran -fvisibility=hidden -fpic -g -O2 -c loessf.f -o loessf.o
gfortran -fvisibility=hidden -fpic -g -O2 -c ppr.f -o ppr.o
gfortran -fvisibility=hidden -fpic -g -O2 -c qsbart.f -o qsbart.o
gfortran -fvisibility=hidden -fpic -g -O2 -c sgram.f -o sgram.o
gfortran -fvisibility=hidden -fpic -g -O2 -c sinerp.f -o sinerp.o
gfortran -fvisibility=hidden -fpic -g -O2 -c sslvrg.f -o sslvrg.o
gfortran -fvisibility=hidden -fpic -g -O2 -c stxwx.f -o stxwx.o
gfortran -fvisibility=hidden -fpic -g -O2 -c hclust.f -o hclust.o
gfortran -fvisibility=hidden -fpic -g -O2 -c kmns.f -o kmns.o
gfortran -fvisibility=hidden -fpic -g -O2 -c eureka.f -o eureka.o
gfortran -fvisibility=hidden -fpic -g -O2 -c stl.f -o stl.o
gfortran -fpic -g -O2 -c portsrc.f -o portsrc.o
gfortran -fvisibility=hidden -fpic -g -O2 -c lminfl.f -o lminfl.o
gcc -std=gnu23 -shared -L../../../../lib -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o stats.so init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o monoSpl.o isoreg.o Srunmed.o dblcen.o distance.o hclust-utils.o nls.o rWishart.o HoltWinters.o PPsum.o arima.o burg.o filter.o mAR.o pacf.o starma.o port.o family.o sbart.o approx.o loglin.o lowess.o massdist.o splines.o lm.o complete_cases.o cov.o deriv.o fft.o fourier.o model.o optim.o optimize.o integrate.o random.o distn.o zeroin.o rcont.o influence.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sgram.o sinerp.o sslvrg.o stxwx.o hclust.o kmns.o eureka.o stl.o portsrc.o lminfl.o -fopenmp -llapack -lblas -lgfortran -lm -L../../../../lib -lR
make[6]: Entering directory '/build/r/src/R-4.5.1/src/library/stats/src'
mkdir -p -- ../../../../library/stats/libs
make[6]: Leaving directory '/build/r/src/R-4.5.1/src/library/stats/src'
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make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/stats'
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/stats'
byte-compiling package 'stats'
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/stats'
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/library/stats'
make[3]: Entering directory '/build/r/src/R-4.5.1/src/library/datasets'
building package 'datasets'
mkdir -p -- ../../../library/datasets
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/datasets'
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/datasets'
mkdir -p -- ../../../library/datasets/data
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/library/datasets'
make[3]: Entering directory '/build/r/src/R-4.5.1/src/library/methods'
building package 'methods'
mkdir -p -- ../../../library/methods
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/methods'
mkdir -p -- ../../../library/methods/R
mv: setting attribute 'security.SMACK64' for 'security.SMACK64': Operation not permitted
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/methods'
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/methods'
make[5]: Entering directory '/build/r/src/R-4.5.1/src/library/methods/src'
making do_substitute_direct.d from do_substitute_direct.c
making init.d from init.c
making methods_list_dispatch.d from methods_list_dispatch.c
making slot.d from slot.c
making class_support.d from class_support.c
making tests.d from tests.c
making utils.d from utils.c
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c do_substitute_direct.c -o do_substitute_direct.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c init.c -o init.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c methods_list_dispatch.c -o methods_list_dispatch.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c slot.c -o slot.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c class_support.c -o class_support.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c tests.c -o tests.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c utils.c -o utils.o
gcc -std=gnu23 -shared -L../../../../lib -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o methods.so do_substitute_direct.o init.o methods_list_dispatch.o slot.o class_support.o tests.o utils.o -L../../../../lib -lR
make[6]: Entering directory '/build/r/src/R-4.5.1/src/library/methods/src'
mkdir -p -- ../../../../library/methods/libs
make[6]: Leaving directory '/build/r/src/R-4.5.1/src/library/methods/src'
make[5]: Leaving directory '/build/r/src/R-4.5.1/src/library/methods/src'
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/methods'
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/methods'
byte-compiling package 'methods'
initializing class and method definitions ... done
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/methods'
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/library/methods'
make[3]: Entering directory '/build/r/src/R-4.5.1/src/library/grid'
building package 'grid'
mkdir -p -- ../../../library/grid
mkdir -p -- ../../../library/grid/doc
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/grid'
mkdir -p -- ../../../library/grid/R
mv: setting attribute 'security.SMACK64' for 'security.SMACK64': Operation not permitted
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/grid'
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/grid'
make[5]: Entering directory '/build/r/src/R-4.5.1/src/library/grid/src'
making clippath.d from clippath.c
making gpar.d from gpar.c
making grid.d from grid.c
making just.d from just.c
making layout.d from layout.c
making mask.d from mask.c
making matrix.d from matrix.c
making path.d from path.c
making register.d from register.c
making state.d from state.c
making typeset.d from typeset.c
making unit.d from unit.c
making util.d from util.c
making viewport.d from viewport.c
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c clippath.c -o clippath.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c gpar.c -o gpar.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c grid.c -o grid.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c just.c -o just.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c layout.c -o layout.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c mask.c -o mask.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c matrix.c -o matrix.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c path.c -o path.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c register.c -o register.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c state.c -o state.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c typeset.c -o typeset.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c unit.c -o unit.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c util.c -o util.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c viewport.c -o viewport.o
gcc -std=gnu23 -shared -L../../../../lib -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o grid.so clippath.o gpar.o grid.o just.o layout.o mask.o matrix.o path.o register.o state.o typeset.o unit.o util.o viewport.o -L../../../../lib -lR
make[6]: Entering directory '/build/r/src/R-4.5.1/src/library/grid/src'
mkdir -p -- ../../../../library/grid/libs
make[6]: Leaving directory '/build/r/src/R-4.5.1/src/library/grid/src'
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make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/grid'
byte-compiling package 'grid'
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/grid'
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/library/grid'
make[3]: Entering directory '/build/r/src/R-4.5.1/src/library/splines'
building package 'splines'
mkdir -p -- ../../../library/splines
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/splines'
mkdir -p -- ../../../library/splines/R
mv: setting attribute 'security.SMACK64' for 'security.SMACK64': Operation not permitted
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/splines'
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/splines'
make[5]: Entering directory '/build/r/src/R-4.5.1/src/library/splines/src'
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c splines.c -o splines.o
making splines.d from splines.c
gcc -std=gnu23 -shared -L../../../../lib -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o splines.so splines.o -L../../../../lib -lR
make[6]: Entering directory '/build/r/src/R-4.5.1/src/library/splines/src'
mkdir -p -- ../../../../library/splines/libs
make[6]: Leaving directory '/build/r/src/R-4.5.1/src/library/splines/src'
make[5]: Leaving directory '/build/r/src/R-4.5.1/src/library/splines/src'
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/splines'
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/splines'
byte-compiling package 'splines'
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/splines'
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/library/splines'
make[3]: Entering directory '/build/r/src/R-4.5.1/src/library/stats4'
building package 'stats4'
mkdir -p -- ../../../library/stats4
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/stats4'
mkdir -p -- ../../../library/stats4/R
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byte-compiling package 'stats4'
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make[3]: Entering directory '/build/r/src/R-4.5.1/src/library/tcltk'
building package 'tcltk'
mkdir -p -- ../../../library/tcltk/R
mv: setting attribute 'security.SMACK64' for 'security.SMACK64': Operation not permitted
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/tcltk'
mkdir -p -- ../../../library/tcltk/exec
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/tcltk'
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/tcltk/src'
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/include -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c init.c -o init.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/include -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c tcltk.c -o tcltk.o
making init.d from init.c
making tcltk.d from tcltk.c
making tcltk_unix.d from tcltk_unix.c
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/include -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c tcltk_unix.c -o tcltk_unix.o
gcc -std=gnu23 -shared -L../../../../lib -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o tcltk.so init.o tcltk.o tcltk_unix.o -L/usr/lib -ltcl8.6 -L/usr/lib -ltk8.6 -lX11 -lXss -lXext -lm -L../../../../lib -lR
make[5]: Entering directory '/build/r/src/R-4.5.1/src/library/tcltk/src'
mkdir -p -- ../../../../library/tcltk/libs
make[5]: Leaving directory '/build/r/src/R-4.5.1/src/library/tcltk/src'
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/tcltk/src'
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/tcltk'
byte-compiling package 'tcltk'
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make[3]: Leaving directory '/build/r/src/R-4.5.1/src/library/tcltk'
make[3]: Entering directory '/build/r/src/R-4.5.1/src/library/parallel'
building package 'parallel'
mkdir -p -- ../../../library/parallel
mkdir -p -- ../../../library/parallel/doc
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/parallel'
mkdir -p -- ../../../library/parallel/R
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make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/parallel'
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/parallel'
make[5]: Entering directory '/build/r/src/R-4.5.1/src/library/parallel/src'
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c init.c -o init.o
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rngstream.c -o rngstream.o
making init.d from init.c
making fork.d from fork.c
making rngstream.d from rngstream.c
gcc -std=gnu23 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c fork.c -o fork.o
gcc -std=gnu23 -shared -L../../../../lib -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o parallel.so init.o rngstream.o fork.o -L../../../../lib -lR
make[6]: Entering directory '/build/r/src/R-4.5.1/src/library/parallel/src'
mkdir -p -- ../../../../library/parallel/libs
make[6]: Leaving directory '/build/r/src/R-4.5.1/src/library/parallel/src'
make[5]: Leaving directory '/build/r/src/R-4.5.1/src/library/parallel/src'
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/parallel'
make[4]: Entering directory '/build/r/src/R-4.5.1/src/library/parallel'
byte-compiling package 'parallel'
make[4]: Leaving directory '/build/r/src/R-4.5.1/src/library/parallel'
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/library/parallel'
make[3]: Entering directory '/build/r/src/R-4.5.1/src/library/base'
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installing parsed NAMESPACE files
make[2]: Leaving directory '/build/r/src/R-4.5.1/src/library'
make[1]: Leaving directory '/build/r/src/R-4.5.1/src'
make[1]: Entering directory '/build/r/src/R-4.5.1/tests'
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you should 'make docs' now ...
make[1]: Entering directory '/build/r/src/R-4.5.1'
configuring Java ...
make[1]: Entering directory '/build/r/src/R-4.5.1/src/library'
make[1]: Entering directory '/build/r/src/R-4.5.1/doc'
building/updating vignettes for package 'grid' ...
Java interpreter : /usr/bin/java
Java version : 24.0.1
Java home path : /usr/lib/jvm/java-24-openjdk
building/updating vignettes for package 'parallel' ...
building/updating vignettes for package 'utils' ...
building/updating vignettes for package 'stats' ...
make[1]: Leaving directory '/build/r/src/R-4.5.1/src/library'
creating doc/NEWS
creating doc/NEWS.pdf
Java compiler : /usr/bin/javac
Java headers gen.:
Java archive tool: /usr/bin/jar
trying to compile and link a JNI program
detected JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
using C compiler: ‘armv7l-unknown-linux-gnueabihf-gcc (GCC) 14.2.1 20250207’
make[2]: Entering directory '/tmp/Rjavareconf.I21CLr'
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -I/usr/lib/jvm/java-24-openjdk/include -I/usr/lib/jvm/java-24-openjdk/include/linux -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c conftest.c -o conftest.o
gcc -std=gnu23 -shared -L/build/r/src/R-4.5.1/lib -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o conftest.so conftest.o -L/usr/lib/jvm/java-24-openjdk/lib/server -ljvm -L/build/r/src/R-4.5.1/lib -lR
make[2]: Leaving directory '/tmp/Rjavareconf.I21CLr'
JAVA_HOME : /usr/lib/jvm/java-24-openjdk
Java library path: $(JAVA_HOME)/lib/server
JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
Updating Java configuration in /build/r/src/R-4.5.1
Done.
make[1]: Leaving directory '/build/r/src/R-4.5.1'
make[2]: Entering directory '/build/r/src/R-4.5.1/doc/manual'
creating doc/manual/version.texi
creating doc/manual/R-FAQ.html
creating doc/manual/R-admin.html
creating doc/manual/R-data.html
creating doc/manual/R-exts.html
creating doc/manual/R-intro.html
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creating doc/manual/R-lang.html
make[3]: Entering directory '/build/r/src/R-4.5.1/doc/html'
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make[2]: Leaving directory '/build/r/src/R-4.5.1/doc/manual'
make[1]: Leaving directory '/build/r/src/R-4.5.1/doc'
make[1]: Entering directory '/build/r/src/R-4.5.1/src/library'
make[2]: Entering directory '/build/r/src/R-4.5.1/src/library'
installing parsed Rd
make[3]: Entering directory '/build/r/src/R-4.5.1/src/library'
datasets
grid
grDevices
graphics
methods
tcltk
compiler
splines
stats4
parallel
tools
utils
stats
base
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/library'
make[2]: Leaving directory '/build/r/src/R-4.5.1/src/library'
make[2]: Entering directory '/build/r/src/R-4.5.1/src/library'
building/updating package metadata ...
make[2]: Leaving directory '/build/r/src/R-4.5.1/src/library'
make[2]: Entering directory '/build/r/src/R-4.5.1/src/library'
writing package indices
make[3]: Entering directory '/build/r/src/R-4.5.1/src/library'
make[3]: Leaving directory '/build/r/src/R-4.5.1/src/library'
make[2]: Leaving directory '/build/r/src/R-4.5.1/src/library'
make[1]: Leaving directory '/build/r/src/R-4.5.1/src/library'
make[1]: Entering directory '/build/r/src/R-4.5.1/src/library/Recommended'
make[2]: Entering directory '/build/r/src/R-4.5.1/src/library/Recommended'
begin installing recommended package lattice
begin installing recommended package MASS
begin installing recommended package codetools
begin installing recommended package foreign
begin installing recommended package KernSmooth
begin installing recommended package rpart
begin installing recommended package nnet
begin installing recommended package spatial
* installing *source* package ‘codetools’ ...
** this is package ‘codetools’ version ‘0.2-20’
** package ‘codetools’ successfully unpacked and MD5 sums checked
** using non-staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (codetools)
* installing *source* package ‘nnet’ ...
** this is package ‘nnet’ version ‘7.3-20’
** package ‘nnet’ successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
using C compiler: ‘armv7l-unknown-linux-gnueabihf-gcc (GCC) 14.2.1 20250207’
make[3]: Entering directory '/tmp/RtmpfIWciR/R.INSTALL423558c34c19/nnet/src'
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c nnet.c -o nnet.o
gcc -std=gnu23 -shared -L/build/r/src/R-4.5.1/lib -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o nnet.so nnet.o -L/build/r/src/R-4.5.1/lib -lR
make[3]: Leaving directory '/tmp/RtmpfIWciR/R.INSTALL423558c34c19/nnet/src'
installing to /build/r/src/R-4.5.1/library/nnet/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (nnet)
* installing *source* package ‘spatial’ ...
** this is package ‘spatial’ version ‘7.3-18’
** package ‘spatial’ successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
using C compiler: ‘armv7l-unknown-linux-gnueabihf-gcc (GCC) 14.2.1 20250207’
make[3]: Entering directory '/tmp/RtmpoPnvl9/R.INSTALL4237308c5709/spatial/src'
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c init.c -o init.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c krc.c -o krc.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pps.c -o pps.o
gcc -std=gnu23 -shared -L/build/r/src/R-4.5.1/lib -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o spatial.so init.o krc.o pps.o -L/build/r/src/R-4.5.1/lib -lR
make[3]: Leaving directory '/tmp/RtmpoPnvl9/R.INSTALL4237308c5709/spatial/src'
installing to /build/r/src/R-4.5.1/library/spatial/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (spatial)
* installing *source* package ‘KernSmooth’ ...
** this is package ‘KernSmooth’ version ‘2.23-26’
** package ‘KernSmooth’ successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
using C compiler: ‘armv7l-unknown-linux-gnueabihf-gcc (GCC) 14.2.1 20250207’
using Fortran compiler: ‘GNU Fortran (GCC) 14.2.1 20250207’
make[3]: Entering directory '/tmp/RtmpxOVGzT/R.INSTALL423071745a03/KernSmooth/src'
gfortran -fpic -g -O2 -c blkest.f -o blkest.o
gfortran -fpic -g -O2 -c cp.f -o cp.o
gfortran -fpic -g -O2 -c dgedi.f -o dgedi.o
gfortran -fpic -g -O2 -c dgefa.f -o dgefa.o
gfortran -fpic -g -O2 -c dgesl.f -o dgesl.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c init.c -o init.o
gfortran -fpic -g -O2 -c linbin.f -o linbin.o
gfortran -fpic -g -O2 -c linbin2D.f -o linbin2D.o
gfortran -fpic -g -O2 -c locpoly.f -o locpoly.o
gfortran -fpic -g -O2 -c rlbin.f -o rlbin.o
gfortran -fpic -g -O2 -c sdiag.f -o sdiag.o
gfortran -fpic -g -O2 -c sstdiag.f -o sstdiag.o
gcc -std=gnu23 -shared -L/build/r/src/R-4.5.1/lib -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o KernSmooth.so blkest.o cp.o dgedi.o dgefa.o dgesl.o init.o linbin.o linbin2D.o locpoly.o rlbin.o sdiag.o sstdiag.o -lblas -lgfortran -lm -L/build/r/src/R-4.5.1/lib -lR
make[3]: Leaving directory '/tmp/RtmpxOVGzT/R.INSTALL423071745a03/KernSmooth/src'
installing to /build/r/src/R-4.5.1/library/KernSmooth/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (KernSmooth)
* installing *source* package ‘foreign’ ...
** this is package ‘foreign’ version ‘0.8-90’
** package ‘foreign’ successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
using C compiler: ‘armv7l-unknown-linux-gnueabihf-gcc (GCC) 14.2.1 20250207’
make[3]: Entering directory '/tmp/RtmpCJGbIA/R.INSTALL42277fb15e86/foreign/src'
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c R_systat.c -o R_systat.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c Rdbfread.c -o Rdbfread.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c Rdbfwrite.c -o Rdbfwrite.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c SASxport.c -o SASxport.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c avl.c -o avl.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dbfopen.c -o dbfopen.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c file-handle.c -o file-handle.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c format.c -o format.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c init.c -o init.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c minitab.c -o minitab.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pfm-read.c -o pfm-read.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c sfm-read.c -o sfm-read.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c spss.c -o spss.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c stataread.c -o stataread.o
gcc -std=gnu23 -shared -L/build/r/src/R-4.5.1/lib -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o foreign.so R_systat.o Rdbfread.o Rdbfwrite.o SASxport.o avl.o dbfopen.o file-handle.o format.o init.o minitab.o pfm-read.o sfm-read.o spss.o stataread.o -L/build/r/src/R-4.5.1/lib -lR
make[3]: Leaving directory '/tmp/RtmpCJGbIA/R.INSTALL42277fb15e86/foreign/src'
installing to /build/r/src/R-4.5.1/library/foreign/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (foreign)
* installing *source* package ‘rpart’ ...
** this is package ‘rpart’ version ‘4.1.24’
** package ‘rpart’ successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
using C compiler: ‘armv7l-unknown-linux-gnueabihf-gcc (GCC) 14.2.1 20250207’
make[3]: Entering directory '/tmp/RtmpnfwUir/R.INSTALL422d565e2e92/rpart/src'
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c anova.c -o anova.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c anovapred.c -o anovapred.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c branch.c -o branch.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c bsplit.c -o bsplit.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c choose_surg.c -o choose_surg.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c fix_cp.c -o fix_cp.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c free_tree.c -o free_tree.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c gini.c -o gini.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c graycode.c -o graycode.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c init.c -o init.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c insert_split.c -o insert_split.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c make_cp_list.c -o make_cp_list.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c make_cp_table.c -o make_cp_table.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c mysort.c -o mysort.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c nodesplit.c -o nodesplit.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c partition.c -o partition.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c poisson.c -o poisson.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pred_rpart.c -o pred_rpart.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c print_tree.c -o print_tree.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rpart.c -o rpart.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rpart_callback.c -o rpart_callback.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rpartexp.c -o rpartexp.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rpartexp2.c -o rpartexp2.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rpcountup.c -o rpcountup.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rpmatrix.c -o rpmatrix.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rundown.c -o rundown.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rundown2.c -o rundown2.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c surrogate.c -o surrogate.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c usersplit.c -o usersplit.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c xpred.c -o xpred.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c xval.c -o xval.o
gcc -std=gnu23 -shared -L/build/r/src/R-4.5.1/lib -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o rpart.so anova.o anovapred.o branch.o bsplit.o choose_surg.o fix_cp.o free_tree.o gini.o graycode.o init.o insert_split.o make_cp_list.o make_cp_table.o mysort.o nodesplit.o partition.o poisson.o pred_rpart.o print_tree.o rpart.o rpart_callback.o rpartexp.o rpartexp2.o rpcountup.o rpmatrix.o rundown.o rundown2.o surrogate.o usersplit.o xpred.o xval.o -L/build/r/src/R-4.5.1/lib -lR
make[3]: Leaving directory '/tmp/RtmpnfwUir/R.INSTALL422d565e2e92/rpart/src'
installing to /build/r/src/R-4.5.1/library/rpart/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rpart)
* installing *source* package ‘MASS’ ...
** this is package ‘MASS’ version ‘7.3-65’
** package ‘MASS’ successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
using C compiler: ‘armv7l-unknown-linux-gnueabihf-gcc (GCC) 14.2.1 20250207’
make[3]: Entering directory '/tmp/RtmplCS7s0/R.INSTALL4224227648fe/MASS/src'
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c MASS.c -o MASS.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c lqs.c -o lqs.o
gcc -std=gnu23 -shared -L/build/r/src/R-4.5.1/lib -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o MASS.so MASS.o lqs.o -L/build/r/src/R-4.5.1/lib -lR
make[3]: Leaving directory '/tmp/RtmplCS7s0/R.INSTALL4224227648fe/MASS/src'
installing to /build/r/src/R-4.5.1/library/MASS/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (MASS)
begin installing recommended package cluster
begin installing recommended package class
* installing *source* package ‘class’ ...
** this is package ‘class’ version ‘7.3-23’
** package ‘class’ successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
using C compiler: ‘armv7l-unknown-linux-gnueabihf-gcc (GCC) 14.2.1 20250207’
make[3]: Entering directory '/tmp/RtmppVvg7I/R.INSTALL441619690a4b/class/src'
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c class.c -o class.o
gcc -std=gnu23 -shared -L/build/r/src/R-4.5.1/lib -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o class.so class.o -L/build/r/src/R-4.5.1/lib -lR
make[3]: Leaving directory '/tmp/RtmppVvg7I/R.INSTALL441619690a4b/class/src'
installing to /build/r/src/R-4.5.1/library/class/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (class)
* installing *source* package ‘lattice’ ...
** this is package ‘lattice’ version ‘0.22-7’
** package ‘lattice’ successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
using C compiler: ‘armv7l-unknown-linux-gnueabihf-gcc (GCC) 14.2.1 20250207’
make[3]: Entering directory '/tmp/Rtmp5LZUlG/R.INSTALL4222581f393/lattice/src'
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c init.c -o init.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c threeDplot.c -o threeDplot.o
gcc -std=gnu23 -shared -L/build/r/src/R-4.5.1/lib -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o lattice.so init.o threeDplot.o -L/build/r/src/R-4.5.1/lib -lR
make[3]: Leaving directory '/tmp/Rtmp5LZUlG/R.INSTALL4222581f393/lattice/src'
installing to /build/r/src/R-4.5.1/library/lattice/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (lattice)
begin installing recommended package nlme
begin installing recommended package Matrix
* installing *source* package ‘cluster’ ...
** this is package ‘cluster’ version ‘2.1.8.1’
** package ‘cluster’ successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
using C compiler: ‘armv7l-unknown-linux-gnueabihf-gcc (GCC) 14.2.1 20250207’
make[3]: Entering directory '/tmp/RtmpydzwEL/R.INSTALL4414145604b9/cluster/src'
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c clara.c -o clara.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c daisy.c -o daisy.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dysta.c -o dysta.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c fanny.c -o fanny.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c init.c -o init.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c mona.c -o mona.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pam.c -o pam.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c sildist.c -o sildist.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c spannel.c -o spannel.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c twins.c -o twins.o
gcc -std=gnu23 -shared -L/build/r/src/R-4.5.1/lib -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o cluster.so clara.o daisy.o dysta.o fanny.o init.o mona.o pam.o sildist.o spannel.o twins.o -L/build/r/src/R-4.5.1/lib -lR
make[3]: Leaving directory '/tmp/RtmpydzwEL/R.INSTALL4414145604b9/cluster/src'
installing to /build/r/src/R-4.5.1/library/cluster/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (cluster)
* installing *source* package ‘nlme’ ...
** this is package ‘nlme’ version ‘3.1-168’
** package ‘nlme’ successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
using C compiler: ‘armv7l-unknown-linux-gnueabihf-gcc (GCC) 14.2.1 20250207’
using Fortran compiler: ‘GNU Fortran (GCC) 14.2.1 20250207’
make[3]: Entering directory '/tmp/RtmpN1aJOy/R.INSTALL44913bd0ca9c/nlme/src'
gfortran -fpic -g -O2 -c chol.f -o chol.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c corStruct.c -o corStruct.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c gnls.c -o gnls.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c init.c -o init.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c matrix.c -o matrix.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c nlOptimizer.c -o nlOptimizer.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c nlme.c -o nlme.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c nlmefit.c -o nlmefit.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pdMat.c -o pdMat.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pythag.c -o pythag.o
gfortran -fpic -g -O2 -c rs.f -o rs.o
gcc -std=gnu23 -shared -L/build/r/src/R-4.5.1/lib -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o pdMat.o pythag.o rs.o -lgfortran -lm -L/build/r/src/R-4.5.1/lib -lR
make[3]: Leaving directory '/tmp/RtmpN1aJOy/R.INSTALL44913bd0ca9c/nlme/src'
installing to /build/r/src/R-4.5.1/library/nlme/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (nlme)
* installing *source* package ‘Matrix’ ...
** this is package ‘Matrix’ version ‘1.7-3’
** package ‘Matrix’ successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
using C compiler: ‘armv7l-unknown-linux-gnueabihf-gcc (GCC) 14.2.1 20250207’
make[3]: Entering directory '/tmp/RtmpuMiHtm/R.INSTALL4492208ca1bf/Matrix/src'
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c Csparse.c -o Csparse.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c attrib.c -o attrib.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c bind.c -o bind.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c cholmod-common.c -o cholmod-common.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c cholmod-etc.c -o cholmod-etc.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c coerce.c -o coerce.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c cs-etc.c -o cs-etc.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dense.c -o dense.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c determinant.c -o determinant.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c expm.c -o expm.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c factor.c -o factor.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c idz.c -o idz.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c init.c -o init.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c kappa.c -o kappa.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c matmult.c -o matmult.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c objects.c -o objects.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c perm.c -o perm.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c solve.c -o solve.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c sparse.c -o sparse.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c subassign.c -o subassign.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c subscript.c -o subscript.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c utils-R.c -o utils-R.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c utils.c -o utils.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c validity.c -o validity.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -fvisibility=hidden -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c vector.c -o vector.o
cd SuiteSparse/CHOLMOD && make clean all CC="gcc -std=gnu23" CPPFLAGS=" -I\"/build/r/src/R-4.5.1/include\" -I\"/build/r/src/R-4.5.1/include\" -DNDEBUG -DNPRINT -DNTIMER" CFLAGS="-march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden" AR="ar" RANLIB="ranlib"
make[4]: Entering directory '/tmp/RtmpuMiHtm/R.INSTALL4492208ca1bf/Matrix/src/SuiteSparse/CHOLMOD'
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Check/cholmod_check.c -o Check/cholmod_check.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Check/cholmod_l_check.c -o Check/cholmod_l_check.o
cd SuiteSparse/CCOLAMD && make clean all CC="gcc -std=gnu23" CPPFLAGS=" -I\"/build/r/src/R-4.5.1/include\" -I\"/build/r/src/R-4.5.1/include\" -DNDEBUG -DNPRINT -DNTIMER" CFLAGS="-march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden" AR="ar" RANLIB="ranlib"
make[4]: Entering directory '/tmp/RtmpuMiHtm/R.INSTALL4492208ca1bf/Matrix/src/SuiteSparse/CCOLAMD'
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/ccolamd.c -o Source/ccolamd.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Check/cholmod_read.c -o Check/cholmod_read.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/ccolamd_l.c -o Source/ccolamd_l.o
cd SuiteSparse/CAMD && make clean all CC="gcc -std=gnu23" CPPFLAGS=" -I\"/build/r/src/R-4.5.1/include\" -I\"/build/r/src/R-4.5.1/include\" -DNDEBUG -DNPRINT -DNTIMER" CFLAGS="-march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden" AR="ar" RANLIB="ranlib"
make[4]: Entering directory '/tmp/RtmpuMiHtm/R.INSTALL4492208ca1bf/Matrix/src/SuiteSparse/CAMD'
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/camd_1.c -o Source/camd_1.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/camd_l1.c -o Source/camd_l1.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Check/cholmod_l_read.c -o Check/cholmod_l_read.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/ccolamd_version.c -o Source/ccolamd_version.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/camd_2.c -o Source/camd_2.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/camd_l2.c -o Source/camd_l2.o
rm -f CCOLAMD.a
ar -cr CCOLAMD.a Source/ccolamd.o Source/ccolamd_l.o Source/ccolamd_version.o
ranlib CCOLAMD.a
make[4]: Leaving directory '/tmp/RtmpuMiHtm/R.INSTALL4492208ca1bf/Matrix/src/SuiteSparse/CCOLAMD'
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/camd_aat.c -o Source/camd_aat.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Check/cholmod_write.c -o Check/cholmod_write.o
cd SuiteSparse/COLAMD && make clean all CC="gcc -std=gnu23" CPPFLAGS=" -I\"/build/r/src/R-4.5.1/include\" -I\"/build/r/src/R-4.5.1/include\" -DNDEBUG -DNPRINT -DNTIMER" CFLAGS="-march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden" AR="ar" RANLIB="ranlib"
make[4]: Entering directory '/tmp/RtmpuMiHtm/R.INSTALL4492208ca1bf/Matrix/src/SuiteSparse/COLAMD'
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/colamd.c -o Source/colamd.o
cd SuiteSparse/AMD && make clean all CC="gcc -std=gnu23" CPPFLAGS=" -I\"/build/r/src/R-4.5.1/include\" -I\"/build/r/src/R-4.5.1/include\" -DNDEBUG -DNPRINT -DNTIMER" CFLAGS="-march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden" AR="ar" RANLIB="ranlib"
make[4]: Entering directory '/tmp/RtmpuMiHtm/R.INSTALL4492208ca1bf/Matrix/src/SuiteSparse/AMD'
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/amd_1.c -o Source/amd_1.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/camd_l_aat.c -o Source/camd_l_aat.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/camd_control.c -o Source/camd_control.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/amd_l1.c -o Source/amd_l1.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Check/cholmod_l_write.c -o Check/cholmod_l_write.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/amd_2.c -o Source/amd_2.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/camd_l_control.c -o Source/camd_l_control.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Cholesky/cholmod_amd.c -o Cholesky/cholmod_amd.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/colamd_l.c -o Source/colamd_l.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/camd_defaults.c -o Source/camd_defaults.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/camd_l_defaults.c -o Source/camd_l_defaults.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Cholesky/cholmod_l_amd.c -o Cholesky/cholmod_l_amd.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/amd_l2.c -o Source/amd_l2.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Cholesky/cholmod_analyze.c -o Cholesky/cholmod_analyze.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/camd_dump.c -o Source/camd_dump.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/amd_aat.c -o Source/amd_aat.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/colamd_version.c -o Source/colamd_version.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/camd_l_dump.c -o Source/camd_l_dump.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Cholesky/cholmod_l_analyze.c -o Cholesky/cholmod_l_analyze.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Cholesky/cholmod_colamd.c -o Cholesky/cholmod_colamd.o
rm -f COLAMD.a
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/amd_l_aat.c -o Source/amd_l_aat.o
ar -cr COLAMD.a Source/colamd.o Source/colamd_l.o Source/colamd_version.o
ranlib COLAMD.a
make[4]: Leaving directory '/tmp/RtmpuMiHtm/R.INSTALL4492208ca1bf/Matrix/src/SuiteSparse/COLAMD'
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Cholesky/cholmod_l_colamd.c -o Cholesky/cholmod_l_colamd.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/camd_info.c -o Source/camd_info.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/camd_l_info.c -o Source/camd_l_info.o
cd SuiteSparse/CXSparse && make clean all CC="gcc -std=gnu23" CPPFLAGS=" -I\"/build/r/src/R-4.5.1/include\" -I\"/build/r/src/R-4.5.1/include\" -DNDEBUG -DNPRINT -DNTIMER" CFLAGS="-march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden" AR="ar" RANLIB="ranlib"
make[4]: Entering directory '/tmp/RtmpuMiHtm/R.INSTALL4492208ca1bf/Matrix/src/SuiteSparse/CXSparse'
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/amd_control.c -o Source/amd_control.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_add.c -o Source/cs_add.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Cholesky/cholmod_etree.c -o Cholesky/cholmod_etree.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Cholesky/cholmod_l_etree.c -o Cholesky/cholmod_l_etree.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/amd_l_control.c -o Source/amd_l_control.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/camd_order.c -o Source/camd_order.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_add.c -o Source/cs_dl_add.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_add.c -o Source/cs_ci_add.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Cholesky/cholmod_factorize.c -o Cholesky/cholmod_factorize.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/amd_defaults.c -o Source/amd_defaults.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/camd_l_order.c -o Source/camd_l_order.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Cholesky/cholmod_l_factorize.c -o Cholesky/cholmod_l_factorize.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_add.c -o Source/cs_cl_add.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/amd_l_defaults.c -o Source/amd_l_defaults.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_amd.c -o Source/cs_amd.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/camd_postorder.c -o Source/camd_postorder.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Cholesky/cholmod_postorder.c -o Cholesky/cholmod_postorder.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Cholesky/cholmod_l_postorder.c -o Cholesky/cholmod_l_postorder.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/amd_dump.c -o Source/amd_dump.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Cholesky/cholmod_rcond.c -o Cholesky/cholmod_rcond.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/camd_l_postorder.c -o Source/camd_l_postorder.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_amd.c -o Source/cs_dl_amd.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/amd_l_dump.c -o Source/amd_l_dump.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/amd_info.c -o Source/amd_info.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_amd.c -o Source/cs_ci_amd.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Cholesky/cholmod_l_rcond.c -o Cholesky/cholmod_l_rcond.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_amd.c -o Source/cs_cl_amd.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/camd_preprocess.c -o Source/camd_preprocess.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_chol.c -o Source/cs_chol.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/amd_l_info.c -o Source/amd_l_info.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/amd_order.c -o Source/amd_order.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Cholesky/cholmod_resymbol.c -o Cholesky/cholmod_resymbol.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/amd_l_order.c -o Source/amd_l_order.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Cholesky/cholmod_l_resymbol.c -o Cholesky/cholmod_l_resymbol.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/camd_l_preprocess.c -o Source/camd_l_preprocess.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Cholesky/cholmod_rowcolcounts.c -o Cholesky/cholmod_rowcolcounts.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Cholesky/cholmod_l_rowcolcounts.c -o Cholesky/cholmod_l_rowcolcounts.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_chol.c -o Source/cs_dl_chol.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/amd_post_tree.c -o Source/amd_post_tree.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/camd_valid.c -o Source/camd_valid.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/camd_l_valid.c -o Source/camd_l_valid.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_chol.c -o Source/cs_ci_chol.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_chol.c -o Source/cs_cl_chol.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/amd_l_post_tree.c -o Source/amd_l_post_tree.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/amd_postorder.c -o Source/amd_postorder.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/amd_l_postorder.c -o Source/amd_l_postorder.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Cholesky/cholmod_rowfac.c -o Cholesky/cholmod_rowfac.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/camd_version.c -o Source/camd_version.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Cholesky/cholmod_l_rowfac.c -o Cholesky/cholmod_l_rowfac.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cholsol.c -o Source/cs_cholsol.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Cholesky/cholmod_solve.c -o Cholesky/cholmod_solve.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_cholsol.c -o Source/cs_dl_cholsol.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/amd_preprocess.c -o Source/amd_preprocess.o
rm -f CAMD.a
ar -cr CAMD.a Source/camd_1.o Source/camd_l1.o Source/camd_2.o Source/camd_l2.o Source/camd_aat.o Source/camd_l_aat.o Source/camd_control.o Source/camd_l_control.o Source/camd_defaults.o Source/camd_l_defaults.o Source/camd_dump.o Source/camd_l_dump.o Source/camd_info.o Source/camd_l_info.o Source/camd_order.o Source/camd_l_order.o Source/camd_postorder.o Source/camd_l_postorder.o Source/camd_preprocess.o Source/camd_l_preprocess.o Source/camd_valid.o Source/camd_l_valid.o Source/camd_version.o
ranlib CAMD.a
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Cholesky/cholmod_l_solve.c -o Cholesky/cholmod_l_solve.o
make[4]: Leaving directory '/tmp/RtmpuMiHtm/R.INSTALL4492208ca1bf/Matrix/src/SuiteSparse/CAMD'
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_cholsol.c -o Source/cs_ci_cholsol.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Cholesky/cholmod_spsolve.c -o Cholesky/cholmod_spsolve.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/amd_l_preprocess.c -o Source/amd_l_preprocess.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/amd_valid.c -o Source/amd_valid.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_cholsol.c -o Source/cs_cl_cholsol.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_compress.c -o Source/cs_compress.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/amd_l_valid.c -o Source/amd_l_valid.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Cholesky/cholmod_l_spsolve.c -o Cholesky/cholmod_l_spsolve.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/amd_version.c -o Source/amd_version.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_compress.c -o Source/cs_dl_compress.o
rm -f AMD.a
ar -cr AMD.a Source/amd_1.o Source/amd_l1.o Source/amd_2.o Source/amd_l2.o Source/amd_aat.o Source/amd_l_aat.o Source/amd_control.o Source/amd_l_control.o Source/amd_defaults.o Source/amd_l_defaults.o Source/amd_dump.o Source/amd_l_dump.o Source/amd_info.o Source/amd_l_info.o Source/amd_order.o Source/amd_l_order.o Source/amd_post_tree.o Source/amd_l_post_tree.o Source/amd_postorder.o Source/amd_l_postorder.o Source/amd_preprocess.o Source/amd_l_preprocess.o Source/amd_valid.o Source/amd_l_valid.o Source/amd_version.o
ranlib AMD.a
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_compress.c -o Source/cs_ci_compress.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_compress.c -o Source/cs_cl_compress.o
make[4]: Leaving directory '/tmp/RtmpuMiHtm/R.INSTALL4492208ca1bf/Matrix/src/SuiteSparse/AMD'
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_convert.c -o Source/cs_convert.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_counts.c -o Source/cs_counts.o
cd SuiteSparse/SuiteSparse_config && make clean all CC="gcc -std=gnu23" CPPFLAGS=" -I\"/build/r/src/R-4.5.1/include\" -I\"/build/r/src/R-4.5.1/include\" -DNDEBUG -DNPRINT -DNTIMER" CFLAGS="-march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden" AR="ar" RANLIB="ranlib"
make[4]: Entering directory '/tmp/RtmpuMiHtm/R.INSTALL4492208ca1bf/Matrix/src/SuiteSparse/SuiteSparse_config'
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c SuiteSparse_config.c -o SuiteSparse_config.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_aat.c -o Utility/cholmod_aat.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_aat.c -o Utility/cholmod_l_aat.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_counts.c -o Source/cs_dl_counts.o
rm -f SuiteSparse_config.a
ar -cr SuiteSparse_config.a SuiteSparse_config.o
ranlib SuiteSparse_config.a
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_counts.c -o Source/cs_ci_counts.o
make[4]: Leaving directory '/tmp/RtmpuMiHtm/R.INSTALL4492208ca1bf/Matrix/src/SuiteSparse/SuiteSparse_config'
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_counts.c -o Source/cs_cl_counts.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cumsum.c -o Source/cs_cumsum.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_add.c -o Utility/cholmod_add.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_cumsum.c -o Source/cs_dl_cumsum.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_add.c -o Utility/cholmod_l_add.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_cumsum.c -o Source/cs_ci_cumsum.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_add_size_t.c -o Utility/cholmod_add_size_t.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_add_size_t.c -o Utility/cholmod_l_add_size_t.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_cumsum.c -o Source/cs_cl_cumsum.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_alloc_factor.c -o Utility/cholmod_alloc_factor.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dfs.c -o Source/cs_dfs.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_dfs.c -o Source/cs_dl_dfs.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_dfs.c -o Source/cs_ci_dfs.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_alloc_factor.c -o Utility/cholmod_l_alloc_factor.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_dfs.c -o Source/cs_cl_dfs.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_alloc_work.c -o Utility/cholmod_alloc_work.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dmperm.c -o Source/cs_dmperm.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_alloc_work.c -o Utility/cholmod_l_alloc_work.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_dmperm.c -o Source/cs_dl_dmperm.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_dmperm.c -o Source/cs_ci_dmperm.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_allocate_dense.c -o Utility/cholmod_allocate_dense.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_dmperm.c -o Source/cs_cl_dmperm.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_droptol.c -o Source/cs_droptol.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_allocate_dense.c -o Utility/cholmod_l_allocate_dense.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_droptol.c -o Source/cs_dl_droptol.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_allocate_factor.c -o Utility/cholmod_allocate_factor.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_droptol.c -o Source/cs_ci_droptol.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_droptol.c -o Source/cs_cl_droptol.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_allocate_factor.c -o Utility/cholmod_l_allocate_factor.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_allocate_sparse.c -o Utility/cholmod_allocate_sparse.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_allocate_sparse.c -o Utility/cholmod_l_allocate_sparse.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dropzeros.c -o Source/cs_dropzeros.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_allocate_triplet.c -o Utility/cholmod_allocate_triplet.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_dropzeros.c -o Source/cs_dl_dropzeros.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_allocate_triplet.c -o Utility/cholmod_l_allocate_triplet.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_dropzeros.c -o Source/cs_ci_dropzeros.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_dropzeros.c -o Source/cs_cl_dropzeros.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_allocate_work.c -o Utility/cholmod_allocate_work.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dupl.c -o Source/cs_dupl.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_allocate_work.c -o Utility/cholmod_l_allocate_work.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_dupl.c -o Source/cs_dl_dupl.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_dupl.c -o Source/cs_ci_dupl.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_dupl.c -o Source/cs_cl_dupl.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_band.c -o Utility/cholmod_band.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_entry.c -o Source/cs_entry.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_band.c -o Utility/cholmod_l_band.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_band_nnz.c -o Utility/cholmod_band_nnz.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_band_nnz.c -o Utility/cholmod_l_band_nnz.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_entry.c -o Source/cs_dl_entry.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_calloc.c -o Utility/cholmod_calloc.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_entry.c -o Source/cs_ci_entry.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_calloc.c -o Utility/cholmod_l_calloc.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_entry.c -o Source/cs_cl_entry.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ereach.c -o Source/cs_ereach.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_ereach.c -o Source/cs_dl_ereach.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_change_factor.c -o Utility/cholmod_change_factor.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_change_factor.c -o Utility/cholmod_l_change_factor.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_clear_flag.c -o Utility/cholmod_clear_flag.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_clear_flag.c -o Utility/cholmod_l_clear_flag.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_copy.c -o Utility/cholmod_copy.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_ereach.c -o Source/cs_ci_ereach.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_copy.c -o Utility/cholmod_l_copy.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_ereach.c -o Source/cs_cl_ereach.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_etree.c -o Source/cs_etree.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_etree.c -o Source/cs_dl_etree.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_etree.c -o Source/cs_ci_etree.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_copy_dense.c -o Utility/cholmod_copy_dense.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_etree.c -o Source/cs_cl_etree.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_copy_dense.c -o Utility/cholmod_l_copy_dense.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_copy_dense2.c -o Utility/cholmod_copy_dense2.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_fkeep.c -o Source/cs_fkeep.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_copy_dense2.c -o Utility/cholmod_l_copy_dense2.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_fkeep.c -o Source/cs_dl_fkeep.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_copy_factor.c -o Utility/cholmod_copy_factor.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_copy_factor.c -o Utility/cholmod_l_copy_factor.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_fkeep.c -o Source/cs_ci_fkeep.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_fkeep.c -o Source/cs_cl_fkeep.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_copy_sparse.c -o Utility/cholmod_copy_sparse.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_copy_sparse.c -o Utility/cholmod_l_copy_sparse.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_copy_triplet.c -o Utility/cholmod_copy_triplet.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_copy_triplet.c -o Utility/cholmod_l_copy_triplet.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_gaxpy.c -o Source/cs_gaxpy.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_gaxpy.c -o Source/cs_dl_gaxpy.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_cumsum.c -o Utility/cholmod_cumsum.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_cumsum.c -o Utility/cholmod_l_cumsum.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_dbound.c -o Utility/cholmod_dbound.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_gaxpy.c -o Source/cs_ci_gaxpy.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_dbound.c -o Utility/cholmod_l_dbound.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_gaxpy.c -o Source/cs_cl_gaxpy.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_defaults.c -o Utility/cholmod_defaults.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_defaults.c -o Utility/cholmod_l_defaults.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_dense_nnz.c -o Utility/cholmod_dense_nnz.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_dense_nnz.c -o Utility/cholmod_l_dense_nnz.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_happly.c -o Source/cs_happly.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_happly.c -o Source/cs_dl_happly.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_dense_to_sparse.c -o Utility/cholmod_dense_to_sparse.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_dense_to_sparse.c -o Utility/cholmod_l_dense_to_sparse.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_divcomplex.c -o Utility/cholmod_divcomplex.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_divcomplex.c -o Utility/cholmod_l_divcomplex.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_happly.c -o Source/cs_ci_happly.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_happly.c -o Source/cs_cl_happly.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_ensure_dense.c -o Utility/cholmod_ensure_dense.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_ensure_dense.c -o Utility/cholmod_l_ensure_dense.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_error.c -o Utility/cholmod_error.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_house.c -o Source/cs_house.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_error.c -o Utility/cholmod_l_error.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_house.c -o Source/cs_dl_house.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_house.c -o Source/cs_ci_house.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_eye.c -o Utility/cholmod_eye.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_house.c -o Source/cs_cl_house.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_eye.c -o Utility/cholmod_l_eye.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_factor_to_sparse.c -o Utility/cholmod_factor_to_sparse.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ipvec.c -o Source/cs_ipvec.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_factor_to_sparse.c -o Utility/cholmod_l_factor_to_sparse.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_finish.c -o Utility/cholmod_finish.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_finish.c -o Utility/cholmod_l_finish.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_ipvec.c -o Source/cs_dl_ipvec.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_ipvec.c -o Source/cs_ci_ipvec.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_free.c -o Utility/cholmod_free.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_ipvec.c -o Source/cs_cl_ipvec.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_free.c -o Utility/cholmod_l_free.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_free_dense.c -o Utility/cholmod_free_dense.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_free_dense.c -o Utility/cholmod_l_free_dense.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_free_factor.c -o Utility/cholmod_free_factor.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_leaf.c -o Source/cs_leaf.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_free_factor.c -o Utility/cholmod_l_free_factor.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_leaf.c -o Source/cs_dl_leaf.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_free_sparse.c -o Utility/cholmod_free_sparse.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_free_sparse.c -o Utility/cholmod_l_free_sparse.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_free_triplet.c -o Utility/cholmod_free_triplet.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_free_triplet.c -o Utility/cholmod_l_free_triplet.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_free_work.c -o Utility/cholmod_free_work.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_leaf.c -o Source/cs_ci_leaf.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_free_work.c -o Utility/cholmod_l_free_work.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_leaf.c -o Source/cs_cl_leaf.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_hypot.c -o Utility/cholmod_hypot.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_hypot.c -o Utility/cholmod_l_hypot.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_malloc.c -o Utility/cholmod_malloc.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_load.c -o Source/cs_load.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_malloc.c -o Utility/cholmod_l_malloc.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_load.c -o Source/cs_dl_load.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_maxrank.c -o Utility/cholmod_maxrank.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_load.c -o Source/cs_ci_load.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_maxrank.c -o Utility/cholmod_l_maxrank.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_memdebug.c -o Utility/cholmod_memdebug.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_load.c -o Source/cs_cl_load.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_lsolve.c -o Source/cs_lsolve.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_mult_size_t.c -o Utility/cholmod_mult_size_t.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_lsolve.c -o Source/cs_dl_lsolve.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_lsolve.c -o Source/cs_ci_lsolve.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_mult_size_t.c -o Utility/cholmod_l_mult_size_t.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_mult_uint64_t.c -o Utility/cholmod_mult_uint64_t.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_nnz.c -o Utility/cholmod_nnz.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_nnz.c -o Utility/cholmod_l_nnz.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_ones.c -o Utility/cholmod_ones.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_lsolve.c -o Source/cs_cl_lsolve.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ltsolve.c -o Source/cs_ltsolve.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_ones.c -o Utility/cholmod_l_ones.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_pack_factor.c -o Utility/cholmod_pack_factor.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_pack_factor.c -o Utility/cholmod_l_pack_factor.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_ptranspose.c -o Utility/cholmod_ptranspose.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_ltsolve.c -o Source/cs_dl_ltsolve.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_ltsolve.c -o Source/cs_ci_ltsolve.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_ltsolve.c -o Source/cs_cl_ltsolve.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_ptranspose.c -o Utility/cholmod_l_ptranspose.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_realloc.c -o Utility/cholmod_realloc.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_realloc.c -o Utility/cholmod_l_realloc.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_realloc_multiple.c -o Utility/cholmod_realloc_multiple.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_lu.c -o Source/cs_lu.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_lu.c -o Source/cs_dl_lu.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_lu.c -o Source/cs_ci_lu.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_realloc_multiple.c -o Utility/cholmod_l_realloc_multiple.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_reallocate_column.c -o Utility/cholmod_reallocate_column.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_reallocate_column.c -o Utility/cholmod_l_reallocate_column.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_lu.c -o Source/cs_cl_lu.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_reallocate_factor.c -o Utility/cholmod_reallocate_factor.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_lusol.c -o Source/cs_lusol.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_reallocate_factor.c -o Utility/cholmod_l_reallocate_factor.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_lusol.c -o Source/cs_dl_lusol.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_reallocate_sparse.c -o Utility/cholmod_reallocate_sparse.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_reallocate_sparse.c -o Utility/cholmod_l_reallocate_sparse.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_reallocate_triplet.c -o Utility/cholmod_reallocate_triplet.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_lusol.c -o Source/cs_ci_lusol.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_lusol.c -o Source/cs_cl_lusol.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_reallocate_triplet.c -o Utility/cholmod_l_reallocate_triplet.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_malloc.c -o Source/cs_malloc.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_sbound.c -o Utility/cholmod_sbound.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_sbound.c -o Utility/cholmod_l_sbound.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_score_comp.c -o Utility/cholmod_score_comp.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_malloc.c -o Source/cs_dl_malloc.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_malloc.c -o Source/cs_ci_malloc.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_malloc.c -o Source/cs_cl_malloc.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_score_comp.c -o Utility/cholmod_l_score_comp.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_set_empty.c -o Utility/cholmod_set_empty.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_set_empty.c -o Utility/cholmod_l_set_empty.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_maxtrans.c -o Source/cs_maxtrans.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_sort.c -o Utility/cholmod_sort.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_maxtrans.c -o Source/cs_dl_maxtrans.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_maxtrans.c -o Source/cs_ci_maxtrans.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_sort.c -o Utility/cholmod_l_sort.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_sparse_to_dense.c -o Utility/cholmod_sparse_to_dense.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_sparse_to_dense.c -o Utility/cholmod_l_sparse_to_dense.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_maxtrans.c -o Source/cs_cl_maxtrans.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_multiply.c -o Source/cs_multiply.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_sparse_to_triplet.c -o Utility/cholmod_sparse_to_triplet.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_multiply.c -o Source/cs_dl_multiply.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_multiply.c -o Source/cs_ci_multiply.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_sparse_to_triplet.c -o Utility/cholmod_l_sparse_to_triplet.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_speye.c -o Utility/cholmod_speye.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_multiply.c -o Source/cs_cl_multiply.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_speye.c -o Utility/cholmod_l_speye.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_spzeros.c -o Utility/cholmod_spzeros.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_norm.c -o Source/cs_norm.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_spzeros.c -o Utility/cholmod_l_spzeros.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_start.c -o Utility/cholmod_start.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_start.c -o Utility/cholmod_l_start.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_transpose.c -o Utility/cholmod_transpose.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_norm.c -o Source/cs_dl_norm.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_norm.c -o Source/cs_ci_norm.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_transpose.c -o Utility/cholmod_l_transpose.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_transpose_sym.c -o Utility/cholmod_transpose_sym.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_transpose_sym.c -o Utility/cholmod_l_transpose_sym.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_transpose_unsym.c -o Utility/cholmod_transpose_unsym.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_transpose_unsym.c -o Utility/cholmod_l_transpose_unsym.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_norm.c -o Source/cs_cl_norm.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_permute.c -o Source/cs_permute.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_permute.c -o Source/cs_dl_permute.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_triplet_to_sparse.c -o Utility/cholmod_triplet_to_sparse.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_permute.c -o Source/cs_ci_permute.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_permute.c -o Source/cs_cl_permute.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_triplet_to_sparse.c -o Utility/cholmod_l_triplet_to_sparse.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_pinv.c -o Source/cs_pinv.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_version.c -o Utility/cholmod_version.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_pinv.c -o Source/cs_dl_pinv.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_version.c -o Utility/cholmod_l_version.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_xtype.c -o Utility/cholmod_xtype.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_pinv.c -o Source/cs_ci_pinv.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_xtype.c -o Utility/cholmod_l_xtype.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_pinv.c -o Source/cs_cl_pinv.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_zeros.c -o Utility/cholmod_zeros.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Utility/cholmod_l_zeros.c -o Utility/cholmod_l_zeros.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c MatrixOps/cholmod_drop.c -o MatrixOps/cholmod_drop.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_post.c -o Source/cs_post.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_post.c -o Source/cs_dl_post.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_post.c -o Source/cs_ci_post.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_post.c -o Source/cs_cl_post.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c MatrixOps/cholmod_l_drop.c -o MatrixOps/cholmod_l_drop.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c MatrixOps/cholmod_horzcat.c -o MatrixOps/cholmod_horzcat.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_print.c -o Source/cs_print.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c MatrixOps/cholmod_l_horzcat.c -o MatrixOps/cholmod_l_horzcat.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c MatrixOps/cholmod_norm.c -o MatrixOps/cholmod_norm.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_print.c -o Source/cs_dl_print.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_print.c -o Source/cs_ci_print.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_print.c -o Source/cs_cl_print.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c MatrixOps/cholmod_l_norm.c -o MatrixOps/cholmod_l_norm.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_pvec.c -o Source/cs_pvec.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c MatrixOps/cholmod_scale.c -o MatrixOps/cholmod_scale.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_pvec.c -o Source/cs_dl_pvec.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c MatrixOps/cholmod_l_scale.c -o MatrixOps/cholmod_l_scale.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c MatrixOps/cholmod_sdmult.c -o MatrixOps/cholmod_sdmult.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_pvec.c -o Source/cs_ci_pvec.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c MatrixOps/cholmod_l_sdmult.c -o MatrixOps/cholmod_l_sdmult.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_pvec.c -o Source/cs_cl_pvec.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c MatrixOps/cholmod_ssmult.c -o MatrixOps/cholmod_ssmult.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c MatrixOps/cholmod_l_ssmult.c -o MatrixOps/cholmod_l_ssmult.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_qr.c -o Source/cs_qr.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_qr.c -o Source/cs_dl_qr.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c MatrixOps/cholmod_submatrix.c -o MatrixOps/cholmod_submatrix.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c MatrixOps/cholmod_l_submatrix.c -o MatrixOps/cholmod_l_submatrix.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c MatrixOps/cholmod_symmetry.c -o MatrixOps/cholmod_symmetry.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_qr.c -o Source/cs_ci_qr.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_qr.c -o Source/cs_cl_qr.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_qrsol.c -o Source/cs_qrsol.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_qrsol.c -o Source/cs_dl_qrsol.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c MatrixOps/cholmod_l_symmetry.c -o MatrixOps/cholmod_l_symmetry.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_qrsol.c -o Source/cs_ci_qrsol.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_qrsol.c -o Source/cs_cl_qrsol.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_randperm.c -o Source/cs_randperm.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c MatrixOps/cholmod_vertcat.c -o MatrixOps/cholmod_vertcat.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c MatrixOps/cholmod_l_vertcat.c -o MatrixOps/cholmod_l_vertcat.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_randperm.c -o Source/cs_dl_randperm.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Modify/cholmod_rowadd.c -o Modify/cholmod_rowadd.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_randperm.c -o Source/cs_ci_randperm.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Modify/cholmod_l_rowadd.c -o Modify/cholmod_l_rowadd.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_randperm.c -o Source/cs_cl_randperm.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Modify/cholmod_rowdel.c -o Modify/cholmod_rowdel.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Modify/cholmod_l_rowdel.c -o Modify/cholmod_l_rowdel.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_reach.c -o Source/cs_reach.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Modify/cholmod_updown.c -o Modify/cholmod_updown.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Modify/cholmod_l_updown.c -o Modify/cholmod_l_updown.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Partition/cholmod_camd.c -o Partition/cholmod_camd.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_reach.c -o Source/cs_dl_reach.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_reach.c -o Source/cs_ci_reach.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Partition/cholmod_l_camd.c -o Partition/cholmod_l_camd.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Partition/cholmod_ccolamd.c -o Partition/cholmod_ccolamd.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_reach.c -o Source/cs_cl_reach.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Partition/cholmod_l_ccolamd.c -o Partition/cholmod_l_ccolamd.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Partition/cholmod_csymamd.c -o Partition/cholmod_csymamd.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Partition/cholmod_l_csymamd.c -o Partition/cholmod_l_csymamd.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Partition/cholmod_metis.c -o Partition/cholmod_metis.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_scatter.c -o Source/cs_scatter.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Partition/cholmod_l_metis.c -o Partition/cholmod_l_metis.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Partition/cholmod_metis_wrapper.c -o Partition/cholmod_metis_wrapper.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Partition/cholmod_nesdis.c -o Partition/cholmod_nesdis.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_scatter.c -o Source/cs_dl_scatter.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Partition/cholmod_l_nesdis.c -o Partition/cholmod_l_nesdis.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Supernodal/cholmod_super_numeric.c -o Supernodal/cholmod_super_numeric.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_scatter.c -o Source/cs_ci_scatter.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_scatter.c -o Source/cs_cl_scatter.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Supernodal/cholmod_l_super_numeric.c -o Supernodal/cholmod_l_super_numeric.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Supernodal/cholmod_super_solve.c -o Supernodal/cholmod_super_solve.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_scc.c -o Source/cs_scc.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Supernodal/cholmod_l_super_solve.c -o Supernodal/cholmod_l_super_solve.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_scc.c -o Source/cs_dl_scc.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_scc.c -o Source/cs_ci_scc.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Supernodal/cholmod_super_symbolic.c -o Supernodal/cholmod_super_symbolic.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_scc.c -o Source/cs_cl_scc.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_schol.c -o Source/cs_schol.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Supernodal/cholmod_l_super_symbolic.c -o Supernodal/cholmod_l_super_symbolic.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_schol.c -o Source/cs_dl_schol.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_schol.c -o Source/cs_ci_schol.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_schol.c -o Source/cs_cl_schol.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_spsolve.c -o Source/cs_spsolve.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_spsolve.c -o Source/cs_dl_spsolve.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_spsolve.c -o Source/cs_ci_spsolve.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_spsolve.c -o Source/cs_cl_spsolve.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_sqr.c -o Source/cs_sqr.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_sqr.c -o Source/cs_dl_sqr.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_sqr.c -o Source/cs_ci_sqr.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_sqr.c -o Source/cs_cl_sqr.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_symperm.c -o Source/cs_symperm.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_symperm.c -o Source/cs_dl_symperm.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_symperm.c -o Source/cs_ci_symperm.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_symperm.c -o Source/cs_cl_symperm.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_tdfs.c -o Source/cs_tdfs.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_tdfs.c -o Source/cs_dl_tdfs.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_tdfs.c -o Source/cs_ci_tdfs.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_tdfs.c -o Source/cs_cl_tdfs.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_transpose.c -o Source/cs_transpose.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_transpose.c -o Source/cs_dl_transpose.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_transpose.c -o Source/cs_ci_transpose.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_transpose.c -o Source/cs_cl_transpose.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_updown.c -o Source/cs_updown.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_updown.c -o Source/cs_dl_updown.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_updown.c -o Source/cs_ci_updown.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_updown.c -o Source/cs_cl_updown.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_usolve.c -o Source/cs_usolve.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_usolve.c -o Source/cs_dl_usolve.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_usolve.c -o Source/cs_ci_usolve.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_usolve.c -o Source/cs_cl_usolve.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_util.c -o Source/cs_util.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_util.c -o Source/cs_dl_util.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_util.c -o Source/cs_ci_util.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_util.c -o Source/cs_cl_util.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_utsolve.c -o Source/cs_utsolve.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_dl_utsolve.c -o Source/cs_dl_utsolve.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_ci_utsolve.c -o Source/cs_ci_utsolve.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cs_cl_utsolve.c -o Source/cs_cl_utsolve.o
gcc -std=gnu23 -I./Include -I../SuiteSparse_config -I"/build/r/src/R-4.5.1/include" -I"/build/r/src/R-4.5.1/include" -DNDEBUG -DNPRINT -DNTIMER -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -fpic -fvisibility=hidden -c Source/cxsparse_version.c -o Source/cxsparse_version.o
rm -f CXSparse.a
ar -cr CXSparse.a Source/cs_add.o Source/cs_dl_add.o Source/cs_ci_add.o Source/cs_cl_add.o Source/cs_amd.o Source/cs_dl_amd.o Source/cs_ci_amd.o Source/cs_cl_amd.o Source/cs_chol.o Source/cs_dl_chol.o Source/cs_ci_chol.o Source/cs_cl_chol.o Source/cs_cholsol.o Source/cs_dl_cholsol.o Source/cs_ci_cholsol.o Source/cs_cl_cholsol.o Source/cs_compress.o Source/cs_dl_compress.o Source/cs_ci_compress.o Source/cs_cl_compress.o Source/cs_convert.o Source/cs_counts.o Source/cs_dl_counts.o Source/cs_ci_counts.o Source/cs_cl_counts.o Source/cs_cumsum.o Source/cs_dl_cumsum.o Source/cs_ci_cumsum.o Source/cs_cl_cumsum.o Source/cs_dfs.o Source/cs_dl_dfs.o Source/cs_ci_dfs.o Source/cs_cl_dfs.o Source/cs_dmperm.o Source/cs_dl_dmperm.o Source/cs_ci_dmperm.o Source/cs_cl_dmperm.o Source/cs_droptol.o Source/cs_dl_droptol.o Source/cs_ci_droptol.o Source/cs_cl_droptol.o Source/cs_dropzeros.o Source/cs_dl_dropzeros.o Source/cs_ci_dropzeros.o Source/cs_cl_dropzeros.o Source/cs_dupl.o Source/cs_dl_dupl.o Source/cs_ci_dupl.o Source/cs_cl_dupl.o Source/cs_entry.o Source/cs_dl_entry.o Source/cs_ci_entry.o Source/cs_cl_entry.o Source/cs_ereach.o Source/cs_dl_ereach.o Source/cs_ci_ereach.o Source/cs_cl_ereach.o Source/cs_etree.o Source/cs_dl_etree.o Source/cs_ci_etree.o Source/cs_cl_etree.o Source/cs_fkeep.o Source/cs_dl_fkeep.o Source/cs_ci_fkeep.o Source/cs_cl_fkeep.o Source/cs_gaxpy.o Source/cs_dl_gaxpy.o Source/cs_ci_gaxpy.o Source/cs_cl_gaxpy.o Source/cs_happly.o Source/cs_dl_happly.o Source/cs_ci_happly.o Source/cs_cl_happly.o Source/cs_house.o Source/cs_dl_house.o Source/cs_ci_house.o Source/cs_cl_house.o Source/cs_ipvec.o Source/cs_dl_ipvec.o Source/cs_ci_ipvec.o Source/cs_cl_ipvec.o Source/cs_leaf.o Source/cs_dl_leaf.o Source/cs_ci_leaf.o Source/cs_cl_leaf.o Source/cs_load.o Source/cs_dl_load.o Source/cs_ci_load.o Source/cs_cl_load.o Source/cs_lsolve.o Source/cs_dl_lsolve.o Source/cs_ci_lsolve.o Source/cs_cl_lsolve.o Source/cs_ltsolve.o Source/cs_dl_ltsolve.o Source/cs_ci_ltsolve.o Source/cs_cl_ltsolve.o Source/cs_lu.o Source/cs_dl_lu.o Source/cs_ci_lu.o Source/cs_cl_lu.o Source/cs_lusol.o Source/cs_dl_lusol.o Source/cs_ci_lusol.o Source/cs_cl_lusol.o Source/cs_malloc.o Source/cs_dl_malloc.o Source/cs_ci_malloc.o Source/cs_cl_malloc.o Source/cs_maxtrans.o Source/cs_dl_maxtrans.o Source/cs_ci_maxtrans.o Source/cs_cl_maxtrans.o Source/cs_multiply.o Source/cs_dl_multiply.o Source/cs_ci_multiply.o Source/cs_cl_multiply.o Source/cs_norm.o Source/cs_dl_norm.o Source/cs_ci_norm.o Source/cs_cl_norm.o Source/cs_permute.o Source/cs_dl_permute.o Source/cs_ci_permute.o Source/cs_cl_permute.o Source/cs_pinv.o Source/cs_dl_pinv.o Source/cs_ci_pinv.o Source/cs_cl_pinv.o Source/cs_post.o Source/cs_dl_post.o Source/cs_ci_post.o Source/cs_cl_post.o Source/cs_print.o Source/cs_dl_print.o Source/cs_ci_print.o Source/cs_cl_print.o Source/cs_pvec.o Source/cs_dl_pvec.o Source/cs_ci_pvec.o Source/cs_cl_pvec.o Source/cs_qr.o Source/cs_dl_qr.o Source/cs_ci_qr.o Source/cs_cl_qr.o Source/cs_qrsol.o Source/cs_dl_qrsol.o Source/cs_ci_qrsol.o Source/cs_cl_qrsol.o Source/cs_randperm.o Source/cs_dl_randperm.o Source/cs_ci_randperm.o Source/cs_cl_randperm.o Source/cs_reach.o Source/cs_dl_reach.o Source/cs_ci_reach.o Source/cs_cl_reach.o Source/cs_scatter.o Source/cs_dl_scatter.o Source/cs_ci_scatter.o Source/cs_cl_scatter.o Source/cs_scc.o Source/cs_dl_scc.o Source/cs_ci_scc.o Source/cs_cl_scc.o Source/cs_schol.o Source/cs_dl_schol.o Source/cs_ci_schol.o Source/cs_cl_schol.o Source/cs_spsolve.o Source/cs_dl_spsolve.o Source/cs_ci_spsolve.o Source/cs_cl_spsolve.o Source/cs_sqr.o Source/cs_dl_sqr.o Source/cs_ci_sqr.o Source/cs_cl_sqr.o Source/cs_symperm.o Source/cs_dl_symperm.o Source/cs_ci_symperm.o Source/cs_cl_symperm.o Source/cs_tdfs.o Source/cs_dl_tdfs.o Source/cs_ci_tdfs.o Source/cs_cl_tdfs.o Source/cs_transpose.o Source/cs_dl_transpose.o Source/cs_ci_transpose.o Source/cs_cl_transpose.o Source/cs_updown.o Source/cs_dl_updown.o Source/cs_ci_updown.o Source/cs_cl_updown.o Source/cs_usolve.o Source/cs_dl_usolve.o Source/cs_ci_usolve.o Source/cs_cl_usolve.o Source/cs_util.o Source/cs_dl_util.o Source/cs_ci_util.o Source/cs_cl_util.o Source/cs_utsolve.o Source/cs_dl_utsolve.o Source/cs_ci_utsolve.o Source/cs_cl_utsolve.o Source/cxsparse_version.o
ranlib CXSparse.a
make[4]: Leaving directory '/tmp/RtmpuMiHtm/R.INSTALL4492208ca1bf/Matrix/src/SuiteSparse/CXSparse'
rm -f CHOLMOD.a
ar -cr CHOLMOD.a Check/cholmod_check.o Check/cholmod_l_check.o Check/cholmod_read.o Check/cholmod_l_read.o Check/cholmod_write.o Check/cholmod_l_write.o Cholesky/cholmod_amd.o Cholesky/cholmod_l_amd.o Cholesky/cholmod_analyze.o Cholesky/cholmod_l_analyze.o Cholesky/cholmod_colamd.o Cholesky/cholmod_l_colamd.o Cholesky/cholmod_etree.o Cholesky/cholmod_l_etree.o Cholesky/cholmod_factorize.o Cholesky/cholmod_l_factorize.o Cholesky/cholmod_postorder.o Cholesky/cholmod_l_postorder.o Cholesky/cholmod_rcond.o Cholesky/cholmod_l_rcond.o Cholesky/cholmod_resymbol.o Cholesky/cholmod_l_resymbol.o Cholesky/cholmod_rowcolcounts.o Cholesky/cholmod_l_rowcolcounts.o Cholesky/cholmod_rowfac.o Cholesky/cholmod_l_rowfac.o Cholesky/cholmod_solve.o Cholesky/cholmod_l_solve.o Cholesky/cholmod_spsolve.o Cholesky/cholmod_l_spsolve.o Utility/cholmod_aat.o Utility/cholmod_l_aat.o Utility/cholmod_add.o Utility/cholmod_l_add.o Utility/cholmod_add_size_t.o Utility/cholmod_l_add_size_t.o Utility/cholmod_alloc_factor.o Utility/cholmod_l_alloc_factor.o Utility/cholmod_alloc_work.o Utility/cholmod_l_alloc_work.o Utility/cholmod_allocate_dense.o Utility/cholmod_l_allocate_dense.o Utility/cholmod_allocate_factor.o Utility/cholmod_l_allocate_factor.o Utility/cholmod_allocate_sparse.o Utility/cholmod_l_allocate_sparse.o Utility/cholmod_allocate_triplet.o Utility/cholmod_l_allocate_triplet.o Utility/cholmod_allocate_work.o Utility/cholmod_l_allocate_work.o Utility/cholmod_band.o Utility/cholmod_l_band.o Utility/cholmod_band_nnz.o Utility/cholmod_l_band_nnz.o Utility/cholmod_calloc.o Utility/cholmod_l_calloc.o Utility/cholmod_change_factor.o Utility/cholmod_l_change_factor.o Utility/cholmod_clear_flag.o Utility/cholmod_l_clear_flag.o Utility/cholmod_copy.o Utility/cholmod_l_copy.o Utility/cholmod_copy_dense.o Utility/cholmod_l_copy_dense.o Utility/cholmod_copy_dense2.o Utility/cholmod_l_copy_dense2.o Utility/cholmod_copy_factor.o Utility/cholmod_l_copy_factor.o Utility/cholmod_copy_sparse.o Utility/cholmod_l_copy_sparse.o Utility/cholmod_copy_triplet.o Utility/cholmod_l_copy_triplet.o Utility/cholmod_cumsum.o Utility/cholmod_l_cumsum.o Utility/cholmod_dbound.o Utility/cholmod_l_dbound.o Utility/cholmod_defaults.o Utility/cholmod_l_defaults.o Utility/cholmod_dense_nnz.o Utility/cholmod_l_dense_nnz.o Utility/cholmod_dense_to_sparse.o Utility/cholmod_l_dense_to_sparse.o Utility/cholmod_divcomplex.o Utility/cholmod_l_divcomplex.o Utility/cholmod_ensure_dense.o Utility/cholmod_l_ensure_dense.o Utility/cholmod_error.o Utility/cholmod_l_error.o Utility/cholmod_eye.o Utility/cholmod_l_eye.o Utility/cholmod_factor_to_sparse.o Utility/cholmod_l_factor_to_sparse.o Utility/cholmod_finish.o Utility/cholmod_l_finish.o Utility/cholmod_free.o Utility/cholmod_l_free.o Utility/cholmod_free_dense.o Utility/cholmod_l_free_dense.o Utility/cholmod_free_factor.o Utility/cholmod_l_free_factor.o Utility/cholmod_free_sparse.o Utility/cholmod_l_free_sparse.o Utility/cholmod_free_triplet.o Utility/cholmod_l_free_triplet.o Utility/cholmod_free_work.o Utility/cholmod_l_free_work.o Utility/cholmod_hypot.o Utility/cholmod_l_hypot.o Utility/cholmod_malloc.o Utility/cholmod_l_malloc.o Utility/cholmod_maxrank.o Utility/cholmod_l_maxrank.o Utility/cholmod_memdebug.o Utility/cholmod_mult_size_t.o Utility/cholmod_l_mult_size_t.o Utility/cholmod_mult_uint64_t.o Utility/cholmod_nnz.o Utility/cholmod_l_nnz.o Utility/cholmod_ones.o Utility/cholmod_l_ones.o Utility/cholmod_pack_factor.o Utility/cholmod_l_pack_factor.o Utility/cholmod_ptranspose.o Utility/cholmod_l_ptranspose.o Utility/cholmod_realloc.o Utility/cholmod_l_realloc.o Utility/cholmod_realloc_multiple.o Utility/cholmod_l_realloc_multiple.o Utility/cholmod_reallocate_column.o Utility/cholmod_l_reallocate_column.o Utility/cholmod_reallocate_factor.o Utility/cholmod_l_reallocate_factor.o Utility/cholmod_reallocate_sparse.o Utility/cholmod_l_reallocate_sparse.o Utility/cholmod_reallocate_triplet.o Utility/cholmod_l_reallocate_triplet.o Utility/cholmod_sbound.o Utility/cholmod_l_sbound.o Utility/cholmod_score_comp.o Utility/cholmod_l_score_comp.o Utility/cholmod_set_empty.o Utility/cholmod_l_set_empty.o Utility/cholmod_sort.o Utility/cholmod_l_sort.o Utility/cholmod_sparse_to_dense.o Utility/cholmod_l_sparse_to_dense.o Utility/cholmod_sparse_to_triplet.o Utility/cholmod_l_sparse_to_triplet.o Utility/cholmod_speye.o Utility/cholmod_l_speye.o Utility/cholmod_spzeros.o Utility/cholmod_l_spzeros.o Utility/cholmod_start.o Utility/cholmod_l_start.o Utility/cholmod_transpose.o Utility/cholmod_l_transpose.o Utility/cholmod_transpose_sym.o Utility/cholmod_l_transpose_sym.o Utility/cholmod_transpose_unsym.o Utility/cholmod_l_transpose_unsym.o Utility/cholmod_triplet_to_sparse.o Utility/cholmod_l_triplet_to_sparse.o Utility/cholmod_version.o Utility/cholmod_l_version.o Utility/cholmod_xtype.o Utility/cholmod_l_xtype.o Utility/cholmod_zeros.o Utility/cholmod_l_zeros.o MatrixOps/cholmod_drop.o MatrixOps/cholmod_l_drop.o MatrixOps/cholmod_horzcat.o MatrixOps/cholmod_l_horzcat.o MatrixOps/cholmod_norm.o MatrixOps/cholmod_l_norm.o MatrixOps/cholmod_scale.o MatrixOps/cholmod_l_scale.o MatrixOps/cholmod_sdmult.o MatrixOps/cholmod_l_sdmult.o MatrixOps/cholmod_ssmult.o MatrixOps/cholmod_l_ssmult.o MatrixOps/cholmod_submatrix.o MatrixOps/cholmod_l_submatrix.o MatrixOps/cholmod_symmetry.o MatrixOps/cholmod_l_symmetry.o MatrixOps/cholmod_vertcat.o MatrixOps/cholmod_l_vertcat.o Modify/cholmod_rowadd.o Modify/cholmod_l_rowadd.o Modify/cholmod_rowdel.o Modify/cholmod_l_rowdel.o Modify/cholmod_updown.o Modify/cholmod_l_updown.o Partition/cholmod_camd.o Partition/cholmod_l_camd.o Partition/cholmod_ccolamd.o Partition/cholmod_l_ccolamd.o Partition/cholmod_csymamd.o Partition/cholmod_l_csymamd.o Partition/cholmod_metis.o Partition/cholmod_l_metis.o Partition/cholmod_metis_wrapper.o Partition/cholmod_nesdis.o Partition/cholmod_l_nesdis.o Supernodal/cholmod_super_numeric.o Supernodal/cholmod_l_super_numeric.o Supernodal/cholmod_super_solve.o Supernodal/cholmod_l_super_solve.o Supernodal/cholmod_super_symbolic.o Supernodal/cholmod_l_super_symbolic.o
ranlib CHOLMOD.a
make[4]: Leaving directory '/tmp/RtmpuMiHtm/R.INSTALL4492208ca1bf/Matrix/src/SuiteSparse/CHOLMOD'
gcc -std=gnu23 -shared -L/build/r/src/R-4.5.1/lib -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o Matrix.so Csparse.o attrib.o bind.o cholmod-common.o cholmod-etc.o coerce.o cs-etc.o dense.o determinant.o expm.o factor.o idz.o init.o kappa.o matmult.o objects.o perm.o solve.o sparse.o subassign.o subscript.o utils-R.o utils.o validity.o vector.o SuiteSparse/CHOLMOD/CHOLMOD.a SuiteSparse/CCOLAMD/CCOLAMD.a SuiteSparse/CAMD/CAMD.a SuiteSparse/COLAMD/COLAMD.a SuiteSparse/AMD/AMD.a SuiteSparse/CXSparse/CXSparse.a SuiteSparse/SuiteSparse_config/SuiteSparse_config.a -llapack -lblas -lgfortran -lm -L/build/r/src/R-4.5.1/lib -lR
make[3]: Leaving directory '/tmp/RtmpuMiHtm/R.INSTALL4492208ca1bf/Matrix/src'
installing to /build/r/src/R-4.5.1/library/Matrix/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘chol2inv’ from ‘base’ in package ‘Matrix’
(from the saved implicit definition)
Creating a generic function for ‘chol2inv’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘diag’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘zapsmall’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘drop’ from package ‘base’ in package ‘Matrix’
in method for ‘coerce’ with signature ‘"matrix.csc","dgCMatrix"’: no definition for class “matrix.csc”
in method for ‘coerce’ with signature ‘"matrix.csr","dgRMatrix"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"matrix.coo","dgTMatrix"’: no definition for class “matrix.coo”
in method for ‘coerce’ with signature ‘"matrix.csr","dgCMatrix"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"matrix.coo","dgCMatrix"’: no definition for class “matrix.coo”
in method for ‘coerce’ with signature ‘"matrix.csc","CsparseMatrix"’: no definition for class “matrix.csc”
in method for ‘coerce’ with signature ‘"matrix.csc","RsparseMatrix"’: no definition for class “matrix.csc”
in method for ‘coerce’ with signature ‘"matrix.csc","TsparseMatrix"’: no definition for class “matrix.csc”
in method for ‘coerce’ with signature ‘"matrix.csr","CsparseMatrix"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"matrix.csr","RsparseMatrix"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"matrix.csr","TsparseMatrix"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"matrix.coo","CsparseMatrix"’: no definition for class “matrix.coo”
in method for ‘coerce’ with signature ‘"matrix.coo","RsparseMatrix"’: no definition for class “matrix.coo”
in method for ‘coerce’ with signature ‘"matrix.coo","TsparseMatrix"’: no definition for class “matrix.coo”
in method for ‘coerce’ with signature ‘"matrix.csc","sparseMatrix"’: no definition for class “matrix.csc”
in method for ‘coerce’ with signature ‘"matrix.csr","sparseMatrix"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"matrix.coo","sparseMatrix"’: no definition for class “matrix.coo”
in method for ‘coerce’ with signature ‘"matrix.csc","Matrix"’: no definition for class “matrix.csc”
in method for ‘coerce’ with signature ‘"matrix.csr","Matrix"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"matrix.coo","Matrix"’: no definition for class “matrix.coo”
in method for ‘coerce’ with signature ‘"dgCMatrix","matrix.csc"’: no definition for class “matrix.csc”
in method for ‘coerce’ with signature ‘"dgRMatrix","matrix.csr"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"dgTMatrix","matrix.coo"’: no definition for class “matrix.coo”
in method for ‘coerce’ with signature ‘"Matrix","matrix.csc"’: no definition for class “matrix.csc”
in method for ‘coerce’ with signature ‘"Matrix","matrix.csr"’: no definition for class “matrix.csr”
in method for ‘coerce’ with signature ‘"Matrix","matrix.coo"’: no definition for class “matrix.coo”
in method for ‘coerce’ with signature ‘"graphAM","TsparseMatrix"’: no definition for class “graphAM”
in method for ‘coerce’ with signature ‘"graphNEL","TsparseMatrix"’: no definition for class “graphNEL”
in method for ‘coerce’ with signature ‘"graph","CsparseMatrix"’: no definition for class “graph”
in method for ‘coerce’ with signature ‘"graph","RsparseMatrix"’: no definition for class “graph”
in method for ‘coerce’ with signature ‘"graph","TsparseMatrix"’: no definition for class “graph”
in method for ‘coerce’ with signature ‘"graph","sparseMatrix"’: no definition for class “graph”
in method for ‘coerce’ with signature ‘"graph","Matrix"’: no definition for class “graph”
in method for ‘coerce’ with signature ‘"TsparseMatrix","graphNEL"’: no definition for class “graphNEL”
in method for ‘coerce’ with signature ‘"Matrix","graphNEL"’: no definition for class “graphNEL”
in method for ‘coerce’ with signature ‘"Matrix","graph"’: no definition for class “graph”
Creating a generic function for ‘colSums’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘colMeans’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘rowSums’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘rowMeans’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘diag<-’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘unname’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘norm’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘rcond’ from ‘base’ in package ‘Matrix’
(from the saved implicit definition)
Creating a generic function for ‘rcond’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘cov2cor’ from package ‘stats’ in package ‘Matrix’
Creating a generic function for ‘qr.Q’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘qr.R’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘qr.X’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘qr.coef’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘qr.fitted’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘qr.resid’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘qr.qty’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘qr.qy’ from package ‘base’ in package ‘Matrix’
Creating a generic function for ‘toeplitz’ from ‘stats’ in package ‘Matrix’
(from the saved implicit definition)
Creating a generic function for ‘toeplitz’ from package ‘stats’ in package ‘Matrix’
Creating a generic function for ‘which’ from package ‘base’ in package ‘Matrix’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Matrix)
begin installing recommended package mgcv
begin installing recommended package survival
* installing *source* package ‘survival’ ...
** this is package ‘survival’ version ‘3.8-3’
** package ‘survival’ successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
using C compiler: ‘armv7l-unknown-linux-gnueabihf-gcc (GCC) 14.2.1 20250207’
make[3]: Entering directory '/tmp/Rtmpel7m2U/R.INSTALL4b0e49abd72b/survival/src'
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c agexact.c -o agexact.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c agfit4.c -o agfit4.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c agfit5.c -o agfit5.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c agmart.c -o agmart.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c agmart3.c -o agmart3.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c agscore2.c -o agscore2.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c agscore3.c -o agscore3.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c agsurv4.c -o agsurv4.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c agsurv5.c -o agsurv5.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c cdecomp.c -o cdecomp.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c chinv2.c -o chinv2.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c chinv3.c -o chinv3.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c cholesky2.c -o cholesky2.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c cholesky3.c -o cholesky3.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c cholesky5.c -o cholesky5.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c chsolve2.c -o chsolve2.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c chsolve3.c -o chsolve3.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c chsolve5.c -o chsolve5.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c collapse.c -o collapse.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c concordance1.c -o concordance1.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c concordance3.c -o concordance3.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c concordance5.c -o concordance5.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c cox_Rcallback.c -o cox_Rcallback.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c coxcount1.c -o coxcount1.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c coxdetail.c -o coxdetail.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c coxexact.c -o coxexact.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c coxfit5.c -o coxfit5.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c coxfit6.c -o coxfit6.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c coxmart.c -o coxmart.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c coxmart2.c -o coxmart2.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c coxph_wtest.c -o coxph_wtest.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c coxsafe.c -o coxsafe.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c coxscho.c -o coxscho.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c coxscore2.c -o coxscore2.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c coxsurv1.c -o coxsurv1.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c coxsurv2.c -o coxsurv2.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c coxsurv3.c -o coxsurv3.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c coxsurv4.c -o coxsurv4.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dmatrix.c -o dmatrix.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c doloop.c -o doloop.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c fastkm.c -o fastkm.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c finegray.c -o finegray.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c gchol.c -o gchol.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c init.c -o init.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c multicheck.c -o multicheck.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c norisk.c -o norisk.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pyears1.c -o pyears1.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pyears2.c -o pyears2.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pyears3b.c -o pyears3b.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pystep.c -o pystep.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c residcsum.c -o residcsum.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c survConcordance.c -o survConcordance.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c survdiff2.c -o survdiff2.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c survfit4.c -o survfit4.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c survfitaj.c -o survfitaj.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c survfitkm.c -o survfitkm.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c survfitresid.c -o survfitresid.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c survpenal.c -o survpenal.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c survreg6.c -o survreg6.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c survreg7.c -o survreg7.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c survregc1.c -o survregc1.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c survregc2.c -o survregc2.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c survsplit.c -o survsplit.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c tmerge.c -o tmerge.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c twoclust.c -o twoclust.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c zph1.c -o zph1.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c zph2.c -o zph2.o
gcc -std=gnu23 -shared -L/build/r/src/R-4.5.1/lib -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o survival.so agexact.o agfit4.o agfit5.o agmart.o agmart3.o agscore2.o agscore3.o agsurv4.o agsurv5.o cdecomp.o chinv2.o chinv3.o cholesky2.o cholesky3.o cholesky5.o chsolve2.o chsolve3.o chsolve5.o collapse.o concordance1.o concordance3.o concordance5.o cox_Rcallback.o coxcount1.o coxdetail.o coxexact.o coxfit5.o coxfit6.o coxmart.o coxmart2.o coxph_wtest.o coxsafe.o coxscho.o coxscore2.o coxsurv1.o coxsurv2.o coxsurv3.o coxsurv4.o dmatrix.o doloop.o fastkm.o finegray.o gchol.o init.o multicheck.o norisk.o pyears1.o pyears2.o pyears3b.o pystep.o residcsum.o survConcordance.o survdiff2.o survfit4.o survfitaj.o survfitkm.o survfitresid.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o survsplit.o tmerge.o twoclust.o zph1.o zph2.o -L/build/r/src/R-4.5.1/lib -lR
make[3]: Leaving directory '/tmp/Rtmpel7m2U/R.INSTALL4b0e49abd72b/survival/src'
installing to /build/r/src/R-4.5.1/library/survival/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (survival)
begin installing recommended package boot
* installing *source* package ‘boot’ ...
** this is package ‘boot’ version ‘1.3-31’
** package ‘boot’ successfully unpacked and MD5 sums checked
** using non-staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (boot)
* installing *source* package ‘mgcv’ ...
** this is package ‘mgcv’ version ‘1.9-3’
** package ‘mgcv’ successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
using C compiler: ‘armv7l-unknown-linux-gnueabihf-gcc (GCC) 14.2.1 20250207’
make[3]: Entering directory '/tmp/RtmpPbXdry/R.INSTALL4b0d5238e7/mgcv/src'
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c coxph.c -o coxph.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c davies.c -o davies.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c discrete.c -o discrete.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c gdi.c -o gdi.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c init.c -o init.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c magic.c -o magic.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c mat.c -o mat.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c matrix.c -o matrix.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c mgcv.c -o mgcv.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c misc.c -o misc.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c mvn.c -o mvn.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c ncv.c -o ncv.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qp.c -o qp.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c soap.c -o soap.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c sparse-smooth.c -o sparse-smooth.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c sparse.c -o sparse.o
gcc -std=gnu23 -I"/build/r/src/R-4.5.1/include" -DNDEBUG -fopenmp -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c tprs.c -o tprs.o
gcc -std=gnu23 -shared -L/build/r/src/R-4.5.1/lib -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o mgcv.so coxph.o davies.o discrete.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o mvn.o ncv.o qp.o soap.o sparse-smooth.o sparse.o tprs.o -llapack -lblas -lgfortran -lm -fopenmp -L/build/r/src/R-4.5.1/lib -lR
make[3]: Leaving directory '/tmp/RtmpPbXdry/R.INSTALL4b0d5238e7/mgcv/src'
installing to /build/r/src/R-4.5.1/library/mgcv/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (mgcv)
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(cd ../../include; make Rmath.h)
Copying source files
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make[1]: Entering directory '/build/r/src/R-4.5.1/src/nmath/standalone'
making mlutils.d from mlutils.c
making d1mach.d from d1mach.c
making i1mach.d from i1mach.c
making fmax2.d from fmax2.c
making fmin2.d from fmin2.c
making fprec.d from fprec.c
making fround.d from fround.c
making ftrunc.d from ftrunc.c
making sign.d from sign.c
making fsign.d from fsign.c
making imax2.d from imax2.c
making imin2.d from imin2.c
making log1p.d from log1p.c
making chebyshev.d from chebyshev.c
making lgammacor.d from lgammacor.c
making gammalims.d from gammalims.c
making stirlerr.d from stirlerr.c
making gamma.d from gamma.c
making bd0.d from bd0.c
making lgamma.d from lgamma.c
making gamma_cody.d from gamma_cody.c
making beta.d from beta.c
making lbeta.d from lbeta.c
making polygamma.d from polygamma.c
making cospi.d from cospi.c
making bessel_i.d from bessel_i.c
making bessel_j.d from bessel_j.c
making bessel_k.d from bessel_k.c
making choose.d from choose.c
making bessel_y.d from bessel_y.c
making snorm.d from snorm.c
making sexp.d from sexp.c
making dgamma.d from dgamma.c
making pgamma.d from pgamma.c
making qgamma.d from qgamma.c
making rgamma.d from rgamma.c
making dbeta.d from dbeta.c
making pbeta.d from pbeta.c
making qbeta.d from qbeta.c
making rbeta.d from rbeta.c
making dunif.d from dunif.c
making punif.d from punif.c
making qunif.d from qunif.c
making runif.d from runif.c
making dnorm.d from dnorm.c
making qnorm.d from qnorm.c
making pnorm.d from pnorm.c
making rnorm.d from rnorm.c
making dlnorm.d from dlnorm.c
making qlnorm.d from qlnorm.c
making plnorm.d from plnorm.c
making rlnorm.d from rlnorm.c
making df.d from df.c
making pf.d from pf.c
making qf.d from qf.c
making rf.d from rf.c
making dnf.d from dnf.c
making dt.d from dt.c
making pt.d from pt.c
making qt.d from qt.c
making rt.d from rt.c
making dnt.d from dnt.c
making dchisq.d from dchisq.c
making pchisq.d from pchisq.c
making qchisq.d from qchisq.c
making rchisq.d from rchisq.c
making rnchisq.d from rnchisq.c
making dbinom.d from dbinom.c
making pbinom.d from pbinom.c
making qbinom.d from qbinom.c
making rbinom.d from rbinom.c
making rmultinom.d from rmultinom.c
making dcauchy.d from dcauchy.c
making pcauchy.d from pcauchy.c
making qcauchy.d from qcauchy.c
making rcauchy.d from rcauchy.c
making dexp.d from dexp.c
making pexp.d from pexp.c
making qexp.d from qexp.c
making rexp.d from rexp.c
making dgeom.d from dgeom.c
making pgeom.d from pgeom.c
making qgeom.d from qgeom.c
making rgeom.d from rgeom.c
making dhyper.d from dhyper.c
making phyper.d from phyper.c
making qhyper.d from qhyper.c
making rhyper.d from rhyper.c
making dnbinom.d from dnbinom.c
making pnbinom.d from pnbinom.c
making qnbinom.d from qnbinom.c
making qnbinom_mu.d from qnbinom_mu.c
making rnbinom.d from rnbinom.c
making dpois.d from dpois.c
making ppois.d from ppois.c
making qpois.d from qpois.c
making rpois.d from rpois.c
making dweibull.d from dweibull.c
making pweibull.d from pweibull.c
making qweibull.d from qweibull.c
making rweibull.d from rweibull.c
making dlogis.d from dlogis.c
making qlogis.d from qlogis.c
making plogis.d from plogis.c
making rlogis.d from rlogis.c
making dnchisq.d from dnchisq.c
making pnchisq.d from pnchisq.c
making qnchisq.d from qnchisq.c
making dnbeta.d from dnbeta.c
making pnbeta.d from pnbeta.c
making qnbeta.d from qnbeta.c
making pnf.d from pnf.c
making pnt.d from pnt.c
making qnf.d from qnf.c
making qnt.d from qnt.c
making ptukey.d from ptukey.c
making qtukey.d from qtukey.c
making toms708.d from toms708.c
making wilcox.d from wilcox.c
making signrank.d from signrank.c
making std_unif.d from std_unif.c
make[1]: Leaving directory '/build/r/src/R-4.5.1/src/nmath/standalone'
make[1]: Entering directory '/build/r/src/R-4.5.1/src/nmath/standalone'
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c mlutils.c -o mlutils.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c d1mach.c -o d1mach.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c i1mach.c -o i1mach.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c fmax2.c -o fmax2.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c fmin2.c -o fmin2.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c fprec.c -o fprec.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c fround.c -o fround.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c ftrunc.c -o ftrunc.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c sign.c -o sign.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c fsign.c -o fsign.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c imax2.c -o imax2.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c imin2.c -o imin2.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c chebyshev.c -o chebyshev.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c log1p.c -o log1p.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c lgammacor.c -o lgammacor.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c gammalims.c -o gammalims.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c stirlerr.c -o stirlerr.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c bd0.c -o bd0.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c gamma.c -o gamma.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c lgamma.c -o lgamma.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c gamma_cody.c -o gamma_cody.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c beta.c -o beta.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c lbeta.c -o lbeta.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c polygamma.c -o polygamma.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c cospi.c -o cospi.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c bessel_i.c -o bessel_i.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c bessel_j.c -o bessel_j.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c bessel_k.c -o bessel_k.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c bessel_y.c -o bessel_y.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c choose.c -o choose.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c snorm.c -o snorm.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c sexp.c -o sexp.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dgamma.c -o dgamma.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pgamma.c -o pgamma.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qgamma.c -o qgamma.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rgamma.c -o rgamma.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dbeta.c -o dbeta.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pbeta.c -o pbeta.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qbeta.c -o qbeta.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rbeta.c -o rbeta.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dunif.c -o dunif.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c punif.c -o punif.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qunif.c -o qunif.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c runif.c -o runif.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dnorm.c -o dnorm.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pnorm.c -o pnorm.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qnorm.c -o qnorm.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rnorm.c -o rnorm.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dlnorm.c -o dlnorm.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c plnorm.c -o plnorm.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qlnorm.c -o qlnorm.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rlnorm.c -o rlnorm.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c df.c -o df.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pf.c -o pf.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qf.c -o qf.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rf.c -o rf.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dnf.c -o dnf.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dt.c -o dt.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pt.c -o pt.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qt.c -o qt.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rt.c -o rt.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dnt.c -o dnt.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dchisq.c -o dchisq.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pchisq.c -o pchisq.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qchisq.c -o qchisq.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rchisq.c -o rchisq.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rnchisq.c -o rnchisq.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dbinom.c -o dbinom.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pbinom.c -o pbinom.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qbinom.c -o qbinom.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rbinom.c -o rbinom.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rmultinom.c -o rmultinom.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dcauchy.c -o dcauchy.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pcauchy.c -o pcauchy.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qcauchy.c -o qcauchy.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rcauchy.c -o rcauchy.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dexp.c -o dexp.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pexp.c -o pexp.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qexp.c -o qexp.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rexp.c -o rexp.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dgeom.c -o dgeom.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pgeom.c -o pgeom.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qgeom.c -o qgeom.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rgeom.c -o rgeom.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dhyper.c -o dhyper.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c phyper.c -o phyper.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qhyper.c -o qhyper.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rhyper.c -o rhyper.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dnbinom.c -o dnbinom.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pnbinom.c -o pnbinom.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qnbinom.c -o qnbinom.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qnbinom_mu.c -o qnbinom_mu.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rnbinom.c -o rnbinom.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dpois.c -o dpois.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c ppois.c -o ppois.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qpois.c -o qpois.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rpois.c -o rpois.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dweibull.c -o dweibull.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pweibull.c -o pweibull.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qweibull.c -o qweibull.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rweibull.c -o rweibull.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dlogis.c -o dlogis.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c plogis.c -o plogis.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qlogis.c -o qlogis.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c rlogis.c -o rlogis.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dnchisq.c -o dnchisq.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pnchisq.c -o pnchisq.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qnchisq.c -o qnchisq.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c dnbeta.c -o dnbeta.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pnbeta.c -o pnbeta.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qnbeta.c -o qnbeta.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pnf.c -o pnf.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c pnt.c -o pnt.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qnf.c -o qnf.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qnt.c -o qnt.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c ptukey.c -o ptukey.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c qtukey.c -o qtukey.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c toms708.c -o toms708.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c wilcox.c -o wilcox.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c signrank.c -o signrank.lo
gcc -std=gnu23 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=armv7-a -mfloat-abi=hard -mfpu=neon -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -ffat-lto-objects -c std_unif.c -o std_unif.lo
gcc -std=gnu23 -shared -fopenmp -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o libRmath.so mlutils.lo d1mach.lo i1mach.lo fmax2.lo fmin2.lo fprec.lo fround.lo ftrunc.lo sign.lo fsign.lo imax2.lo imin2.lo chebyshev.lo log1p.lo lgammacor.lo gammalims.lo stirlerr.lo bd0.lo gamma.lo lgamma.lo gamma_cody.lo beta.lo lbeta.lo polygamma.lo cospi.lo bessel_i.lo bessel_j.lo bessel_k.lo bessel_y.lo choose.lo snorm.lo sexp.lo dgamma.lo pgamma.lo qgamma.lo rgamma.lo dbeta.lo pbeta.lo qbeta.lo rbeta.lo dunif.lo punif.lo qunif.lo runif.lo dnorm.lo pnorm.lo qnorm.lo rnorm.lo dlnorm.lo plnorm.lo qlnorm.lo rlnorm.lo df.lo pf.lo qf.lo rf.lo dnf.lo dt.lo pt.lo qt.lo rt.lo dnt.lo dchisq.lo pchisq.lo qchisq.lo rchisq.lo rnchisq.lo dbinom.lo pbinom.lo qbinom.lo rbinom.lo rmultinom.lo dcauchy.lo pcauchy.lo qcauchy.lo rcauchy.lo dexp.lo pexp.lo qexp.lo rexp.lo dgeom.lo pgeom.lo qgeom.lo rgeom.lo dhyper.lo phyper.lo qhyper.lo rhyper.lo dnbinom.lo pnbinom.lo qnbinom.lo qnbinom_mu.lo rnbinom.lo dpois.lo ppois.lo qpois.lo rpois.lo dweibull.lo pweibull.lo qweibull.lo rweibull.lo dlogis.lo plogis.lo qlogis.lo rlogis.lo dnchisq.lo pnchisq.lo qnchisq.lo dnbeta.lo pnbeta.lo qnbeta.lo pnf.lo pnt.lo qnf.lo qnt.lo ptukey.lo qtukey.lo toms708.lo wilcox.lo signrank.lo std_unif.lo -lm
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[]\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber []\T1/pcr/m/n/
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\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . oracle
. com / cd / E19957-[]01 / 806-[]3568 / ncg _
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]make[2]: Leaving directory '/build/r/src/R-4.5.1/src/main'
make[2]: Entering directory '/build/r/src/R-4.5.1/src/modules'
make[3]: Entering directory '/build/r/src/R-4.5.1/src/modules/internet'
[28]mkdir -p -- /build/r/pkg/r/usr/lib/R/modules
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[] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em
pty.names = TRUE,[]
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[]\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more
than 256 (or
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[33]make[2]: Entering directory '/build/r/src/R-4.5.1/src/library'
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[]\T1/pcr/m/n/9 names(dL <- as.data.frame(L))
# "NA."[]
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[]\T1/pcr/m/n/9 names(dL1 <- as.data.frame(L, col.names = names(L)))
# "NA."[]
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[]\T1/pcr/m/n/9 names(dL1.<- as.data.frame(L, check.name
s=FALSE)) # "NA"[]
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[]\T1/pcr/m/n/9 names(dL2 <- as.data.frame(L, col.names = names(L), check.name
s=FALSE)) # NA[]
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[]\T1/pcr/m/n/9 names(dLn <- as.data.frame(L, new.names = TRUE, check.name
s=FALSE)) # NA[]
mkdir -p -- /build/r/pkg/r/usr/lib/R/library
[34]installing packages ...
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[]\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[]
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[]\T1/ptm/m/n/10 If [][][]\T1/pcr/m/n/10 is.object[][][](x) []\T1/ptm/m/n/10 is
true and it has a [][][]\T1/pcr/m/n/10 class[][][] []\T1/ptm/m/n/10 for which
an
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[]\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla
ss "POSIXlt"[]
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[]\T1/pcr/m/n/9 if(file.exists(tab)) { # typically on Windows; on Linux when
\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 configure --with-internal-tzcode\TS1/cmtt/m/n/9
`[]
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[]\T1/ptm/m/n/10 There are no re-stric-tions on the name given as []\T1/pcr/m/n
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[]\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse1(substitute(what), back
tick=FALSE),
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[]\T1/pcr/m/n/10 unCfillPOSIXlt(x) []\T1/ptm/m/n/10 is a fast [][]prim-i-tive[]
[][] ver-sion of []\T1/pcr/m/n/10 balancePOSIXlt(x,
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[]\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2,
lwd = 1, bty="n")[]
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[]\T1/pcr/m/n/9 plot(range(x0), c(1e-40, 1), log = "xy", xlab = "x", ylab = ""
, type = "n",[]
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[] \T1/pcr/m/n/9 main = "Bessel Functions J_nu(x) near 0\n log - log sc
ale") ; axis(2, at=1)[]
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[]\T1/pcr/m/n/9 plot(range(x0), 10^c(-100, 80), log = "xy", xlab = "x", ylab =
"", type = "n",[]
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[] \T1/pcr/m/n/9 main = "Bessel Functions K_nu(x) near 0\n log - log sc
ale") ; axis(2, at=1)[]
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[]\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5,
sep = ", ")),[]
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[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
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[]\T1/pcr/m/n/9 L <- as.list(E <- setNames( , c("if", "for", "while", "repeat"
, "function",[]
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[] \T1/pcr/m/n/9 "(", "{", "[", "<-", "<<-",
"->", "=")))[]
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[]\T1/pcr/m/n/9 for(i in seq_along(L)) L[[i]] <- call(E[[i]]) # instead of lap
ply(E, call) ..[]
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[]\T1/pcr/m/n/9 list_ <- function (...) \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 names<-
\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 (list(...), vapply(sys.call()[-1L], as.character
, ""))[]
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[]\T1/pcr/m/n/9 (Tab <- noquote(sapply(list_(is.call, typeof, class, mode), \(
F) sapply(L, F))))[]
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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an
ob-ject
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\T1/ptm/m/n/10 of class []\T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"[]\T1/ptm/
m/n/10 , []\T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" []\T1/ptm/m/n/10 o
r
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[] \T1/pcr/m/n/10 Xchk = any(nas %in% c("X11", "jpeg", "png", "tif
f")))[]
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[]\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par
-i-son[][][] and
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[]\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[]
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[]\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na
med ar-gu-
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[]\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu
e and valid
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[]\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[]
[81] building HTML index ...
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[]\T1/pcr/m/n/9 as.character(list(A = "Abc", xy = c("x", "y"))) # "Abc" "c(\"
x\", \"y\")"[]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c
har-ac-ter by
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[88]make[2]: Leaving directory '/build/r/src/R-4.5.1/src/library'
make[1]: Leaving directory '/build/r/src/R-4.5.1/src'
[89]make[1]: Entering directory '/build/r/src/R-4.5.1/tests'
make[1]: Nothing to be done for 'install'.
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[]\T1/ptm/m/n/10 When a generic func-tion []\T1/pcr/m/n/10 fun []\T1/ptm/m/n/10
is ap-plied to an ob-ject with class at-tribute []\T1/pcr/m/n/10 c("first",
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[]\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i
n-tro-duc-tion see [][]$\T1/pcr/m/n/10 https : / /
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[]\T1/pcr/m/n/9 stopifnot(identical(as.complex(NA_real_), NA_real_ + 0i)) # ha
s always been true[]
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[]\T1/pcr/m/n/9 NAs <- vapply(list(NA, NA_integer_, NA_real_, NA_character_, N
A_complex_),[]
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[]\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile
r, math-library:[]
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[]\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[]
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[]\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class []\T1/pcr/m/n
/10 interrupt []\T1/ptm/m/n/10 that in-her-its di-rectly from class
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[]\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols.
They can be es-tab-lished us-ing
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[]\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i
s []\T1/pcr/m/n/10 interactive[]\T1/ptm/m/n/10 . This should
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[]\T1/pcr/m/n/10 zstdfile(description, open = "", encoding = getOption("encodi
ng"),[]
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[]\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[]
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[]\T1/ptm/m/n/10 character string, par-tially matched to []\T1/pcr/m/n/10 c("de
fault", "internal",
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[]\T1/pcr/m/n/10 file[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pipe[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 fifo[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 url[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 gzfile[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 bzfile[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 xzfile[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 zstdfile[]\T1/
ptm/m/n/10 , []\T1/pcr/m/n/10 unz[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 socketConnection[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 socketAcce
pt []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 serverSocket []\T1/ptm/m/n/10 re-turn
a con-nec-tion ob-ject
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[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
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[]\T1/pcr/m/n/10 file []\T1/ptm/m/n/10 can be used with []\T1/pcr/m/n/10 descri
ption = "clipboard" []\T1/ptm/m/n/10 in mode []\T1/pcr/m/n/10 "r" []\T1/ptm/m/n
/10 only. This
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[]\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[]
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[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
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[]\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect
s to https://[]
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[]\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[]
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[]\T1/pcr/m/n/10 data.frame []\T1/ptm/m/n/10 con-verts each of its ar-gu-ments
to a data frame by call-ing
Underfull \hbox (badness 1975) in paragraph at lines 8897--8907
[][][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)[]\T1/ptm/m/n/10 . As
that is a generic func-tion, meth-ods can be
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[] \T1/pcr/m/n/9 c = seq(as.Date("2004-01-01"), by = "week", l
ength.out = 3),[]
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\T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") []\T1/ptm/m
/n/10 may give []\T1/pcr/m/n/10 NA[]\T1/ptm/m/n/10 , and
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[]\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: --------
-------------[]
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[]\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO
!\n"); pi+2})[]
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[] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "(
", "function"),[]
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[] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh
owAttributes"),[]
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[]\T1/pcr/m/n/10 ..deparseOpts []\T1/ptm/m/n/10 is the [][][]\T1/pcr/m/n/10 cha
racter[][][] []\T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used b
y
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[]\T1/ptm/m/n/10 Surround un-eval-u-ated ex-pres-sions, but not [][][]\T1/pcr/m
/n/10 formula[][][][]\T1/ptm/m/n/10 s, with
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[]\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t
er-mi-nant if
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[] \T1/pcr/m/n/10 z <- as.POSIXct(c("2016-12-31 23:59:59", "2017-01-01 00:0
0:01"))[]
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[]\T1/pcr/m/n/10 provideDimnames(x) []\T1/ptm/m/n/10 pro-vides []\T1/pcr/m/n/10
dimnames []\T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has
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[]\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE
RS)))) # recycling[]
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[]\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
on both levels[]
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[]\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of []\
T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . Cur-rently this is only used by
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[]\T1/pcr/m/n/9 ## From R 4.1.0 to 4.1.2, ...names() sometimes did not match n
ames(list(...));[]
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[]\T1/pcr/m/n/9 chk.n2 <- function(...) stopifnot(identical(print(...names()),
names(list(...))))[]
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19
85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .
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\T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr
/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _
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\T1/pcr/m/n/10 754-[]2019$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / /
en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/
pcr/m/n/10 https :
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[] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA
ttributes"))[]
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[]\T1/pcr/m/n/9 ## Write an ASCII version of the \TS1/pcr/m/n/9 '\T1/pcr/m/n/9
base\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 function mean() to our temp file, ..[]
[169]
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[]\T1/pcr/m/n/9 drop(1:3 %*% 2:4) # scalar product - w/o drop(.), would retur
n 1x1 matrix[]
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[]\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9]))
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[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for
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[]\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) []\T1/ptm/m/n/10 is equiv-a-len
t to but faster than
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[]\T1/ptm/m/n/10 Do not use []\T1/pcr/m/n/10 dyn.unload []\T1/ptm/m/n/10 on a D
LL loaded by [][][]\T1/pcr/m/n/10 library.dynam[][][][]\T1/ptm/m/n/10 : use
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[]\T1/ptm/m/n/10 Changing the cur-rent en-cod-ing from a run-ning R ses-sion ma
y lead to con-fu-sion (see
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[]\T1/pcr/m/n/9 Encoding(x.) # "unknown" (UTF-8 loc.) | "latin1" (8859-1/CP-12
52 loc.) | ....[]
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[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of
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[]\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][][]\T1/pcr/m/n/1
0 dev2bitmap[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 bitmap[][][] []\T1/pt
m/m/n/10 and
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[]\T1/ptm/m/n/10 The path to HTML []\T1/pcr/m/n/10 tidy[]\T1/ptm/m/n/10 . Used
by []\T1/pcr/m/n/10 R CMD check []\T1/ptm/m/n/10 if
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[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
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[]\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing []\T1/pc
r/m/n/10 where []\T1/ptm/m/n/10 as
Underfull \hbox (badness 5970) in paragraph at lines 13268--13270
[]\T1/pcr/m/n/10 get0(): []\T1/ptm/m/n/10 The object---as from [][][]\T1/pcr/m/
n/10 get[][][](x, *)[]\T1/ptm/m/n/10 --- if []\T1/pcr/m/n/10 exists(x, *) []\T1
/ptm/m/n/10 is true, oth-er-wise
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[]\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide
a constructor[]
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[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
done: see
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[]\T1/ptm/m/n/10 Junction points and sym-bolic links are fol-lowed, so in-for-m
a-tion is given about the
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[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as []\T1/pcr
/m/n/10 PATH []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 R_LIBS []\T1/ptm/m/n/10 with
[]\T1/pcr/m/n/10 fsep =
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[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
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[][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil
e.access[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.path[][][][]\T1/ptm/
m/n/10 , [][][]\T1/pcr/m/n/10 file.show[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m
/n/10 list.files[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 unlink[][][][]\T1
/ptm/m/n/10 ,
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .
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[] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B
as it exists already[]
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[]\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
= "0777")[]
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[][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil
e.exists[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.path[][][][]\T1/ptm/
m/n/10 , [][][]\T1/pcr/m/n/10 list.files[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/
m/n/10 unlink[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 basename[][][][]\T1/
ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive = TRUE)[]
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[]\T1/pcr/m/n/10 packageNotFoundError []\T1/ptm/m/n/10 cre-ates an er-ror con-d
i-tion ob-ject of class
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[]\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio
ns it is found:[]
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[]\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE,
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[] \T1/pcr/m/n/10 left.open = FALSE, checkSorted = TRUE, checkNA =
TRUE)[]
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[]\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr
i-bu-tion func-tion, and in-deed,
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[]\T1/pcr/m/n/9 stopifnot(identical(it, ## suppressing the checks is faster *B
UT* dangerous, unless[]
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[] \T1/pcr/m/n/9 ## you *know* that X is sorted and
tt contains no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[]
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[] \T1/pcr/m/n/9 findInterval(tt, X, checkSorted=FALSE, che
ckNA=FALSE)))[]
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[] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)
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[] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[]
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[]\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have
type symbol (aka name).[]
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[]\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co
mbination with[]
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[]\T1/ptm/m/n/10 either a log-i-cal spec-i-fy-ing whether el-e-ments of a real
or com-plex vec-
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\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger
penalty (see
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[]\T1/pcr/m/n/10 big.mark[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 big.interval[]\T1/
ptm/m/n/10 , []\T1/pcr/m/n/10 small.mark[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sma
ll.interval[]\T1/ptm/m/n/10 ,
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[][][]\T1/pcr/m/n/10 formatC[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 paste
[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 as.character[][][][]\T1/ptm/m/n/1
0 , [][][]\T1/pcr/m/n/10 sprintf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 p
rint[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 prettyNum[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 toString[][][][]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[]
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[]\T1/pcr/m/n/10 prettyNum() []\T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (p
os-si-bly for-mat-ted) num-bers, also in
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[] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark =
decimal.mark,[]
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[]\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric
(x)),[]
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[]\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][]
[]\T1/pcr/m/n/10 complex[][][] []\T1/ptm/m/n/10 only for
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[]\T1/pcr/m/n/10 "f" []\T1/ptm/m/n/10 gives num-bers in the usual []\T1/pcr/m/n
/10 xxx.xxx []\T1/ptm/m/n/10 for-mat; []\T1/pcr/m/n/10 "e" []\T1/ptm/m/n/10 and
[]\T1/pcr/m/n/10 "E" []\T1/ptm/m/n/10 give
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[]\T1/ptm/m/n/10 This works via []\T1/pcr/m/n/10 prettyNum()[]\T1/ptm/m/n/10 ,
which calls []\T1/pcr/m/n/10 .format.zeros(*,
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[]\T1/ptm/m/n/10 For num-bers, []\T1/pcr/m/n/10 formatC() []\T1/ptm/m/n/10 call
s []\T1/pcr/m/n/10 prettyNum() []\T1/ptm/m/n/10 when needed which it-self calls
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[]\T1/ptm/m/n/10 If you set []\T1/pcr/m/n/10 format []\T1/ptm/m/n/10 it over-ri
des the set-ting of []\T1/pcr/m/n/10 mode[]\T1/ptm/m/n/10 , so []\T1/pcr/m/n/10
formatC(123.45, mode =
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[]\T1/pcr/m/n/10 prettyNum []\T1/ptm/m/n/10 is the util-ity func-tion for pret-
ti-fy-ing []\T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 x []\T1/ptm/m/n
/10 can be com-plex (or
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[]\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big
.mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[]
Underfull \vbox (badness 10000) has occurred while \output is active
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[]\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you
want see the effect[]
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[]\T1/pcr/m/n/10 Reduce(f, x, init, right = FALSE, accumulate = FALSE, simplif
y = TRUE)
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[]\T1/pcr/m/n/9 ## very low-level: get()ing the "missing argument", e.g., insi
de browser()[]
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[] \T1/pcr/m/n/9 is.symbol(E$m) # => valid argument to get(), and *also* ge
ts \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 missing arg\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[]
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[]\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil
l a DLLInfoList[]
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\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing [
]\T1/pcr/m/n/10 CRoutine[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 CallRoutine[]\T1/pt
m/m/n/10 ,
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 name []\T1/ptm/m/n/10 con-tains only one s
ym-bol name and []\T1/pcr/m/n/10 unlist []\T1/ptm/m/n/10 is []\T1/pcr/m/n/10 TR
UE[]\T1/ptm/m/n/10 , then the sin-gle
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[][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][][]\T1/ptm/m/n/10 , [][][]\T1
/pcr/m/n/10 is.loaded[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .C[][][][]\T
1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .Fortran[][][][]\T1/ptm/m/n/10 , [][][]\T1/
pcr/m/n/10 .External[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .Call[][][][]
\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 ## Not run: ## for translation, those strings should appear in
R-pkg.pot as[]
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[]\T1/pcr/m/n/9 if(is.na(thisLang) || !nzchar(thisLang)) thisLang <- "en" # "f
actory" default[]
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[]\T1/pcr/m/n/9 gettext(enT, domain="R-stats")# "leeres Modell angegeben" (if
translation works)[]
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[]\T1/pcr/m/n/9 ## Here, we reset to the *original* setting before the full ex
ample started:[]
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[]\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE,
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[]\T1/pcr/m/n/10 grepv(pattern, x, ignore.case = FALSE, perl = FALSE, value =
TRUE,[]
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[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
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[] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around
"checking hack"[]
Underfull \vbox (badness 10000) has occurred while \output is active
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[]\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[]
Underfull \vbox (badness 10000) has occurred while \output is active
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[] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[]
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[]\T1/pcr/m/n/9 (ii <- grouping(x <- c(1, 1, 3:1, 1:4, 3), y <- c(9, 9:1), z <
- c(2, 1:9)))
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[]\T1/pcr/m/n/9 z <- gzcon(url("https://www.stats.ox.ac.uk/pub/datasets/csb/ch
12.dat.gz"))[]
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[]\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE)
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[]\T1/ptm/m/n/10 The most portable name for the ISO 8859-15 en-cod-ing, com-mon
ly known as `Latin 9',
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\T1/ptm/m/n/10 is []\T1/pcr/m/n/10 "iso885915"[]\T1/ptm/m/n/10 : most plat-form
s sup-port both []\T1/pcr/m/n/10 "latin-9" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/1
0 "latin9" []\T1/ptm/m/n/10 but GNU
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[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 https : / / unicode-[]org . github . io / icu /
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19525--19525
[]\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s
ettings, we can only reset to the default.[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 19555--19555
[]\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE,
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[] \T1/pcr/m/n/10 num.eq = FALSE, single.NA = FALSE, attrib.as.se
t = FALSE,[]
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[] \T1/pcr/m/n/10 ignore.bytecode = FALSE, ignore.environment = F
ALSE,[]
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[]\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------
----------------[]
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[]\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is
ignored by default[]
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[]\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share
an environment:[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19718--19718
[]\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi
ng "srcref" :[]
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[]\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u
se ifelse(),[]
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[]\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[]
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[]\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][][]\T
1/pcr/m/n/10 stop[][][] []\T1/ptm/m/n/10 and
[289]
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[][][]\T1/pcr/m/n/10 as.character[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
as.complex[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 as.double[][][][]\T1/pt
m/m/n/10 , [][][]\T1/pcr/m/n/10 as.integer[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc
r/m/n/10 as.logical[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 as.raw[][][][]
\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . oracle
. com / cd / E19957-[]01 / 806-[]3568 / ncg _
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[]\T1/pcr/m/n/10 is.atomic []\T1/ptm/m/n/10 is true for the [][]atomic[][][] ty
pes ([]\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "integer"[]\
T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "numeric"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[]
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[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
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[]\T1/pcr/m/n/9 isSymmetric(D3) # FALSE (as row and co
lumn names differ)[]
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[]\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE (as names are
not checked)[]
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[]\T1/pcr/m/n/10 .kappa_tri(z, exact = FALSE, LINPACK = TRUE, norm = NULL, upl
o = "U", ...)[]
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[]\T1/pcr/m/n/10 rcond(x, norm = c("O","I","1"), triangular = FALSE, uplo = "U
", ...)[]
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[]\T1/ptm/m/n/10 LAPACK and LIN-PACK are from [][]$\T1/pcr/m/n/10 https : / / n
etlib . org / lapack/$[][] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / /
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[]\T1/pcr/m/n/9 ## Moore-Penrose inverse { ~= MASS::ginv(); differing tol (val
ue & meaning)}:[]
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[]\T1/pcr/m/n/9 try( kappa(m76, exact=TRUE, norm="1") )# error in solve().. m
ust be square[]
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[]\T1/pcr/m/n/9 ## ==> use pseudo-inverse instead of solve() for rectangular {
and norm != "2"}:[]
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[] \T1/pcr/m/n/9 inv_z = solve(A, tol = 1e-19))) # 5.22057e16 on x86_
64 Linux with GCC[]
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[]\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p
hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to
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[]\T1/ptm/m/n/10 In late 2017 a []\T1/pcr/m/n/10 libcurl []\T1/ptm/m/n/10 in-st
al-la-tion was seen di-vided into two li-braries, []\T1/pcr/m/n/10 libcurl []\T
1/ptm/m/n/10 and
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[][][]$\T1/pcr/m/n/10 https : / / curl . se / docs / sslcerts . html$[][] \T1/p
tm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / curl . se / docs /
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[]\T1/ptm/m/n/10 At startup, the li-brary search path is ini-tial-ized from the
en-vi-ron-ment vari-ables []\T1/pcr/m/n/10 R_LIBS[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 LOCALAPPDATA []\T1/ptm/m/n/10 (usu-ally []\T1/pcr/m/n/10 C:\Us
ers\username\AppData\Local[]\T1/ptm/m/n/10 ) on Win-dows is a
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\T1/ptm/m/n/10 hid-den di-rec-tory and may not be viewed by some soft-ware. It
may be opened by
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[]\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use
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[][][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][][]\T1/ptm/m/n/10 : thi
s will sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 library []\T1/ptm/m/n/10 is called with no
[]\T1/pcr/m/n/10 package []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 help []\T1/ptm/m
/n/10 ar-gu-ment, it lists all avail-able pack-
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[][][]\T1/pcr/m/n/10 attach[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 detach
[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 search[][][][]\T1/ptm/m/n/10 , []
[][]\T1/pcr/m/n/10 objects[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 autoloa
d[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 requireNamespace[][][][]\T1/ptm/
m/n/10 ,
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[]\T1/ptm/m/n/10 Do not use [][][]\T1/pcr/m/n/10 dyn.unload[][][] []\T1/ptm/m/n
/10 on a DLL loaded by []\T1/pcr/m/n/10 library.dynam[]\T1/ptm/m/n/10 : use
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[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
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[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
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[][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil
e.access[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 files[][][] []\T1/ptm/
m/n/10 for many more file han-dling func-tions and
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[] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments
as for lists[]
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[] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
prob = 0.2))),[]
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[]\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the
same names ![]
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[]\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w
/ same name in .GlobalEnv[]
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[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways
be sup-
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[]\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/
ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of
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[]\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other
Unix-alikes[]
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[]\T1/pcr/m/n/9 c(m = months(then), wd = weekdays(then)) # in C_TIME locale \T
S1/pcr/m/n/9 '\T1/pcr/m/n/9 cT\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 ; typically German
[]
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[]\T1/pcr/m/n/9 c(m = months(then), wd = weekdays(then)) # "standard" (still p
latform specific ?)[]
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[]\T1/pcr/m/n/9 ## Not run: Sys.setlocale("LC_COLLATE", "C") # turn off loca
le-specific sorting,[]
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[]\T1/pcr/m/n/9 Sys.setenv("LANGUAGE" = "es") # set the language for error/war
ning messages[]
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[][][]\T1/pcr/m/n/10 raw[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logical[]
[][] []\T1/ptm/m/n/10 or `number-like' vec-tors (i.e., of types [][][]\T1/pcr/m
/n/10 double[][][] []\T1/ptm/m/n/10 (class
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[]\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary = r ), complex(real =
r , imaginary = NA ),[]
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[] \T1/pcr/m/n/9 complex(real = r , imaginary = NaN), complex(real = N
aN, imaginary = r ))[]
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[]\T1/pcr/m/n/9 zM ##--> many "NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s" (= 1) and th
e four non-NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s (3 different ones, at 7,9,10)[]
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[]\T1/pcr/m/n/9 match.arg(c("a", ""), c("", NA, "bb", "abc"), several.ok=TRUE
) # |--> "abc"[]
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[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion
(also known as a `clo-sure'):
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[]\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross \T1/ptm/m/n/10 prod-ucts, []
[][]\T1/pcr/m/n/10 crossprod[][][]() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 tcro
ssprod() []\T1/ptm/m/n/10 are typ-i-cally prefer-able.
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[]\T1/pcr/m/n/10 memCompress(from, type = c("gzip", "bzip2", "xz", "zstd", "no
ne"))
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\T1/ptm/m/n/10 al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 https : / / lea
rn . microsoft . com / en-[]gb / windows /
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\T1/pcr/m/n/10 desktop / Memory / physical-[]address-[]extension$[][] \T1/ptm/m
/n/10 and [][]$\T1/pcr/m/n/10 https : / / learn .
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[] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
all,[]
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[]\T1/pcr/m/n/10 anyNA(recursive = FALSE) []\T1/ptm/m/n/10 works the same way a
s []\T1/pcr/m/n/10 is.na[]\T1/ptm/m/n/10 ; []\T1/pcr/m/n/10 anyNA(recursive =
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[]\T1/pcr/m/n/10 as.name []\T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-
nally to a char-ac-ter vec-tor (so meth-ods for
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[]\T1/ptm/m/n/10 For an [][][]\T1/pcr/m/n/10 environment[][][] env[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 names(env) []\T1/ptm/m/n/10 gives the names of the cor-r
e-spond-ing list,
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\T1/ptm/m/n/10 i.e., []\T1/pcr/m/n/10 names(as.list(env, all.names = TRUE)) []\
T1/ptm/m/n/10 which are also given by [][][]\T1/pcr/m/n/10 ls[][][](env,
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\T1/pcr/m/n/10 all.names = TRUE, sorted = FALSE)[]\T1/ptm/m/n/10 . If the en-vi
-ron-ment is used as a hash ta-ble,
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[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of []\T1/pcr/m/n/1
0 c("bytes", "chars",
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[]\T1/ptm/m/n/10 optional [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 e
ven-tu-ally to be passed to []\T1/pcr/m/n/10 print()[]\T1/ptm/m/n/10 , used by
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\T1/ptm/m/n/10 tion []\T1/pcr/m/n/10 GetFinalPathNameByHandle []\T1/ptm/m/n/10
and in case of an er-ror (such as in-suf-fi-cient per-
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[]\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s
tartup mes-sages given by
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[]\T1/pcr/m/n/10 .onAttach[]\T1/ptm/m/n/10 . These mes-sages (and any es-sen-ti
al ones from []\T1/pcr/m/n/10 .onLoad[]\T1/ptm/m/n/10 ) should use
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[]\T1/ptm/m/n/10 Uses of []\T1/pcr/m/n/10 library []\T1/ptm/m/n/10 with ar-gu-m
ent []\T1/pcr/m/n/10 help []\T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion ab
out the pack-
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\T1/ptm/m/n/10 age should use []\T1/pcr/m/n/10 format []\T1/ptm/m/n/10 on the c
om-puted pack-age in-for-ma-tion ob-ject and pass this to
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[]\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ
e.only)
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[] \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk
gs"))[]
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[]\T1/pcr/m/n/10 loadNamespace []\T1/ptm/m/n/10 does not at-tach the name space
it loads to the search path.
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[]\T1/pcr/m/n/10 attachNamespace []\T1/ptm/m/n/10 can be used to at-tach a fram
e con-tain-ing the ex-ported val-ues of a
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[]\T1/pcr/m/n/10 isNamespaceLoaded(pkg) []\T1/ptm/m/n/10 is equiv-a-lent to but
more ef-fi-cient than []\T1/pcr/m/n/10 pkg %in%
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[] \T1/pcr/m/n/9 ## The string "foo" and the symbol \TS1/pcr/m/n/9 '\T1/pcr/m/
n/9 foo\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 can be used interchangeably here:[]
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[]\T1/ptm/m/n/10 The de-fault method for []\T1/pcr/m/n/10 is.numeric []\T1/ptm/
m/n/10 re-turns []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 if its ar-gu-ment is of
[][]mode[][][]
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\T1/ptm/m/n/10 ject as ob-tained by [][][]\T1/pcr/m/n/10 R.version[][][][]\T1/p
tm/m/n/10 . For []\T1/pcr/m/n/10 as.numeric_version []\T1/ptm/m/n/10 and
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[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
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[]\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/
10 R \T1/ptm/m/n/10 starts up. Ini-
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[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
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[]\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][][]\T1/pcr/
m/n/10 setRepositories[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 28609--28615
\T1/ptm/m/n/10 e.g. the de-fault `[]\T1/pcr/m/n/10 "https://bioconductor.org"[]
\T1/ptm/m/n/10 ' or the Eu-ro-pean mir-ror
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\T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de
"[]\T1/ptm/m/n/10 '. Can be set by
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[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
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[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by
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[]\T1/ptm/m/n/10 Used by [][][]\T1/pcr/m/n/10 install.packages[][][] []\T1/ptm/
m/n/10 (and in-di-rectly
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[]\T1/ptm/m/n/10 default email-ing method used by [][][]\T1/pcr/m/n/10 create.p
ost[][][] []\T1/ptm/m/n/10 and hence [][][]\T1/pcr/m/n/10 bug.report[][][] []\T
1/ptm/m/n/10 and
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[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see
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[]\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec,
300X faster[]
Underfull \vbox (badness 10000) has occurred while \output is active
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[]\T1/ptm/m/n/10 where el-e-ment []\T1/pcr/m/n/10 A[c(arrayindex.x, arrayindex.
y)] = FUN(X[arrayindex.x],
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[]\T1/pcr/m/n/10 str2expression(s) []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 str2la
ng(s) []\T1/ptm/m/n/10 re-turn spe-cial ver-sions of []\T1/pcr/m/n/10 parse(tex
t=s,
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[]\T1/pcr/m/n/9 tryCatch(parse(text = txt, srcfile = sf), error = function(e)
"Syntax error.")[]
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\T1/ptm/m/n/10 zero-length [][][]\T1/pcr/m/n/10 character[][][](0)[]\T1/ptm/m/n
/10 . Note that when []\T1/pcr/m/n/10 collapse []\T1/ptm/m/n/10 is a string,
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[][][]\T1/pcr/m/n/10 toString[][][] []\T1/ptm/m/n/10 typ-i-cally calls []\T1/pc
r/m/n/10 paste(*, collapse=", ")[]\T1/ptm/m/n/10 . String ma-nip-u-la-tion with
Overfull \hbox (42.18039pt too wide) in paragraph at lines 29580--29580
[]\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as
the longest input.[]
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[]\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha
t you wanted[]
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[]\T1/pcr/m/n/9 ## zero length arguments recycled as \TS1/cmtt/m/n/9 `\T1/pcr/
m/n/9 ""\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 -- NB: \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 {
}\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 <==> character(0) here[]
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[]\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 recycle0 = TRUE\TS1/pcr/m/n/9
' \T1/pcr/m/n/9 allows standard vectorized behaviour, i.e., zero-length[]
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[]\T1/pcr/m/n/9 ## recycling resulting in zero-length result
character(0):[]
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[]\T1/pcr/m/n/9 paste("The value is", val[valid], "-- not so good!") # -> "..
value is -- not .."[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 29613--29613
[]\T1/pcr/m/n/9 paste("The value is", val[valid], "-- good: empty!", recycle0=
TRUE) # -> character(0)[]
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[]\T1/pcr/m/n/9 paste("foo", {}, "bar", collapse = "|") # |--
> "foo bar"[]
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[]\T1/pcr/m/n/9 ## If all arguments are empty (and collapse a string), "" r
esults always[]
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[]\T1/pcr/m/n/9 mtcars |> subset(cyl == 4) |> nrow() # same as nrow(subset(mt
cars, cyl == 4))[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 29824--29824
[]\T1/pcr/m/n/9 stop() |> (function(...) {})() # stop() is not used on RHS so
is not evaluated[]
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[]\T1/ptm/m/n/10 All other []\T1/pcr/m/n/10 type[]\T1/ptm/m/n/10 s give a warn-
ing or an er-ror; us-ing, e.g., []\T1/pcr/m/n/10 type =
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Underfull \hbox (badness 2277) in paragraph at lines 30191--30196
\T1/ptm/m/n/10 i.e., strictly in-clude the bounds of []\T1/pcr/m/n/10 x[]\T1/pt
m/m/n/10 . New from \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0, al-low-ing
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Underfull \hbox (badness 1701) in paragraph at lines 30310--30314
[]\T1/ptm/m/n/10 This func-tion is al-most never used: []\TS1/cmtt/m/n/10 `\T1/
pcr/m/n/10 name\TS1/cmtt/m/n/10 ` []\T1/ptm/m/n/10 or, more care-fully, [][][]\
T1/pcr/m/n/10 get[][][](name, envir =
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[]\T1/pcr/m/n/9 try(structure(mysqrt, comment = "primitive function")) # depre
cation warning; soon an error[]
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Underfull \hbox (badness 1796) in paragraph at lines 30380--30383
[]\T1/ptm/m/n/10 character string (or []\T1/pcr/m/n/10 NULL[]\T1/ptm/m/n/10 ) i
n-di-cat-ing [][][]\T1/pcr/m/n/10 NA[][][] []\T1/ptm/m/n/10 val-ues in printed
out-put, see
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Underfull \hbox (badness 10000) in paragraph at lines 30591--30594
[]\T1/ptm/m/n/10 Option []\T1/pcr/m/n/10 width []\T1/ptm/m/n/10 con-trols the p
rint-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion
[441]
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[]\T1/pcr/m/n/9 (x <- 2^seq(-8, 30, by=1/4)) # auto-prints; by default all in
"exponential" format[]
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Underfull \hbox (badness 2961) in paragraph at lines 31146--31149
[]\T1/ptm/m/n/10 LAPACK and LIN-PACK are from [][]$\T1/pcr/m/n/10 https : / / n
etlib . org / lapack/$[][] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / /
[449]
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[] \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 =
rep(c(0,0,1),2))[]
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Overfull \hbox (15.18042pt too wide) in paragraph at lines 31588--31588
[]\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3
\u147b\u203c")[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 31599--31599
[]\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\
U147b\U203c"[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 31605--31605
[]\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm
l#Literal-constants[]
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[]\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[]
Underfull \vbox (badness 10000) has occurred while \output is active
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[]\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use []\T1/pcr/m/n/10 R.v
ersion$os []\T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use
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[]\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[]
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[]\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind =
NULL)[]
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Underfull \hbox (badness 3713) in paragraph at lines 31921--31932
[]\T1/pcr/m/n/10 normal.kind []\T1/ptm/m/n/10 can be []\T1/pcr/m/n/10 "Kinderma
n-Ramage"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Buggy Kinderman-Ramage" []\T1/ptm
/m/n/10 (not
[460]
Underfull \hbox (badness 2932) in paragraph at lines 32073--32080
\T1/ptm/m/n/10 Now see [][]$\T1/pcr/m/n/10 https : / / www . math . sci . hiros
hima-[]u . ac . jp / ~m-[]mat / MT / VERSIONS /
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Underfull \hbox (badness 1533) in paragraph at lines 32191--32194
[]\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca
n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the
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[] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m
ax", "min"))[]
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[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no []\T1/pcr/m/n/10 N
A[]\T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
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Overfull \hbox (15.18042pt too wide) in paragraph at lines 32506--32506
[]\T1/pcr/m/n/9 rapply(X, function(x) x, how = "replace") -> X.; stopifnot(ide
ntical(X, X.))[]
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[]\T1/pcr/m/n/9 rapply(X, deparse, control = "all") # passing extras. argument
of deparse()[]
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[]\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "list")[]
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[]\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[]
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[]\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", h
ow = "unlist")[]
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[]\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[]
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Overfull \hbox (25.98041pt too wide) in paragraph at lines 32828--32828
[]\T1/pcr/m/n/9 ## Bit representation [ sign | exponent | mantissa ] of doubl
e prec numbers :[]
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[]\T1/pcr/m/n/9 bitC <- function(x) noquote(vapply(as.double(x), function(x) {
# split one double[]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 32840--32840
[]\T1/pcr/m/n/9 d2bI <- function(x) vapply(as.double(x), function(x) intToBits
(numToInts(x)), raw(64L))[]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 32841--32841
[]\T1/pcr/m/n/9 d2b <- function(x) vapply(as.double(x), function(x)
numToBits(x) , raw(64L))[]
Underfull \vbox (badness 10000) has occurred while \output is active
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Underfull \hbox (badness 6300) in paragraph at lines 32910--32912
[]\T1/ptm/m/n/10 The sec-tion `Pro-cess-ing doc-u-men-ta-tion files' in the `Wr
it-ing R Ex-ten-sions' man-ual:
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Underfull \hbox (badness 4048) in paragraph at lines 32936--32941
[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
to
Underfull \hbox (badness 4582) in paragraph at lines 32936--32941
\T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the
mode:
Underfull \hbox (badness 1824) in paragraph at lines 32936--32941
\T1/ptm/m/n/10 one of []\T1/pcr/m/n/10 "numeric"[]\T1/ptm/m/n/10 , []\T1/pcr/m/
n/10 "double"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "integer"[]\T1/ptm/m/n/10 , []
\T1/pcr/m/n/10 "int"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/
10 ,
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Underfull \hbox (badness 2080) in paragraph at lines 33477--33487
[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 infoRDS[]\T1/ptm/m/n/10 , an \T1/phv/m/n/
10 R \T1/ptm/m/n/10 list with el-e-ments []\T1/pcr/m/n/10 version []\T1/ptm/m/n
/10 (ver-sion num-ber, cur-rently 2 or 3),
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[]\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[]
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[]\T1/pcr/m/n/10 regexpr []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 gregexpr []\T1/p
tm/m/n/10 sup-port `named cap-ture'. If groups are named, e.g.,
Underfull \hbox (badness 1968) in paragraph at lines 34049--34051
[]\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P
OSIX stan-dard, and the
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Underfull \hbox (badness 10000) in paragraph at lines 34060--34062
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 https : / /
pubs . opengroup . org / onlinepubs /
Underfull \hbox (badness 1975) in paragraph at lines 34063--34067
[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 pcre2pattern []\T1/ptm/m/n/10 or []\T1/pc
r/m/n/10 pcrepattern man []\T1/ptm/m/n/10 page (found as part of [][]$\T1/pcr/m
/n/10 https : / / www .
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 34435--34435
[]\T1/pcr/m/n/9 rep(1:4, each = 2, times = 3) # length 24, 3 complete
replications[]
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Underfull \hbox (badness 10000) in paragraph at lines 34506--34510
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
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Underfull \hbox (badness 2302) in paragraph at lines 34739--34742
[]\T1/pcr/m/n/10 signif []\T1/ptm/m/n/10 rounds the val-ues in its first ar-gu-
ment to the spec-i-fied num-ber of \T1/ptm/m/it/10 sig-nif-i-cant
Underfull \hbox (badness 1824) in paragraph at lines 34739--34742
\T1/ptm/m/n/10 dig-its. Hence, for []\T1/pcr/m/n/10 numeric x[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 signif(x, dig) []\T1/ptm/m/n/10 is the same as []\T1/pcr/m/n/
10 round(x, dig -
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[] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"))[]
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[] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[]
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[] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[]
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[] \T1/pcr/m/n/10 useHash = (n > 1e+07 && !replace && is.null(prob)
&& size <= n/2))[]
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[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
FALSE)[]
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 strip.white []\T1/ptm/m/n/10 is of length
1, it ap-plies to all fields; oth-er-wise, if
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[]\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n")
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[]\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence []\T1/pcr/
m/n/10 1, 2, ..., length(along.with)[]\T1/ptm/m/n/10 .
Underfull \hbox (badness 5563) in paragraph at lines 36321--36327
[]\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence []\T1/pcr/m/n/10 1, 2
, ..., length(from) []\T1/ptm/m/n/10 (as if ar-gu-ment
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[]\T1/ptm/m/n/10 A vec-tor of class []\T1/pcr/m/n/10 "Date"[]\T1/ptm/m/n/10 . T
ype []\T1/pcr/m/n/10 "[][]integer[][][]" []\T1/ptm/m/n/10 is of-ten pre-served
on pur-pose, sav-ing
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[]\T1/pcr/m/n/9 ## find all 7th of the month _strictly_ inside two dates, the
last being a 7th.[]
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Underfull \hbox (badness 6094) in paragraph at lines 36948--36952
[]\T1/pcr/m/n/10 getAllConnections []\T1/ptm/m/n/10 re-turns a se-quence of in-
te-ger con-nec-tion de-scrip-tors for use
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\T1/ptm/m/n/10 with []\T1/pcr/m/n/10 getConnection[]\T1/ptm/m/n/10 , cor-re-spo
nd-ing to the row names of the ta-ble re-turned by
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[]\T1/ptm/m/n/10 In Win-dows, com-mand line in-ter-pre-ta-tion is done by the a
p-pli-ca-tion as well as the
Underfull \hbox (badness 3492) in paragraph at lines 37039--37050
\T1/ptm/m/n/10 shell. It may de-pend on the com-piler used: Mi-crosoft's rules
for the C run-time
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\T1/ptm/m/n/10 are given at [][]$\T1/pcr/m/n/10 https : / / learn . microsoft .
com / en-[]us / cpp / c-[]language /
Underfull \hbox (badness 1635) in paragraph at lines 37039--37050
\T1/pcr/m/n/10 parsing-[]c-[]command-[]line-[]arguments ? view = msvc-[]160$[][
]\T1/ptm/m/n/10 . It may de-pend on the
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Overfull \hbox (66.78088pt too wide) in paragraph at lines 37591--37591
[] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index
.return = FALSE)[]
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[]\T1/pcr/m/n/9 sort_by.data.frame(mtcars, ~ list(am, -mpg)) |> subset(select
= c(am, mpg))[]
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[] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length
= Inf,[]
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[] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes"
, "keepNA"),[]
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[][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 vec-tor, passed as []\T1/
pcr/m/n/10 control []\T1/ptm/m/n/10 to [][][]\T1/pcr/m/n/10 deparse[][][]()[]\T
1/ptm/m/n/10 , see also
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[][][]\T1/pcr/m/n/10 .deparseOpts[][][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \
T1/ptm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to
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[]\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments
should print:)[]
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 38437--38437
[]\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m
/n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[]
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[]\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
being added[]
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Underfull \hbox (badness 10000) in paragraph at lines 38678--38680
[][][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919
799 / functions /
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[]\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known")
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[]\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
FALSE)[]
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[]\T1/ptm/m/n/10 Stack over-flow er-rors can be caught and han-dled by ex-it-in
g han-dlers es-tab-lished with
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Overfull \hbox (63.78036pt too wide) in paragraph at lines 39235--39235
[]\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three
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Underfull \hbox (badness 6110) in paragraph at lines 39331--39341
[]\T1/ptm/m/n/10 A func-tion []\T1/pcr/m/n/10 .First []\T1/ptm/m/n/10 (and [][]
[]\T1/pcr/m/n/10 .Last[][][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-at
e `\T1/pcr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or
Underfull \hbox (badness 2635) in paragraph at lines 39331--39341
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have been
saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want a dif-fer-ent
Underfull \hbox (badness 1237) in paragraph at lines 39331--39341
\T1/ptm/m/n/10 set of pack-ages than the de-fault ones when you start, in-sert
a call to [][][]\T1/pcr/m/n/10 options[][][] []\T1/ptm/m/n/10 in the
Underfull \hbox (badness 1231) in paragraph at lines 39331--39341
\T1/pcr/m/n/10 = character()) []\T1/ptm/m/n/10 will at-tach no ex-tra pack-ages
on startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (or
Underfull \hbox (badness 1112) in paragraph at lines 39331--39341
\T1/ptm/m/n/10 set []\T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL []\T1/ptm/m/n/10 as
an en-vi-ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/10 ).
Us-ing
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[]\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file
s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 '
Underfull \hbox (badness 10000) in paragraph at lines 39387--39393
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for
first in architecture-specific di-rec-to-ries,
Underfull \hbox (badness 1496) in paragraph at lines 39387--39393
\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be
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[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is
also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/pt
m/m/n/10 ' which is read
Underfull \hbox (badness 1038) in paragraph at lines 39402--39409
\T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron-
ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the
Underfull \hbox (badness 2573) in paragraph at lines 39402--39409
\T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i
n site or user en-vi-ron-ment
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[]\T1/pcr/m/n/9 # Variable expansion in double quotes, string literals with ba
ckslashes in[]
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Underfull \hbox (badness 5985) in paragraph at lines 39549--39552
[]\T1/ptm/m/n/10 The de-fault han-dler stores the er-ror mes-sage in a buffer;
it can be re-trieved by
Underfull \hbox (badness 1460) in paragraph at lines 39549--39552
[]\T1/pcr/m/n/10 geterrmessage()[]\T1/ptm/m/n/10 . It also stores a trace of th
e call stack that can be re-trieved by
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[]\T1/ptm/m/n/10 alternative to []\T1/pcr/m/n/10 exprs []\T1/ptm/m/n/10 or []\T
1/pcr/m/n/10 ...[]\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an
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[] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e
xprs = exprs)))
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[]\T1/pcr/m/n/9 stopifnot(all.equal(pi, 3.141593), 2 < 2, (1:10 < 12), "a" <
"b") |> try()[]
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[]\T1/pcr/m/n/9 stopifnot(all.equal(rep(list(pi),4), list(3.1, 3.14, 3.141, 3.
1415))) |> try()[]
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[]\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 {Yes, learn how to use do.c
all(substitute, ...) in a powerful manner !!}[]
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[]\T1/pcr/m/n/9 bdy <- do.call(substitute, list(bdy, list(stopifnot =
quote(warnifnot))))[]
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[]\T1/pcr/m/n/9 bdy[[N-1]] <- do.call(substitute, list(bdy[[N-1]], list(stop =
quote(warning))))[]
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[]\T1/ptm/m/n/10 integer de-ter-min-ing the []\T1/pcr/m/n/10 format()[]\T1/ptm/
m/n/10 ing of sec-onds when needed. Note
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[]\T1/pcr/m/n/9 ## time with fractional seconds (setting \TS1/cmtt/m/n/9 `\T1/
pcr/m/n/9 tz = ..\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 for reproducible output)[]
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[]\T1/pcr/m/n/9 z3 # prints without fractional seconds by default, digits.sec
= NULL ("= 0")[]
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[]\T1/pcr/m/n/9 format(s1 <- seq.Date(as.Date(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 19
78-01-01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ), by = \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 day
\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , len = 7), "%a")[]
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[]\T1/pcr/m/n/9 format(s2 <- seq.Date(as.Date(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 20
00-01-01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ), by = \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 mon
th\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , len = 12), "%b")[]
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[] \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[]
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[] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[]
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[]\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[]
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Overfull \hbox (52.98038pt too wide) in paragraph at lines 41140--41140
[]\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e
verything gets added.[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 41143--41143
[]\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also
missing, ....[]
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[]\T1/pcr/m/n/10 format(x, digits = max(3L, getOption("digits") - 3L), zdigits
= 4L, ...)[]
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[]\T1/pcr/m/n/10 print(x, digits = max(3L, getOption("digits") - 3L), zdigits
= 4L, ...)[]
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[]\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision
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[] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[]
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[]\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux,
macOS, FreeBSD:[]
Underfull \hbox (badness 2293) in paragraph at lines 41814--41820
[]\T1/ptm/m/n/10 This ex-pands tilde (see [][]tilde ex-pan-sion[][][]) and wild
-cards in file paths. For pre-cise de-
Underfull \hbox (badness 1237) in paragraph at lines 41814--41820
\T1/ptm/m/n/10 tails of wild-cards ex-pan-sion, see your sys-tem's doc-u-men-ta
-tion on the []\T1/pcr/m/n/10 glob []\T1/ptm/m/n/10 sys-tem call.
[603]
Underfull \hbox (badness 4792) in paragraph at lines 41832--41837
[]\T1/ptm/m/n/10 If a file-name starts with []\T1/pcr/m/n/10 . []\T1/ptm/m/n/10
this may need to be matched ex-plic-itly: for ex-am-ple
Underfull \hbox (badness 1107) in paragraph at lines 41832--41837
[]\T1/pcr/m/n/10 Sys.glob("*.RData") []\T1/ptm/m/n/10 may or may not match `\T1
/pcr/m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match
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Underfull \hbox (badness 10000) in paragraph at lines 42124--42128
[]\T1/pcr/m/n/10 sys.status() []\T1/ptm/m/n/10 re-turns a list with com-po-nent
s []\T1/pcr/m/n/10 sys.calls[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sys.parents []\
T1/ptm/m/n/10 and
Underfull \hbox (badness 1584) in paragraph at lines 42139--42142
[]\T1/pcr/m/n/10 sys.call []\T1/ptm/m/n/10 re-turns a call, []\T1/pcr/m/n/10 sy
s.function []\T1/ptm/m/n/10 a func-tion def-i-ni-tion, and []\T1/pcr/m/n/10 sys
.frame []\T1/ptm/m/n/10 and
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Overfull \hbox (25.98041pt too wide) in paragraph at lines 42277--42277
[]\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths
), keepNA=TRUE))[]
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[]\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/cmtt
/m/n/9 `\T1/pcr/m/n/9 A+C\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 could also be used
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Underfull \hbox (badness 1082) in paragraph at lines 42502--42505
[]\T1/ptm/m/n/10 logical. If []\T1/pcr/m/n/10 TRUE[]\T1/ptm/m/n/10 , func-tions
keep their source in-clud-ing com-ments, see
Underfull \hbox (badness 10000) in paragraph at lines 42529--42531
[][][]\T1/pcr/m/n/10 source[][][][]\T1/ptm/m/n/10 , and [][][]\T1/pcr/m/n/10 lo
adNamespace[][][] []\T1/ptm/m/n/10 which is called from [][][]\T1/pcr/m/n/10 li
brary[][][](.) []\T1/ptm/m/n/10 and uses
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Underfull \hbox (badness 1038) in paragraph at lines 42696--42699
[]\T1/ptm/m/n/10 a log-i-cal (not []\T1/pcr/m/n/10 NA[]\T1/ptm/m/n/10 ) in-di-c
at-ing whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or
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Underfull \hbox (badness 1442) in paragraph at lines 43080--43084
\T1/ptm/m/n/10 con-sider it to be piped or redi-rected: []\T1/pcr/m/n/10 stdout
= TRUE []\T1/ptm/m/n/10 uses a pipe whereas []\T1/pcr/m/n/10 stdout =
[623]
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[]\T1/ptm/m/n/10 Use [][][]\T1/pcr/m/n/10 ftable[][][] []\T1/ptm/m/n/10 for pri
nt-ing (and more) of mul-ti-di-men-sional ta-bles. [][][]\T1/pcr/m/n/10 margin.
table[][][][]\T1/ptm/m/n/10 ,
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Underfull \hbox (badness 7888) in paragraph at lines 43453--43457
[]\T1/ptm/m/n/10 On 64-bit plat-forms []\T1/pcr/m/n/10 bin []\T1/ptm/m/n/10 can
have $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., []\T1/pcr/
m/n/10 length(bin) >
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Overfull \hbox (63.78036pt too wide) in paragraph at lines 43715--43715
[] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1"
, "2"), c("A", "B")))),[]
Overfull \hbox (30.0281pt too wide) in paragraph at lines 43717--43717
[] \T1/pcr/m/n/9 array(list(\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 2\TS1/cm
tt/m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), names = nq),[]
Overfull \hbox (55.67578pt too wide) in paragraph at lines 43719--43719
[] \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 4\TS1/cmtt/m/n/9 ` \T1/pcr/m
/n/9 = NULL, \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 5\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 =
NULL), dim=4, dimnames=list(as.character(2:5)))))[]
Underfull \hbox (badness 10000) in paragraph at lines 43732--43734
[]\T1/pcr/m/n/10 removeTaskCallback []\T1/ptm/m/n/10 un-registers a func-tion t
hat was reg-is-tered ear-lier via
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Underfull \hbox (badness 3872) in paragraph at lines 43931--43934
[]\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call
-backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer .
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Underfull \hbox (badness 1655) in paragraph at lines 44420--44427
\T1/ptm/m/n/10 may also be known as `[]\T1/pcr/m/n/10 GB[]\T1/ptm/m/n/10 ', `[]
\T1/pcr/m/n/10 GB-Eire[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 Europe/Belfast[]\T1
/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 Europe/Guernsey[]\T1/ptm/m/n/10 ',
Underfull \hbox (badness 2253) in paragraph at lines 44428--44433
[]\T1/pcr/m/n/10 OlsonNames []\T1/ptm/m/n/10 re-turns a char-ac-ter vec-tor, se
e the ex-am-ples for typ-i-cal cases. It may
Underfull \hbox (badness 1655) in paragraph at lines 44428--44433
\T1/ptm/m/n/10 have an at-tribute []\T1/pcr/m/n/10 "Version"[]\T1/ptm/m/n/10 ,
some-thing like `[]\T1/pcr/m/n/10 "2023a"[]\T1/ptm/m/n/10 '. (It does on sys-te
ms us-ing
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Underfull \hbox (badness 4467) in paragraph at lines 44482--44491
[]\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 OlsonNames []\T1/ptm/m/n/10 re-
turns the time-zone names known to the cur-rently se-
Underfull \hbox (badness 3954) in paragraph at lines 44482--44491
\T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t
he file sys-tem varies,
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Underfull \hbox (badness 1337) in paragraph at lines 44579--44587
\T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de
r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 /
usr/local/etc\T1/ptm/m/n/10 ' or
Underfull \hbox (badness 10000) in paragraph at lines 44588--44591
[]\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym
-link tar-get name of
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Underfull \hbox (badness 3460) in paragraph at lines 44647--44650
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / data . iana . org /
Underfull \hbox (badness 4429) in paragraph at lines 44651--44653
[][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h
tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol-
Overfull \hbox (31.3804pt too wide) in paragraph at lines 44660--44660
[]\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET",
"Eire", ..., but[]
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Overfull \hbox (15.18042pt too wide) in paragraph at lines 45001--45001
[]\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15
g)\n", ncp))),[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 45003--45003
[]\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp
root finding:[]
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Overfull \hbox (84.78088pt too wide) in paragraph at lines 45100--45100
[] \T1/pcr/m/n/10 getOption("deparse
.max.lines", -1L)))[]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 45102--45102
[] \T1/pcr/m/n/10 getOption("deparse
.max.lines", -1L)))[]
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Underfull \hbox (badness 6542) in paragraph at lines 45376--45378
[]\T1/pcr/m/n/10 cospi(x)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sinpi(x)[]\T1/ptm/
m/n/10 , and []\T1/pcr/m/n/10 tanpi(x)[]\T1/ptm/m/n/10 , com-pute []\T1/pcr/m/n
/10 cos(pi*x)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sin(pi*x)[]\T1/ptm/m/n/10 , an
d
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[]\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[
\t\r\n]")
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Underfull \hbox (badness 1708) in paragraph at lines 45563--45571
[]\T1/pcr/m/n/10 try []\T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any
er-rors that oc-cur dur-ing the eval-u-a-tion. If
Underfull \hbox (badness 3713) in paragraph at lines 45563--45571
\T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][
][]\T1/pcr/m/n/10 stderr[][][] []\T1/ptm/m/n/10 con-nec-tion un-less
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Underfull \hbox (badness 4859) in paragraph at lines 45603--45608
[][][]\T1/pcr/m/n/10 options[][][] []\T1/ptm/m/n/10 for set-ting er-ror han-dle
rs and sup-press-ing the print-ing of er-ror mes-sages;
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Underfull \hbox (badness 3895) in paragraph at lines 45665--45678
[]\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the
struc-ture []\T1/pcr/m/n/10 TypeTable []\T1/ptm/m/n/10 in
Underfull \hbox (badness 1303) in paragraph at lines 45665--45678
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue
s are the vec-tor types []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/
m/n/10 "integer"[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2452) in paragraph at lines 45665--45678
[]\T1/pcr/m/n/10 "promise"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "object"[]\T1/ptm
/m/n/10 , []\T1/pcr/m/n/10 "language"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "char"
[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "..."[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "a
ny"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "expression"[]\T1/ptm/m/n/10 ,
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Overfull \hbox (9.78043pt too wide) in paragraph at lines 46018--46018
[]\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[]
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[667]
Underfull \hbox (badness 1137) in paragraph at lines 46157--46164
[]\T1/ptm/m/n/10 When a func-tion call-ing []\T1/pcr/m/n/10 UseMethod("fun") []
\T1/ptm/m/n/10 is ap-plied to an ob-ject with class vec-tor
[668]
[669]
[670]
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 46536--46536
[]\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local
es and fonts[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 46545--46545
[]\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little-
endian platforms[]
[673]
Underfull \hbox (badness 1721) in paragraph at lines 46607--46624
[][][]\T1/pcr/m/n/10 file.rename[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 f
ile.symlink[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 dir.create[][][][]\
T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 dir.exists[][][][]\T1/ptm/m/n/10 , [][][]\
T1/pcr/m/n/10 normalizePath[][][][]\T1/ptm/m/n/10 ,
[674]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 46709--46709
[]\T1/pcr/m/n/9 try( substr(x, 1,1) ) # gives \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 in
valid multibyte string\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 error in a UTF-8 locale[]
[675]
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[]\T1/ptm/m/n/10 The atomic modes are []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/1
0 , []\T1/pcr/m/n/10 "integer"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "numeric" []\
T1/ptm/m/n/10 (syn-onym []\T1/pcr/m/n/10 "double"[]\T1/ptm/m/n/10 ),
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 mode = "any"[]\T1/ptm/m/n/10 , []\T1/pcr/m
/n/10 is.vector []\T1/ptm/m/n/10 may re-turn []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/
n/10 for the atomic modes, [][][]\T1/pcr/m/n/10 list[][][] []\T1/ptm/m/n/10 and
[676]
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[678]
Underfull \hbox (badness 1014) in paragraph at lines 47004--47007
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the warn-ing should be out-put im-me
-di-ately, even if
[679]
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Overfull \hbox (36.78088pt too wide) in paragraph at lines 47113--47113
[] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes
sages:\n"),[]
[681]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 47190--47190
[]\T1/pcr/m/n/9 ## at the end prints all three warnings, from the \TS1/pcr/m/n
/9 '\T1/pcr/m/n/9 option(warn = 0)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 above[]
Overfull \hbox (90.78033pt too wide) in paragraph at lines 47198--47198
[]\T1/pcr/m/n/9 x <- 1:36; for(n in 1:13) for(m in 1:12) A <- matrix(x, n,m) #
There were 105 warnings ...[]
[682]
Underfull \hbox (badness 1783) in paragraph at lines 47263--47265
[]\T1/pcr/m/n/10 weekdays []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 months []\T1/pt
m/m/n/10 re-turn a char-ac-ter vec-tor of names in the lo-cale in use, i.e.,
[683]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 47293--47293
[]\T1/pcr/m/n/9 ## Show how easily you get month, day, year, day (of {month, w
eek, yr}), ... :[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 47305--47305
[]\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Even simpler: Date -> Matrix
- dropping time info {sec,min,hour, isdst}[]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 47308--47308
[]\T1/pcr/m/n/9 d2mat(seq(as.Date("2000-02-02"), by=1, length.out=30)) # has R
1.0.0\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s release date[]
[684]
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 arr.ind == TRUE []\T1/ptm/m/n/10 and []\T1
/pcr/m/n/10 x []\T1/ptm/m/n/10 is an [][][]\T1/pcr/m/n/10 array[][][] []\T1/ptm
/m/n/10 (has a [][][]\T1/pcr/m/n/10 dim[][][] []\T1/ptm/m/n/10 at-tribute), the
re-sult is
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[]\T1/pcr/m/n/10 arrayInd(which(x), dim(x), dimnames(x))[]\T1/ptm/m/n/10 , name
ly a ma-trix whose rows each
[685]
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[]\T1/ptm/m/n/10 For a [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 vec-
tor []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 with both []\T1/pcr/m/n/10 FALSE []\T1/
ptm/m/n/10 and []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 val-ues, []\T1/pcr/m/n/10
which.min(x) []\T1/ptm/m/n/10 and
[686]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 47503--47503
[]\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is
at least one:[]
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[693]
Underfull \hbox (badness 2846) in paragraph at lines 47999--48003
[]\T1/pcr/m/n/10 .packages() []\T1/ptm/m/n/10 re-turns the names of the cur-ren
tly at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[694]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 48039--48039
[]\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[]
Underfull \hbox (badness 3209) in paragraph at lines 48060--48064
[]\T1/pcr/m/n/10 .standard_regexps []\T1/ptm/m/n/10 re-turns a list of `stan-da
rd' reg-exps, in-clud-ing el-e-ments named
[695]) (./compiler-pkg.tex
[696]
Chapter 2.
[697]
Underfull \hbox (badness 2884) in paragraph at lines 107--121
[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 options []\T1/ptm/m/n/10 ar-gu-ment can b
e used to con-trol com-piler op-er-a-tion. There are cur-
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\T1/ptm/m/n/10 rently four op-tions: []\T1/pcr/m/n/10 optimize[]\T1/ptm/m/n/10
, []\T1/pcr/m/n/10 suppressAll[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 suppressUndef
ined[]\T1/ptm/m/n/10 , and
[698]
[699]
[700]) (./datasets-pkg.tex
Chapter 3.
[701]
[702]
[703]
[704]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 297--297
[] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[]
[705]
[706]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 375--375
[]\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi
ven = FALSE)[]
[707]
[708]
[709]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 613--613
[] \T1/pcr/m/n/9 start = c(lrc = log(.35)), algorithm = "plinear", t
race = TRUE)[]
[710]
[711]
Underfull \hbox (badness 4779) in paragraph at lines 700--703
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[712]
[713]
Underfull \hbox (badness 4779) in paragraph at lines 832--835
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[714]
[715]
Underfull \hbox (badness 1097) in paragraph at lines 1034--1038
[]\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th
e iden-ti-fi-ca-tion of crim-i-nals.
[716]
[717]
Underfull \hbox (badness 4779) in paragraph at lines 1149--1152
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[718]
[719]
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[721]
[722]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1463--1463
[]\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
time (sec)")[]
[723]
[724]
Underfull \hbox (badness 10000) in paragraph at lines 1548--1551
[]\T1/ptm/m/n/10 Finally, []\T1/pcr/m/n/10 freeny []\T1/ptm/m/n/10 is a data fr
ame with vari-ables []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lag.q
uarterly.revenue[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2903) in paragraph at lines 1548--1551
[]\T1/pcr/m/n/10 price.index[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 income.level[]\
T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 market.potential []\T1/ptm/m/n/10 ob-taine
d from the above
[725]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1641--1641
[] \T1/pcr/m/n/9 xlab = "Hip Angle", ylab = "Knee Angle", main = "\TS1/pcr
/m/n/9 '\T1/pcr/m/n/9 gait\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 data : Boy 1")[]
Overfull \hbox (112.38031pt too wide) in paragraph at lines 1643--1643
[]\T1/pcr/m/n/9 matlines(gait[, -1, 1], gait[, -1, 2], type = "l", lty = 1, co
l = adjustcolor("thistle", 1/3))[]
[726]
[727]
[728]
Underfull \hbox (badness 4779) in paragraph at lines 1809--1812
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[729]
[730]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1907--1907
[]\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil
y = binomial())[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1915--1915
[] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
data = infert)[]
[731]
[732]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 2032--2032
[]\T1/pcr/m/n/9 ## Iris versicolor "differs twice as much from I. setosa as fr
om I. virginica"[]
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[]\T1/pcr/m/n/9 ## equivalence of legacy array (iris3) and data.frame (iris) r
epresentation[]
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[] \T1/pcr/m/n/9 sub(" W.",".Width", dn
i3[[2]])))),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2042--2042
[] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d
ni3[[3]]))))[]
[733]
[734]
[735]
Underfull \hbox (badness 4779) in paragraph at lines 2245--2248
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[736]
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[741]
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[744]
Underfull \hbox (badness 4779) in paragraph at lines 2810--2813
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[745]
[746]
[747]
[748]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3084--3084
[]\T1/pcr/m/n/9 plot(bill_dep ~ bill_len, data = penguins, pch = sym[sex], col
= pal[species])[]
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[]\T1/pcr/m/n/9 m <- glm(sex ~ bill_len + bill_dep + body_mass, data = adelie,
family = binomial)[]
[749]
[750]
[751]
[752]
[753]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3420--3420
[]\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main =
1.2, pch = ".")[]
[754]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3467--3467
[]\T1/pcr/m/n/9 myrandu <- matrix(NA_real_, 400, 3, dimnames = list(NULL, c("x
","y","z")))[]
[755]
[756]
[757]
[758]
[759]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 3773--3773
[]\T1/pcr/m/n/9 ## Alaska and Hawaii are placed just off the West Coast (for c
ompact map drawing):[]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 3775--3775
[]\T1/pcr/m/n/9 ## state.center2 := version of state.center with "correct" coo
rdinates for AK & HI:[]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 3776--3776
[]\T1/pcr/m/n/9 ## From https://pubs.usgs.gov/gip/Elevations-Distances/elvadis
t.html#Geographic%20Centers[]
[760]
Underfull \hbox (badness 1259) in paragraph at lines 3833--3836
\T1/ptm/m/n/10 Av. Cir-cu-laire, 3, B-1180 BRUS-SELS Cur-rently at [][]$\T1/pcr
/m/n/10 https : / / www . sidc . be / SILSO /
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3883--3883
[]\T1/pcr/m/n/9 ## How to recreate the "old" sunspot.month (R <= 3.0.3) =: sun
spot.month.0[]
[761]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3936--3936
[]\T1/pcr/m/n/9 (t2 <- c(min( end(sm)[1],end(sy)[1]), 12)) # Dec 1983 (will n
ot be updated!)[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3940--3940
[] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[]
[762] [763]
[764]
Underfull \hbox (badness 4779) in paragraph at lines 4088--4091
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[765]
[766]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4297--4297
[] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
supplement")[]
[767]
Underfull \hbox (badness 10000) in paragraph at lines 4333--4335
[]\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/pcr/m/n/10 h
ttps : / / web . archive . org / web /
Underfull \hbox (badness 10000) in paragraph at lines 4333--4335
\T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma
n / sitephotos /
[768]
[769]
[770]
[771]
[772]
[773] [774]
[775]
[776]
[777]
[778]
[779]
[780]
[781]) (./grDevices-pkg.tex
[782]
Chapter 4.
[783]
[784]
[785]
[786]
Underfull \hbox (badness 4752) in paragraph at lines 299--304
[]\T1/ptm/m/n/10 Apart from that, []\T1/pcr/m/n/10 axisTicks() []\T1/ptm/m/n/10
just calls the C func-tion []\T1/pcr/m/n/10 CreateAtVector() []\T1/ptm/m/n/10
in
Underfull \hbox (badness 2865) in paragraph at lines 299--304
\T1/ptm/m/n/10 `\T1/ptm/m/sl/10 R\T1/pcr/m/n/10 /src/main/plot.c\T1/ptm/m/n/10
' which is also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack
-age func-tion
[787]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 351--351
[]\T1/pcr/m/n/9 aX(2, print(ya <- axisTicks(pu[3:4], log = TRUE))) # 10 20 50
100 (y axis)[]
[788]
[789]
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Overfull \hbox (6.78088pt too wide) in paragraph at lines 537--537
[]\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[]
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Underfull \hbox (badness 2245) in paragraph at lines 919--924
[]\T1/ptm/m/n/10 Hexadecimal string col-ors can be in the long hex-adec-i-mal f
orm (e.g., []\T1/pcr/m/n/10 "#rrggbb" []\T1/ptm/m/n/10 or
[797]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 983--983
[]\T1/pcr/m/n/9 names(clmult) <- sapply(clmult, function(x) paste(crgb[,x[1]],
collapse = ","))[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 990--990
[] \T1/pcr/m/n/9 lattice::cloud(blue ~ red + green, data = as.data.frame(tc
), col = cNms)[]
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[]\T1/pcr/m/n/9 cNms[isC] # "white" "black" "blue" "cyan" "green" "magenta" "r
ed" "yellow"[]
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[] \T1/pcr/m/n/9 plot3d (tc, col = cNms, size = 11) # --> rotate w/ mouse; e
nlarged corners:[]
Underfull \vbox (badness 10000) has occurred while \output is active
[798]
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[801]
Underfull \hbox (badness 5175) in paragraph at lines 1239--1241
[]\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm
. The source code is in
[802]
[803]
[804]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1410--1410
[]\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab",
scale.in = 255))[]
[805]
[806]
[807]
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[]\T1/ptm/m/n/10 character: Does the de-vice sup-port pat-tern fills? One or mo
re of
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[]\T1/pcr/m/n/10 c("LinearGradient", "RadialGradient", "TilingPattern")
[808]
[809]
[810]
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[812]
Underfull \hbox (badness 1565) in paragraph at lines 1962--1967
[]\T1/ptm/m/n/10 The de-fault for []\T1/pcr/m/n/10 dev.print []\T1/ptm/m/n/10 i
s to pro-duce and print a postscript copy. This will not
Underfull \hbox (badness 1354) in paragraph at lines 1962--1967
\T1/ptm/m/n/10 sys-tem: see [][][]\T1/pcr/m/n/10 postscript[][][] []\T1/ptm/m/n
/10 for how to set this up. Win-dows users may pre-fer to use
[813]
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[]\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res
= 72,[]
[814]
Underfull \hbox (badness 1184) in paragraph at lines 2086--2096
[]\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of []\T1/pcr
/m/n/10 ghostscript[]\T1/ptm/m/n/10 , but are likely to in-
Underfull \hbox (badness 2057) in paragraph at lines 2086--2096
[]\T1/pcr/m/n/10 "tiffg4"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiffgray"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "tifflzw"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiffp
ack"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiff12nc"[]\T1/ptm/m/n/10 , []\T1/pcr/
m/n/10 "tiff24nc"[]\T1/ptm/m/n/10 ,
[815]
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[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the
set-ting of
[816]
[817]
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[]\T1/pcr/m/n/10 embedGlyphs(file, glyphInfo, outfile = file, options = charac
ter())[]
[818]
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[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
doc-u-men-ta-tion) are
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[]\T1/pcr/m/n/10 embedGlyphs() []\T1/ptm/m/n/10 is rec-om-mended for []\T1/pcr/
m/n/10 pdf() []\T1/ptm/m/n/10 files that con-tain type-set glyphs (see
[819]
[820]
Underfull \hbox (badness 2326) in paragraph at lines 2509--2519
[]\T1/ptm/m/n/10 are given, then it uses those in a call to []\T1/pcr/m/n/10 se
tGraphicsEventHandlers []\T1/ptm/m/n/10 to re-place
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\T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co
m-pat-i-bil-ity with pre-2.12.0
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\T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e
vent han-dlers is to set them us-ing
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[]\T1/pcr/m/n/10 setGraphicsEventHandlers []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10
setGraphicsEventEnv []\T1/ptm/m/n/10 on one or more graph-ics
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[]\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[]
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[]\T1/pcr/m/n/10 gray.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re
v = FALSE)
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[]\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re
v = FALSE)[]
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[]\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized
= FALSE)[]
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[]\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv",
scale.in = 255))[]
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[]\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale.
out = NULL))[]
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[]\T1/pcr/m/n/10 nclass.FD []\T1/ptm/m/n/10 uses the Freedman-Diaconis choice b
ased on the inter-quartile range
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[]\T1/pcr/m/n/10 palette.colors(n = NULL, palette = "Okabe-Ito", alpha, recycl
e = FALSE,[]
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[]\T1/pcr/m/n/9 (palette(gray(seq(0,.9,length.out = 25)))) # gray scales; prin
t old palette[]
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[]\T1/pcr/m/n/9 ## Demonstrate the colors 1:8 in different palettes using a cu
stom matplot()[]
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[] \T1/pcr/m/n/9 matplot(x, type = "l", lwd = 4, lty = 1, col = 1:n, ylab =
"", main=main)[]
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[]\T1/pcr/m/n/9 palROB <- colorRampPalette(c("red", "darkorange2", "blue"), sp
ace = "Lab")[]
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[]\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE,
fixup = TRUE)
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[]\T1/ptm/m/n/10 the type of palettes to list: []\T1/pcr/m/n/10 "qualitative"[]
\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sequential"[]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 For ex-am-ple, []\T1/pcr/m/n/10 "Dark 3" []\T1/ptm/m/n/10 work
s well for shad-ing points or lines in up to five groups,
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\T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space
& oldid = 883465135$[][]\T1/ptm/m/n/10 .
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[]\T1/ptm/m/n/10 as `\T1/pcr/m/n/10 "CP1250.enc"\T1/ptm/m/n/10 ' (Cen-tral Eu-r
o-pean), []\T1/pcr/m/n/10 "CP1251.enc"
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\T1/ptm/m/n/10 PostScript fonts fam-i-lies of those names which are in-cluded (
or cloned) in all com-mon
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\T1/ptm/m/n/10 cod-ings (ex-cept []\T1/pcr/m/n/10 "TeXtext"[]\T1/ptm/m/n/10 ) a
gree over that range. Some en-cod-ings are su-per-sets of
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\T1/ptm/m/n/10 ISO-Latin1. How-ever, if ac-cented and spe-cial char-ac-ters do
not come out as you ex-
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[]\T1/ptm/m/n/10 arguments []\T1/pcr/m/n/10 width[]\T1/ptm/m/n/10 , []\T1/pcr/m
/n/10 height[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 onefile[]\T1/ptm/m/n/10 , []\T1
/pcr/m/n/10 family[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 title[]\T1/ptm/m/n/10 , [
]\T1/pcr/m/n/10 fonts[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 version[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 paper[]\T1/ptm/m/n/
10 , []\T1/pcr/m/n/10 encoding[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 bg[]\T1/ptm/m
/n/10 , []\T1/pcr/m/n/10 fg[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pointsize[]\T1/p
tm/m/n/10 , []\T1/pcr/m/n/10 pagecentre[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 colormodel[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 useDingbats[]\T1
/ptm/m/n/10 , []\T1/pcr/m/n/10 useKerning[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 fi
llOddEven[]\T1/ptm/m/n/10 ,
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pdfTeX warning (ext4): destination with the same identifier (name{Rfn.symbol})
has been already used, duplicate ignored
<to be read again>
\relax
l.4896 \aliasA{symbol}{plotmath}{symbol}
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[]\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, [][]$\T1/pcr/m/n/10 https : / / ww
w . iso . org / standard / 34342 . html$[][]\T1/ptm/m/n/10 . See also
[863]
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[]\T1/pcr/m/n/9 ## Not run: dev.print(png, filename = "myplot.png", width = 10
24, height = 768)[]
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[]\T1/ptm/m/n/10 For use with []\T1/pcr/m/n/10 onefile = FALSE[]\T1/ptm/m/n/10
, give a C in-te-ger for-mat such as
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[]\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t
ion by Brian D'Urso
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[][][]\T1/pcr/m/n/10 postscriptFonts[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 Devices[][][][]\T1/ptm/m/n/10 , and [][][]\T1/pcr/m/n/10 check.options[][][]
[]\T1/ptm/m/n/10 which is called from both
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[]\T1/pcr/m/n/10 "AvantGarde"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Bookman"[]\T1
/ptm/m/n/10 , []\T1/pcr/m/n/10 "Courier"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "He
lvetica"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Helvetica-Narrow"[]\T1/ptm/m/n/10
,
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[]\T1/pcr/m/n/10 "NewCenturySchoolbook"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Pal
atino" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "Times"[]\T1/ptm/m/n/10 ; []\T1/pc
r/m/n/10 "URWGothic"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 "URWBookman"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "NimbusMon"[]\
T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "NimbusSan" []\T1/ptm/m/n/10 (syn-onym []\T1/p
cr/m/n/10 "URWHelvetica"[]\T1/ptm/m/n/10 ),
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[]\T1/ptm/m/n/10 There are also map-pings for []\T1/pcr/m/n/10 "ComputerModern"
[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ComputerModernItalic" []\T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/10 "Japan1"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Japan1HeiMin"[]\T
1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Japan1GothicBBB"[]\T1/ptm/m/n/10 , and []\T1/p
cr/m/n/10 "Japan1Ryumin" []\T1/ptm/m/n/10 for
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[]\T1/pcr/m/n/10 BousungEG-Light-GB []\T1/ptm/m/n/10 can be found at [][]$\T1/p
cr/m/n/10 https : / / ftp . gnu . org / pub / non-[]gnu /
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[]\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[]
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[]\T1/ptm/m/n/10 Calling []\T1/pcr/m/n/10 quartz() []\T1/ptm/m/n/10 sets [][][]
\T1/pcr/m/n/10 .Device[][][] []\T1/ptm/m/n/10 to []\T1/pcr/m/n/10 "quartz" []\T
1/ptm/m/n/10 for on-screen de-vices and to
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[] \T1/pcr/m/n/9 quartzFonts("mono") # the list(mono = ..) sublist o
f quartzFonts()[]
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\T1/ptm/m/n/10 play List", [][]$\T1/pcr/m/n/10 https : / / stattech . wordpress
. fos . auckland . ac . nz / 2015 / 12 / 21 /
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[]\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15,
sep = "."))[]
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[]\T1/pcr/m/n/10 rgb2hsv []\T1/ptm/m/n/10 trans-forms col-ors from RGB space (r
ed/green/blue) into HSV space
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[]\T1/pcr/m/n/9 p <- persp(x, y, fxy <- outer(x,y), phi = 20, theta = 15, r =
3, ltheta = -75,[]
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[]\T1/pcr/m/n/9 ## now some "horizontal rays" (going from center to very left
or very right):[]
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[] \T1/pcr/m/n/9 lines(trans3d(x=seq(x1, x2, by=0.5), y= -0.7, z = z, pmat
= p, continuous = CNT),[]
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[]\T1/pcr/m/n/9 doHor(-10, 0, z = -0.5, col = 2) # x in [-10, 0] -- to the v
ery left : fine[]
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[]\T1/pcr/m/n/9 doHor(-.5, 2, z = -0.52,col = 4) # x in [-0.5, 2] only {to th
e right} --> all fine[]
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[]\T1/pcr/m/n/9 ## but now, x in [-0.5, 20] -- "too far" ==> "wrap around" pro
blem (without \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 continuous=TRUE\TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 ):[]
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[]\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp
inch,
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[]\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize
= 12,[]
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[]\T1/ptm/m/n/10 arguments []\T1/pcr/m/n/10 width[]\T1/ptm/m/n/10 , []\T1/pcr/m
/n/10 height[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pointsize[]\T1/ptm/m/n/10 , []\
T1/pcr/m/n/10 record[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 rescale[]\T1/ptm/m/n/10
,
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[]\T1/pcr/m/n/10 xpinch[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 ypinch[]\T1/ptm/m/n/
10 , []\T1/pcr/m/n/10 bg[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 canvas[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 gamma[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 xpos[]\T1/ptm/m
/n/10 , []\T1/pcr/m/n/10 ypos[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 buffered[]\T1/
ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 restoreConsole[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 clickToConfi
rm[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 title[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10
fillOddEven []\T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/9 windows() # make sure we have the right device type (availabl
e on Windows only)[]
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[]\T1/ptm/m/n/10 The \T1/phv/m/n/10 R \T1/ptm/m/n/10 func-tion is a wrap-per fo
r two de-vices, one based on Xlib ([][]$\T1/pcr/m/n/10 https : / /
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\T1/pcr/m/n/10 en . wikipedia . org / wiki / Xlib$[][]\T1/ptm/m/n/10 ) and one
us-ing cairo-graph-ics ([][]$\T1/pcr/m/n/10 https : / / www .
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[] \T1/pcr/m/n/10 fonts, family, xpos, ypos, title, type, antialias, symbol
family)[]
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[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
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[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" []\T1/ptm/m/n/10 for CJ
K lan-guages and
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[]\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of []
\T1/pcr/m/n/10 quote(pi) []\T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/10 expression(10^degree)[]\T1/ptm/m/n/10 ) have been seen on Linu
x sys-tems which have the Wine
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[]\T1/pcr/m/n/10 type = "Xlib" []\T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-d
o-Color', `GrayScale', []\T1/pcr/m/n/10 StaticGray []\T1/ptm/m/n/10 and
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[] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
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[]\T1/pcr/m/n/9 op <- options(warn = 2)# ==> warnings would be errors, we supp
ress the one "we know":[]
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[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., []\T1/pcr/m/n/10
number[i] []\T1/ptm/m/n/10 is the mul-ti-plic-ity of
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[]\T1/pcr/m/n/9 xy <- data.frame(x = round(sort(stats::rnorm(100))), y = stats
::rnorm(100))[]
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[903]) (./graphics-pkg.tex
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Chapter 5.
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[]\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag
es, use []\T1/pcr/m/n/10 library(help =
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[] \T1/pcr/m/n/10 gap.axis <- if(perpendicular(side, las)) 0.25 else 1[]
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[]\T1/ptm/m/n/10 When []\T1/pcr/m/n/10 at = NULL[]\T1/ptm/m/n/10 , pretty tick
mark lo-ca-tions are com-puted in-ter-nally (the same way
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[]\T1/pcr/m/n/9 ## now shrink the window (in x- and y-direction) and observe t
he axis labels drawn[]
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[]\T1/pcr/m/n/9 axis.Date(3, at = as.integer(as.Date("2023-04-01")), col.axis
= "darkgreen")[]
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[]\T1/pcr/m/n/9 axis.POSIXct(3, at = as.POSIXct("2022-10-01 00:01:30"), col.ax
is = "orange")[]
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[]\T1/pcr/m/n/9 axis.POSIXct(3, at = as.numeric(as.POSIXct("2022-10-01 00:00:3
0")) + 0.25,[]
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[] \T1/pcr/m/n/9 col.axis = "forestgreen", col = "darkgreen", m
gp = c(3,2,0))[]
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[]\T1/pcr/m/n/9 plot(data.frame(HST, y = 1), xaxt = "n", xlab = "Hawaii Standa
rd Time (HST)")[]
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[]\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][][]\T1/pcr
/m/n/10 par[][][]("xaxp") []\T1/ptm/m/n/10 or
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[][][]\T1/pcr/m/n/10 par[][][]("yaxp") []\T1/ptm/m/n/10 de-pend-ing on the []\T
1/pcr/m/n/10 side []\T1/ptm/m/n/10 ar-gu-ment ([]\T1/pcr/m/n/10 par("xaxp") []\
T1/ptm/m/n/10 if
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[] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[]
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[] \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend =
NULL, ...)[]
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[][][]\T1/pcr/m/n/10 plot[][][](..., type = "h")[]\T1/ptm/m/n/10 , [][][]\T1/pc
r/m/n/10 dotchart[][][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 hist[][][] []\T1
/ptm/m/n/10 for bars of a \T1/ptm/m/it/10 con-tin-u-ous \T1/ptm/m/n/10 vari-abl
e.
[920]
Overfull \hbox (133.98029pt too wide) in paragraph at lines 1038--1038
[] \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = "
# {passengers}", legend.text = TRUE)[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1040--1040
[]\T1/pcr/m/n/9 (xt <- xtabs(Freq ~ Survived + Class + Sex, d.Titanic, subset
= Age=="Adult"))[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 1042--1042
[]\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur
vived, *)", color=TRUE)[]
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Overfull \hbox (31.3804pt too wide) in paragraph at lines 1325--1325
[]\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches ..
outside hinges"):[]
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[927]
Underfull \hbox (badness 2503) in paragraph at lines 1487--1496
\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 horizontal []\T1/ptm/m/n/10 is false, and
[]\T1/pcr/m/n/10 xlim []\T1/ptm/m/n/10 hor-i-zon-tally. []\T1/pcr/m/n/10 xaxt[]
\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 yaxt[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3375) in paragraph at lines 1522--1524
[]\T1/ptm/m/n/10 whisker line type (de-fault: []\T1/pcr/m/n/10 "dashed"[]\T1/pt
m/m/n/10 ),
[928]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1594--1594
[]\T1/pcr/m/n/9 boxplot(z, col.axis = "skyblue3", main = "boxplot(*, col.axi
s=..,main=..)")[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1595--1595
[]\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main = "plot(*, col.axi
s=..,main=..)")[]
[929]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1601--1601
[]\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill
= "grey40",[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1602--1602
[] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 1635--1635
[] \T1/pcr/m/n/10 yaxlabels = NULL, xlim = NULL, ylim = c(0, 1), weights = NU
LL, ...)[]
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[933]
[934]
Underfull \hbox (badness 10000) in paragraph at lines 1908--1914
[][][]\T1/pcr/m/n/10 contourLines[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
filled.contour[][][] []\T1/ptm/m/n/10 for color-filled con-tours, [][][]\T1/pcr
/m/n/10 contourplot[][][] []\T1/ptm/m/n/10 (and
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1928--1928
[]\T1/pcr/m/n/9 contour(x, x, z, ylim = c(-6, 6), nlevels = 20, lty = 2, metho
d = "simple",[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1940--1940
[]\T1/pcr/m/n/9 contour(z, levels=levs[-c(1,length(levs))], col = 1:5, lwd = 1
:3 *1.5, lty = 1:3)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1956--1956
[]\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1965--1965
[]\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[]
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[936]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2050--2050
[]\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns,
[937]
[938]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 2179--2179
[]\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.values = given
.depth, rows = 1)[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2184--2184
[]\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c(
TRUE, FALSE))[]
[939]
[940]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 2358--2358
[]\T1/pcr/m/n/10 dotchart(x, labels = NULL, groups = NULL, gdata = NULL, offse
t = 1/8,
Overfull \hbox (54.78088pt too wide) in paragraph at lines 2359--2359
[] \T1/pcr/m/n/10 ann = par("ann"), xaxt = par("xaxt"), frame.plot = T
RUE, log = "",[]
[941]
Underfull \hbox (badness 1430) in paragraph at lines 2389--2391
[]\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use []\T1/pcr/m/n/10
"n" []\T1/ptm/m/n/10 to sup-press and see also
[942]
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[] \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO
rRd", rev = TRUE),[]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 2472--2472
[] \T1/pcr/m/n/10 plot.title, plot.axes, key.title, key.axes, ke
y.border = NULL,[]
Underfull \hbox (badness 1009) in paragraph at lines 2482--2489
\T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n
ot ap-ply to
[943]
Underfull \hbox (badness 7273) in paragraph at lines 2565--2569
[][][]\T1/pcr/m/n/10 contour[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 image
[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 hcl.colors[][][][]\T1/ptm/m/n/10
, [][][]\T1/pcr/m/n/10 gray.colors[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
palette[][][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 contourplot[][][] []\T1/p
tm/m/n/10 and
[944]
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[947]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2822--2822
[]\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c
(mx, my, 7))[]
[948]
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[]\T1/pcr/m/n/9 plot(8:270, log="xy") ; grid() # at (1, 10, 100); if preferrin
g "all" grid lines:[]
[949]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2882--2882
[] \T1/pcr/m/n/10 density = NULL, angle = 45, col = "lightgray", border =
NULL,[]
[950]
Underfull \hbox (badness 1226) in paragraph at lines 3009--3013
\T1/pcr/m/n/10 1)[]\T1/ptm/m/n/10 , they are the rel-a-tive fre-quen-cies []\T1
/pcr/m/n/10 counts/n []\T1/ptm/m/n/10 and in gen-eral sat-isfy
[951]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 3062--3062
[]\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe
r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3066--3066
[]\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a
suggestion only"[]
[952]
Underfull \hbox (badness 10000) in paragraph at lines 3128--3131
[][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][][]\T1
/pcr/m/n/10 hist.default[][][] []\T1/ptm/m/n/10 such as
[953]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 3179--3179
[]\T1/pcr/m/n/9 ## The default fuzz in hist.default() "kills" this, with a "w
rong" message:[]
[954]
[955]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3343--3343
[]\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL
SE, pch = 19, ...)[]
Overfull \hbox (79.98035pt too wide) in paragraph at lines 3348--3348
[] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel)
, n = 1, plot = plot, ...)[]
[956]
[957]
Underfull \hbox (badness 10000) in paragraph at lines 3490--3495
[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 useRaster []\T1/ptm/m/n/10 is not spec-i-f
ied, raster im-ages are used when the
Underfull \hbox (badness 10000) in paragraph at lines 3490--3495
[][][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") []\T1/ptm/m/n/10 is true,
the grid is reg-u-lar and ei-ther
Underfull \hbox (badness 10000) in paragraph at lines 3490--3495
[][][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage []\T1/pt
m/m/n/10 is []\T1/pcr/m/n/10 "yes" []\T1/ptm/m/n/10 or it is
[958]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 3525--3525
[]\T1/pcr/m/n/9 # Visualize as matrix. Need to transpose matrix and then flip
it horizontally:[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 3527--3527
[]\T1/pcr/m/n/9 imageM <- function(m, grid = max(dim(m)) <= 25, asp = (nrow(m)
-1)/(ncol(m)-1), ...) {[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 3530--3530
[] \T1/pcr/m/n/9 axis(side, at=at, labels=as.character(j+1L), col="gray
", col.axis=1, ...)[]
[959]
[960]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3687--3687
[]\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space =
0, horiz = TRUE)[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 3706--3706
[] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col =
par("fg"),[]
[961]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3710--3710
[] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
FALSE,[]
[962]
[963]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3895--3895
[] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c
ex = 0.8, adj = 0)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3896--3896
[] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3900--3900
[] \T1/pcr/m/n/9 cex = 1+(-1:2)/8, trace = TRUE)# trace: show computed l
engths & coords[]
[964]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 3910--3910
[] \T1/pcr/m/n/9 title("legend(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 top\TS1/pcr/m/n/
9 '\T1/pcr/m/n/9 , lty = c(2, -1, 1), pch = c(NA, 3, 4), merge = TRUE)",[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3941--3941
[] \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj
= c(0, 0.3))[]
Underfull \vbox (badness 10000) has occurred while \output is active
[965]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3967--3967
[]\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Filled\TS1/pcr/m/n/9 ' \T1/pc
r/m/n/9 boxes -- see also example(barplot) which may call legend(*, fill=)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3969--3969
[]\T1/pcr/m/n/9 legend("topright", rownames(VADeaths), fill = gray.colors(nrow
(VADeaths)))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3980--3980
[]\T1/pcr/m/n/9 legend("bottomright", paste("sin(", 1:7, "pi * x)"), col = 1:7
, lty = 1:7,[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3995--3995
[]\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c
ol = "blue")[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 4003--4003
[]\T1/pcr/m/n/9 legend("topleft", "(x,y)", pch=1, title= "topleft, inset =
.05", inset = .05)[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 4005--4005
[]\T1/pcr/m/n/9 legend("topright", "(x,y)", pch=1, title= "topright, inset
= .02",inset = .02)[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 4013--4013
[] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[]
Underfull \vbox (badness 10000) has occurred while \output is active
[966]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4023--4023
[]\T1/pcr/m/n/9 legend("bottomleft", c("This legend", "has", "optimally sized"
, "columns."),[]
Underfull \hbox (badness 10000) in paragraph at lines 4085--4089
[][][]\T1/pcr/m/n/10 lines.formula[][][] []\T1/ptm/m/n/10 for the for-mula meth
od; [][][]\T1/pcr/m/n/10 points[][][][]\T1/ptm/m/n/10 , par-tic-u-larly for []\
T1/pcr/m/n/10 type %in%
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[] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb
ose"))[]
[969]
[970]
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[]\T1/pcr/m/n/9 nd <- length(dv <- seq(as.Date("1959-02-21"), by = "weeks", le
ngth.out = 100))[]
Underfull \vbox (badness 10000) has occurred while \output is active
[971]
[972]
Underfull \hbox (badness 3930) in paragraph at lines 4432--4434
[]\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a
mul-ti-ple of
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[977]
Underfull \hbox (badness 1286) in paragraph at lines 4748--4751
[]\T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify []\T1/pcr/m/n
/10 oma []\T1/ptm/m/n/10 when chang-ing
Underfull \hbox (badness 3229) in paragraph at lines 4756--4761
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are
to be used, see
[978]
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[]\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel
= panel.cor,[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4857--4857
[] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma
=c(2,2,3,2))[]
[979]
[980]
Underfull \hbox (badness 1264) in paragraph at lines 5118--5131
\T1/ptm/m/n/10 func-tions such as [][][]\T1/pcr/m/n/10 plot.default[][][][]\T1/
ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.window[][][][]\T1/ptm/m/n/10 , [][][]\T1
/pcr/m/n/10 points[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lines[][][][]\T
1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 abline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc
r/m/n/10 axis[][][][]\T1/ptm/m/n/10 ,
[981]
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[984 </build/r/src/R-4.5.1/library/graphics/help/figures/mai.pdf>]
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Underfull \vbox (badness 10000) has occurred while \output is active
[985]
[986 </build/r/src/R-4.5.1/library/graphics/help/figures/oma.pdf>]
[987]
[988]
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[]\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9,
physicians = 9,[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5696--5696
[] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[]
[989]
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[991]
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[]\T1/pcr/m/n/9 points(trans3d(xy[,1], xy[,2], z = 6, pmat = res), co
l = 2, pch = 16)[]
[992]
[993]
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[]\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p
yramid" = 5),[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 6061--6061
[] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow
3"), border = FALSE)[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot}) ha
s been already used, duplicate ignored
<to be read again>
\relax
l.6120 \aliasA{plot}{plot.default}{plot}
[995]
[996]
[997]
[998]
[999]
[1000]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6463--6463
[]\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext
remely silly[]
[1001]
[1002]
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[] \T1/pcr/m/n/10 main = paste("Histogram of", paste(x$xname, co
llapse = "\n")),[]
[1003]
[1004]
[1005]
[1006]
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[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[1007]
[1008]
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[]\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th
is works as a mul-ti-ple of
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[][]
[1009 </build/r/src/R-4.5.1/library/graphics/help/figures/pch.pdf>]
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[]\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b
lue", cex = .6,[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 7124--7124
[]\T1/pcr/m/n/9 ## Illustration of pch = 0:25 (as in the figure shown above in
PDF/HTML help)[]
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[]\T1/pcr/m/n/9 ## Not run: png("pch.png", height = 0.7, width = 7, res = 100,
units = "in")[]
[1010]
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[] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab =
"", main = main)[]
Underfull \vbox (badness 10000) has occurred while \output is active
[1011]
[1012]
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[]\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev
in Buhr
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[] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b
order = "red")[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7304--7304
[]\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats::
rnorm(n)))))[]
[1013]
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[]\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther []\T
1/pcr/m/n/10 "winding" []\T1/ptm/m/n/10 or
[1014]
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[1016]
[1017]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7593--7593
[]\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7
, end = 0.1))[]
[1018]
[1019]
[1020]
[1021]
[1022]
[1023]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7980--7980
[]\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
ace = "Lab")[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7984--7984
[]\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit
h obs.number):[]
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[]\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE),[]
[1024]
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[] \T1/pcr/m/n/10 xlim = NULL, ylim = c(0, 1), axes = TRUE, weights =
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[] \T1/pcr/m/n/10 subset = NULL, weights = NULL, drop.unused.levels =
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us = FALSE,[]
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[]\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us = FALSE,[]
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[] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
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[]\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL,
...,[]
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[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 number[i] == 1[]\T1/ptm/m/n/10 , a (sligh
tly en-larged) usual plot-ting sym-bol ([]\T1/pcr/m/n/10 pch[]\T1/ptm/m/n/10 )
is drawn. For
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[]\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035
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[]\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100,
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[] \T1/pcr/m/n/9 "Le fran�ais, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est facile:
R�gles, Libert�, Egalit�, Fraternit�...")[]
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[]\T1/ptm/m/n/10 The po-si-tions of []\T1/pcr/m/n/10 xlab[]\T1/ptm/m/n/10 , []\
T1/pcr/m/n/10 ylab []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 sub []\T1/ptm/m/n/10 a
re []\T1/pcr/m/n/10 line []\T1/ptm/m/n/10 (de-fault for []\T1/pcr/m/n/10 xlab [
]\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 ylab []\T1/ptm/m/n/10 be-ing
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[]\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th
e poly-gon. See
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[]\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code =
2, length = 0.1)[]
[1046]) (./grid-pkg.tex
Chapter 6.
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[]\T1/ptm/m/n/10 Modification of the view-port (should all be valid ar-gu-ments
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[] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un
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[] \T1/pcr/m/n/9 vpList(vpStack(viewport(x=0.1, y=0.1, width=0.5
, height=0.5,[]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="B"),[]
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject
de-scrib-ing a cir-cle), but only
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[] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[]
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ck"), name="r1")[]
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), name="r2")[]
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te"), name="r3")[]
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[]\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio
ns []\T1/pcr/m/n/10 preDrawDetails[]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 Both func-tions call []\T1/pcr/m/n/10 editDetails []\T1/ptm/m/
n/10 to al-low a grob to per-form cus-tom ac-tions and
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de
-scrib-ing a frame), but only
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[]\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global =
FALSE)[]
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[]\T1/ptm/m/n/10 The jus-ti-fi-ca-tion of the glyphs rel-a-tive to the ([]\T1/p
cr/m/n/10 x[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 ) lo-ca-tion.
Can be
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[]\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs =
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[] \T1/pcr/m/n/9 children=gList(grob(name="child", vp
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[] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp =
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[]\T1/ptm/m/n/10 A func-tion that re-turns an affine trans-for-ma-tion ma-trix;
see
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[]\T1/ptm/m/n/10 Another pos-si-ble use of []\T1/pcr/m/n/10 grid.group() []\T1/
ptm/m/n/10 is to spec-ify both []\T1/pcr/m/n/10 src []\T1/ptm/m/n/10 and []\T1/
pcr/m/n/10 dst []\T1/ptm/m/n/10 and com-bine
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[]\T1/pcr/m/n/10 "multiply"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "screen"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "overlay"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "darke
n"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lighten"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n
/10 "color.dodge"[]\T1/ptm/m/n/10 ,
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[] \T1/pcr/m/n/9 mask <- as.mask(rectGrob(gp=gpar(col=NA, fill="grey50")), ty
pe="luminance")[]
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[] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
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[] \T1/pcr/m/n/9 children=vpList(viewpor
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[]\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, width=0.25, height=0.25, just=
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[]\T1/ptm/m/n/10 There are two hooks called []\T1/pcr/m/n/10 "before.grid.newpa
ge" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "grid.newpage" []\T1/ptm/m/n/10 (see
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[] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
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[] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant
i-clockwise")[]
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[] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other
anti-clockwise")[]
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[]\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s
ame path, thus[]
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec
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[] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un
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[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
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[]\T1/pcr/m/n/9 grid.text(quote(frac(e^{-x^2/2}, sqrt(2*pi))), x=x, y=y, rot=s
tats::runif(20, -45,45),[]
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[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 gridCoords []\T1/ptm/m/n/10 a nu-meric ve
c-tor. For []\T1/pcr/m/n/10 gridGrobCoords []\T1/ptm/m/n/10 a list
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\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 "GridCoords" []\T1/ptm/m/n/10 ob-jects. For
[]\T1/pcr/m/n/10 gridGTreeCoords []\T1/ptm/m/n/10 a list of ei-ther
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[]\T1/ptm/m/n/10 Either a []\T1/pcr/m/n/10 "GridGrobCoords" []\T1/ptm/m/n/10 ob
-ject (a list of lists with com-po-nents []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 an
d []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 ) or a
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[]\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 grid.legend()[]\T1/ptm/m/n/10 : all the a
r-gu-ments above are passed to
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[]\T1/pcr/m/n/9 unitType(min(unit(1, "in"), unit(1, "npc") + unit(1, "mm")), r
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[]\T1/pcr/m/n/10 viewportTransform(group, shear=groupShear(), flip=groupFlip()
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[]\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for
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[][][]\T1/pcr/m/n/10 viewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 push
Viewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 popViewport[][][][]\T1/pt
m/m/n/10 , [][][]\T1/pcr/m/n/10 downViewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/
pcr/m/n/10 seekViewport[][][][]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp
ar(col="red"))))[]
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Chapter 7.
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[]\T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how
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[][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] []\T1/ptm/m/n/10 for other in-
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[]\T1/pcr/m/n/9 ## vector. The next method will always be the default, usuall
y a primitive.[]
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[]\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w
ith no arguments[]
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[]\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho
ut arguments[]
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[]\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th
e default method[]
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[]\T1/pcr/m/n/9 ## call f() with 1 argument: the default "B0" is not passed b
y callNextMethod[]
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[]\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the
"B0" method[]
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[]\T1/pcr/m/n/9 ## Although the argument here is numeric, it\TS1/pcr/m/n/9 '\T
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]
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[]\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N
umber" method[]
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[]\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE))
) # the default[]
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[]\T1/ptm/m/n/10 The ar-gu-ment to []\T1/pcr/m/n/10 insertSource []\T1/ptm/m/n/
10 can be an ob-ject of class
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[]\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age
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[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an [][][]\T1/pcr/m/n/10 environment
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[]\T1/pcr/m/n/10 getMethods(f, where, table = FALSE) # deprecated -> use getMe
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[]\T1/ptm/m/n/10 As you might ex-pect [][][]\T1/pcr/m/n/10 setGeneric[][][] []\
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re-ate ob-jects of class
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[]\T1/ptm/m/n/10 Object of class []\T1/pcr/m/n/10 "optionalMethod" []\T1/ptm/m/
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[]\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[]
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[]\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[]
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[]\T1/ptm/m/n/10 Function []\T1/pcr/m/n/10 implicitGeneric() []\T1/ptm/m/n/10 r
e-turns the im-plicit generic ver-sion,
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[]\T1/pcr/m/n/10 setGenericImplicit() []\T1/ptm/m/n/10 turns a generic im-plici
t, []\T1/pcr/m/n/10 prohibitGeneric() []\T1/ptm/m/n/10 pre-vents
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[]\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][][]\T1/pcr/m/n/10
getClass[][][] []\T1/ptm/m/n/10 and the de-scrip-tion of class
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[]
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[] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longit
ude =
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[]\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) {
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[]\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character")
,
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[]\T1/ptm/m/n/10 A call to [][][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) []
\T1/ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to
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[]\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char
acter(),
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[] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac
cess,[]
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[]\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here)
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[]\T1/ptm/m/n/10 For ad-di-tional in-for-ma-tion see doc-u-men-ta-tion for the
im-por-tant steps: ([][][]\T1/pcr/m/n/10 setMethod[][][]()[]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha
t eval-u-ates a call to
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[]\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
inheritance[]
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[]\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli
er fails here)[]
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[]\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho
d for classB[]
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[]\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...)
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[]\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p
assed to
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[]\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o
ds for this class are found (us-ing
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[]\T1/ptm/m/n/10 The de-fault method for []\T1/pcr/m/n/10 $initialize() []\T1/p
tm/m/n/10 is equiv-a-lent to in-vok-ing the method
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[]\T1/ptm/m/n/10 Typically, a spe-cial-ized []\T1/pcr/m/n/10 $initialize() []\T
1/ptm/m/n/10 method car-ries out its own com-pu-ta-tions,
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\T1/ptm/m/n/10 then in-vokes []\T1/pcr/m/n/10 $initFields() []\T1/ptm/m/n/10 to
per-form stan-dard ini-tial-iza-tion, as shown in the
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[]\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func-
tion re-turned by
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[]\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen
se as any S4 class (see
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[][][]\T1/pcr/m/n/10 setValidity[][][][]\T1/ptm/m/n/10 ). Such meth-ods are of-
ten a good idea; they will be called by call-ing
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pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has
been already used, duplicate ignored
<to be read again>
\relax
l.6911 \aliasA{S4}{S3Part}{S4}
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[]\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement
version of as().[]
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[]\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data =
datasets::iris)[]
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[]\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con
tains = "mlm")[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Complex})
has been already used, duplicate ignored
<to be read again>
\relax
l.7167 \aliasA{Complex}{S4groupGeneric}{Complex}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Logic}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.7169 \aliasA{Logic}{S4groupGeneric}{Logic}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) ha
s been already used, duplicate ignored
<to be read again>
\relax
l.7170 \aliasA{Math}{S4groupGeneric}{Math}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.matrixOps
}) has been already used, duplicate ignored
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\relax
l.7172 ...sA{matrixOps}{S4groupGeneric}{matrixOps}
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been already used, duplicate ignored
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\relax
l.7173 \aliasA{Ops}{S4groupGeneric}{Ops}
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l.7174 \aliasA{Summary}{S4groupGeneric}{Summary}
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[]\T1/ptm/m/n/10 There are also S3 groups []\T1/pcr/m/n/10 Math[]\T1/ptm/m/n/10
, []\T1/pcr/m/n/10 Ops[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Summary[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 Complex []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 matrixOps[
]\T1/ptm/m/n/10 , see
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[]\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic
can be ob-tained by call-ing
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[]\T1/pcr/m/n/10 "abs"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sign"[]\T1/ptm/m/n/1
0 , []\T1/pcr/m/n/10 "sqrt"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ceiling"[]\T1/p
tm/m/n/10 , []\T1/pcr/m/n/10 "floor"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "trunc"
[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cummax"[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2012) in paragraph at lines 7249--7261
[]\T1/pcr/m/n/10 "acosh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "asin"[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 "asinh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "atan"[]\T1/p
tm/m/n/10 , []\T1/pcr/m/n/10 "atanh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "exp"[]
\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "expm1"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "c
os"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 "cosh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cospi"[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 "sin"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sinh"[]\T1/ptm
/m/n/10 , []\T1/pcr/m/n/10 "sinpi"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tan"[]\T
1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tanh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tanp
i"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 selectMethod("Re", signature = "testComplex") # shows Generic:
.. "Re" & .."Complex"[]
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[]\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t
ion ob-ject (see
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[]\T1/ptm/m/n/10 The typ-i-cal user level func-tion is []\T1/pcr/m/n/10 selectS
uperClasses() []\T1/ptm/m/n/10 which calls
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[]\T1/pcr/m/n/9 selectSuperClasses("C", dropVirtual=TRUE, directOnly=FALSE)# d
itto w/o "Root"[]
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[]\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(),
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[] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[]
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[]\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[]
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[] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
"setCount")[]
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[]\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo
rmal arguments[]
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[]\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre
es of freedom[]
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[]\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][]
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[]\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][]
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[]\T1/ptm/m/n/10 Chambers, John M. (2009) \T1/ptm/m/it/10 Class In-her-i-tance
in R [][]$\T1/pcr/m/n/10 https : / / johnmchambers . su .
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[]\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., []\T1/pcr/m/n/10 "functi
on" []\T1/ptm/m/n/10 for class
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[]\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl
ass, from the data part; e.g.,
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[]\T1/pcr/m/n/10 "functionWithTrace" []\T1/ptm/m/n/10 ex-tends []\T1/pcr/m/n/10
"function"[]\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends
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Chapter 8.
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[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `[]\T1/p
cr/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"[]\T1/ptm/m/n/10 ' [][]
RNG[][][]: see
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[]\T1/ptm/m/n/10 a vec-tor for []\T1/pcr/m/n/10 clusterApply []\T1/ptm/m/n/10 a
nd []\T1/pcr/m/n/10 clusterApplyLB[]\T1/ptm/m/n/10 , a ma-trix for
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[]\T1/ptm/m/n/10 Two ex-cep-tions: []\T1/pcr/m/n/10 parLapply []\T1/ptm/m/n/10
has ar-gu-ment []\T1/pcr/m/n/10 X []\T1/ptm/m/n/10 not []\T1/pcr/m/n/10 x []\T1
/ptm/m/n/10 for con-sis-tency with [][][]\T1/pcr/m/n/10 lapply[][][][]\T1/ptm/m
/n/10 , and
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[]\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD,
So-laris and Win-dows.
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[]\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for []\T1/pcr/m/
n/10 Rscript []\T1/ptm/m/n/10 such as
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[]\T1/pcr/m/n/10 mcfork []\T1/ptm/m/n/10 re-turns an ob-ject of the class []\T1
/pcr/m/n/10 "childProcess" []\T1/ptm/m/n/10 to the mas-ter and of class
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[]\T1/pcr/m/n/10 "masterProcess" []\T1/ptm/m/n/10 to the child: both the classe
s in-herit from class []\T1/pcr/m/n/10 "process"[]\T1/ptm/m/n/10 . If
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[] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini
ty.list = NULL)[]
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[]\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit
y.list = affL)[]
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[]\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch
eduled to suitable CPUs[]
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[]\T1/pcr/m/n/10 mcparallel []\T1/ptm/m/n/10 re-turns an ob-ject of the class [
]\T1/pcr/m/n/10 "parallelJob" []\T1/ptm/m/n/10 which in-her-its from
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[]\T1/ptm/m/n/10 The be-haviour with []\T1/pcr/m/n/10 mc.set.seed = TRUE []\T1/
ptm/m/n/10 is dif-fer-ent only if
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[]\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin
ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[]
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[] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[]
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[]\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format =
"%Y-%m-%d")))[]
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[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by []\T1/pcr/m/n/10
.Random.seed []\T1/ptm/m/n/10 when the
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[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 nextRNGStream []\T1/ptm/m/n/10 and []\T1/
pcr/m/n/10 nextRNGSubStream[]\T1/ptm/m/n/10 , a value which can be as-signed to
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Chapter 9.
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[]\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
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[]\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl
ine = TRUE))[]
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[]\T1/ptm/m/n/10 An in-te-ger be-tween 0 and []\T1/pcr/m/n/10 splineOrder(objec
t) - 1 []\T1/ptm/m/n/10 spec-i-fy-ing the
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[]\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37,
sparse = TRUE)))[]
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[1348]) (./stats-pkg.tex
Chapter 10.
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Underfull \hbox (badness 1077) in paragraph at lines 71--74
[]\T1/pcr/m/n/10 .MFclass() []\T1/ptm/m/n/10 re-turns a char-ac-ter string, one
of []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ordered"[]\T
1/ptm/m/n/10 , []\T1/pcr/m/n/10 "factor"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 (xl <- .getXlevels(terms(mf), mf)) # a list with one entry " $
Species" with 3 levels:[]
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[] \T1/pcr/m/n/9 identical(.getXlevels(terms(mc), mc), xl[0]) # a empty named
list, as no factors[]
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[]\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[]
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[]\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet =
FALSE)
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[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from []\T1/pcr/m/n/10 l
m []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 aov[]\T1/ptm/m/n/10 , or a for-mula for
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[] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm
= TRUE)[]
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[] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm
= TRUE)[]
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[] \T1/pcr/m/n/9 approx(xn, yn, xout=xout, method=M, rule=R, n
a.rm=na.)$y),[]
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[]\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$y) # warning, can be avoided by
specifying \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ties=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[
]
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[]\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE)
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[]\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[]
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[]\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Bartlett test of homo
geneity of
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[]\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p =
FALSE)[]
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[]\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p =
FALSE)[]
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Package amsmath Warning: Foreign command \atopwithdelims;
(amsmath) \frac or \genfrac should be used instead
(amsmath) on input line 3684.
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[]\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[]
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[]\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0)
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[]\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p
= FALSE)[]
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[]\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p
= FALSE)[]
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[]\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful
, but is ok![]
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[] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
df, ncp = L)),[]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10
(\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/
it/10 g[] \OT1/cmr/m/n/10 =
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[]\T1/pcr/m/n/10 confint(object, parm, level = 0.95, trace = FALSE, test=c("LR
T", "Rao"), ...)[]
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[]\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1))
, ci = c(-1,-1))[]
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[]\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci
= c(-0.9,0.1))[]
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[]\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works
with these :[]
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[]\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter"))
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[]\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i
ng co-vari-ances
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\T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi
-a-tion of)
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\T1/ptm/m/n/10 one of the strings []\T1/pcr/m/n/10 "everything"[]\T1/ptm/m/n/10
, []\T1/pcr/m/n/10 "all.obs"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "complete.obs"
[]\T1/ptm/m/n/10 ,
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[] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
...)[]
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[]\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
TRUE,
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[]\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
NULL)
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[]\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en
v = parent.frame())[]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor in-dex-ing []\T1/pcr/m/n/10 labels(termobj)
[]\T1/ptm/m/n/10 (that is, the
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
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[]\T1/ptm/m/n/10 Objects of class []\T1/pcr/m/n/10 "hclust" []\T1/ptm/m/n/10 ca
n be con-verted to class []\T1/pcr/m/n/10 "dendrogram" []\T1/ptm/m/n/10 us-ing
method
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[]\T1/pcr/m/n/10 rev.dendrogram []\T1/ptm/m/n/10 sim-ply re-turns the den-dro-g
ram []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 with re-versed nodes, see also
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\T1/ptm/m/n/10 has []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 y [
]\T1/ptm/m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be-
fore \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.1.2,
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[][][]\T1/pcr/m/n/10 dendrapply[][][] []\T1/ptm/m/n/10 for ap-ply-ing a func-ti
on to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][][]\T1/pcr/m/n/10 order.dend
rogram[][][] []\T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/9 str(dend1, max.level = 2, last.str = "\TS1/pcr/m/n/9 '\T1/pcr
/m/n/9 ") # only the first two sub-levels[]
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[]\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE,
type = "tr")[]
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[]\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p
cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[]
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[]\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[]
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[]\T1/pcr/m/n/9 abline(h = 1/1022, v = range(x), lty=2); axis(2, at=1/1022, "1
/(2n-2)", las=1)[]
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[] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[]
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[]\T1/pcr/m/n/10 "maximum"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "manhattan"[]\T1/
ptm/m/n/10 , []\T1/pcr/m/n/10 "canberra"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "bi
nary" []\T1/ptm/m/n/10 or
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[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from []\T1/
pcr/m/n/10 dist()[]\T1/ptm/m/n/10 , the
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[]\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht
tps : / / CRAN . R-[]project . org / view =
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[]\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences []
\T1/pcr/m/n/10 x[t][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 x[t-1][]\T1/ptm/m/n/10 ,
...,
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[]\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 na.action[][][] []\T1/ptm/m/n/10 to b
e used if []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 is used as a for-mula, in which c
ase
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[]\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q
uasipoisson())[]
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[1482]
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[]\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link
= "log")) # fails[]
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[]\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[]
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[] \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4
0k", "> 40k"),[]
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[] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod
erateS", "VeryS")))[]
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[]\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Fligner-Killeen test
of homogeneity of
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[][][]\T1/pcr/m/n/10 ftable.formula[][][] []\T1/ptm/m/n/10 for the for-mula in-
ter-face (which al-lows a []\T1/pcr/m/n/10 data = . []\T1/ptm/m/n/10 ar-gu-ment
);
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[]\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org
/ wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or
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[] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL
, ...)[]
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[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
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[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
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[]\T1/ptm/m/n/10 A spec-i-fi-ca-tion of the form []\T1/pcr/m/n/10 first:second
[]\T1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak-
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[]\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][][]\T1/pcr/m/n/10 coeffic
ients[][][][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 effects[]\T1/ptm/m/n/10 , []\T1/
pcr/m/n/10 fitted.values []\T1/ptm/m/n/10 and
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[]\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p
tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1
0 dev \OMS/cmsy/m/n/10 ^^@
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[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
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Underfull \hbox (badness 10000) in paragraph at lines 11235--11241
[][][]\T1/pcr/m/n/10 glm[][][] []\T1/ptm/m/n/10 for com-put-ing []\T1/pcr/m/n/1
0 glm.obj[]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 anova.glm[][][][]\T1/ptm/m/n/1
0 ; the cor-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions,
Underfull \hbox (badness 1418) in paragraph at lines 11273--11278
[]\T1/pcr/m/n/10 "average" []\T1/ptm/m/n/10 (= UP-GMA), []\T1/pcr/m/n/10 "mcqui
tty" []\T1/ptm/m/n/10 (= WPGMA), []\T1/pcr/m/n/10 "median" []\T1/ptm/m/n/10 (=
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\T1/ptm/m/n/10 There are [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/n/10 , [][
][]\T1/pcr/m/n/10 plot[][][] []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 identify []\
T1/ptm/m/n/10 (see [][][]\T1/pcr/m/n/10 identify.hclust[][][][]\T1/ptm/m/n/10 )
meth-ods and the
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[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these
de-fault to
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[]\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[]
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[] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma =
0.1),[]
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[]\T1/ptm/m/n/10 Character string to se-lect an []\T1/pcr/m/n/10 "additive" []\
T1/ptm/m/n/10 (the de-fault) or
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[]\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has
been already used, duplicate ignored
<to be read again>
\relax
l.12089 \aliasA{hat}{influence.measures}{hat}
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Overfull \hbox (0.78088pt too wide) in paragraph at lines 12152--12152
[]\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12164--12164
[]\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
...)[]
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[]\T1/ptm/m/n/10 The op-tional []\T1/pcr/m/n/10 infl[]\T1/ptm/m/n/10 , []\T1/pc
r/m/n/10 res []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 sd []\T1/ptm/m/n/10 ar-gu-me
nts are there to en-cour-age the use of these di-
Underfull \hbox (badness 1052) in paragraph at lines 12234--12236
[]\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 hat() []\T1/ptm/m/n/10 ex-ists
mainly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
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[]\T1/pcr/m/n/9 integrate(dnorm, 0, 20000) ## "fails" on many systems -- "wron
gly" giving \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 0\TS1/pcr/m/n/9 '[]
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[] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend =
TRUE,[]
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[] \T1/pcr/m/n/10 trace.label = deparse1(substitute(trace.fact
or)),[]
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[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][][]\T1/pcr/m/n/10 solve.de
fault[][][] []\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 SSinit =
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[]\T1/ptm/m/n/10 the es-ti-mate at time $\OML/cmm/m/it/10 t \OMS/cmsy/m/n/10 ^^
@ \OT1/cmr/m/n/10 1$ \T1/ptm/m/n/10 of the state un-cer-tainty ma-trix $\OML/cm
m/m/it/10 Q$ \T1/ptm/m/n/10 (not up-dated by
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[]\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class []\T1/pcr/
m/n/10 "kmeans"[]\T1/ptm/m/n/10 , typ-i-cally the re-sult []\T1/pcr/m/n/10 ob [
]\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 ob <-
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[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
Underfull \hbox (badness 1038) in paragraph at lines 13163--13167
\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 "Hartigan-Wong"[]\T1/ptm/m/n/10 ): if pos-i-ti
ve (or true), trac-ing in-for-ma-tion on the
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Underfull \hbox (badness 1496) in paragraph at lines 13591--13597
[]\T1/ptm/m/n/10 Gunar Schr�er and Di-et-rich Tren-kler (1995). Ex-act and Ran-
dom-iza-tion Dis-tri-bu-tions of
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 13846--13846
[]\T1/pcr/m/n/9 lag.plot(sqrt(sunspots), set.lags = c(1:4, 9:12), pch = ".", c
ol = "gold")[]
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Overfull \hbox (9.78043pt too wide) in paragraph at lines 13946--13946
[]\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep
t", "slope"))[]
Underfull \hbox (badness 4518) in paragraph at lines 13994--13999
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
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Underfull \hbox (badness 10000) in paragraph at lines 14194--14198
[]\T1/ptm/m/n/10 More []\T1/pcr/m/n/10 lm() []\T1/ptm/m/n/10 ex-am-ples are ava
il-able e.g., in [][][]\T1/pcr/m/n/10 anscombe[][][][]\T1/ptm/m/n/10 , [][][]\T
1/pcr/m/n/10 attitude[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 freeny[][][]
[]\T1/ptm/m/n/10 ,
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Underfull \hbox (badness 1163) in paragraph at lines 14561--14569
\T1/ptm/m/n/10 els, [][][]\T1/pcr/m/n/10 influence[][][] []\T1/ptm/m/n/10 (etc
on that page) for re-gres-sion di-ag-nos-tics, [][][]\T1/pcr/m/n/10 weighted.re
siduals[][][][]\T1/ptm/m/n/10 ,
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Underfull \hbox (badness 4518) in paragraph at lines 14683--14688
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
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[]\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p =
FALSE)[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14874--14874
[]\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
FALSE)[]
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[]\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p =
FALSE)[]
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[]\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p =
FALSE)[]
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[]\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x)))
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[]\T1/ptm/m/n/10 character; one of []\T1/pcr/m/n/10 "logit"[]\T1/ptm/m/n/10 , [
]\T1/pcr/m/n/10 "probit"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cauchit"[]\T1/ptm/
m/n/10 , []\T1/pcr/m/n/10 "cloglog"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i
n R <= 3.5.0[]
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[] \T1/pcr/m/n/10 T = Thin.row(Proj(M) - Proj(X)), M = diag(nrow =
p), X = ~0,[]
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[]\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph)
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Underfull \hbox (badness 1490) in paragraph at lines 16594--16599
\T1/ptm/m/n/10 those spec-i-fied in []\T1/pcr/m/n/10 ... []\T1/ptm/m/n/10 which
are re-cy-cled to the num-ber of data frame rows. Un-like
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[]\T1/pcr/m/n/9 model.frame(dist ~ speed, data = cars, subset = speed < 10, z
= log(dist))[]
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[]\T1/ptm/m/n/10 a data frame cre-ated with [][][]\T1/pcr/m/n/10 model.frame[][
][][]\T1/ptm/m/n/10 . If an-other sort of ob-ject,
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[]\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts.arg = list(a = "contr.sum"
, b = contr.poly))[]
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[]\T1/pcr/m/n/9 m.orth <- model.matrix(~a+b, dd, contrasts.arg = list(a = "con
tr.helmert"))[]
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[]\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3)) # does not affect objects
with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[]
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[]\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x,
s, prob = 0.4)),[]
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Underfull \vbox (badness 10000) has occurred while \output is active
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Overfull \hbox (42.18039pt too wide) in paragraph at lines 18260--18260
[]\T1/pcr/m/n/9 ## adjusting the convergence test by adding \TS1/pcr/m/n/9 '\T
1/pcr/m/n/9 scaleOffset\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 to its denominator RSS:[]
Underfull \vbox (badness 10000) has occurred while \output is active
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Overfull \hbox (74.58035pt too wide) in paragraph at lines 18279--18279
[]\T1/pcr/m/n/9 ## Here, requiring close convergence, must use more accurate n
umerical differentiation,[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 18280--18280
[]\T1/pcr/m/n/9 ## as this typically gives Error: "step factor .. reduced belo
w \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 minFactor\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 .."[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 18284--18284
[]\T1/pcr/m/n/9 ## central differencing works here typically (PR#18165: not co
nverging on *some*):[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18285--18285
[]\T1/pcr/m/n/9 ctr2 <- nls.control(nDcentral=TRUE, tol = 8e-8, # <- even smal
ler than above[]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 18288--18288
[] \T1/pcr/m/n/9 (grepl("^aarch64.*linux", R.version$platform) && grepl
("^NixOS", osVersion)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18320--18320
[] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[]
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Overfull \hbox (9.78043pt too wide) in paragraph at lines 18496--18496
[]\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[]
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Overfull \hbox (20.58041pt too wide) in paragraph at lines 18543--18543
[]\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18590--18590
[]\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[]
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Overfull \hbox (102.78088pt too wide) in paragraph at lines 18807--18807
[] \T1/pcr/m/n/10 eps = .Machine$double.eps ^ (1/if(central) 3 els
e 2), central = FALSE)[]
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Underfull \hbox (badness 10000) in paragraph at lines 19092--19098
[]\T1/ptm/m/n/10 Method []\T1/pcr/m/n/10 "Brent" []\T1/ptm/m/n/10 is for one-di
mensional prob-lems only, us-ing [][][]\T1/pcr/m/n/10 optimize[][][](<ff>,
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Underfull \hbox (badness 1248) in paragraph at lines 19128--19131
[]\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma
-tion to the gra-di-ent, on
Underfull \hbox (badness 1661) in paragraph at lines 19141--19145
[]\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i
t is un-able to re-duce
Underfull \hbox (badness 1478) in paragraph at lines 19149--19153
\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 control$trace []\T1/ptm/m/n/10 is pos-i-tive
. De-faults to ev-ery 10 it-er-a-tions for []\T1/pcr/m/n/10 "BFGS" []\T1/ptm/m/
n/10 and
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Underfull \hbox (badness 2042) in paragraph at lines 19207--19209
[]\T1/ptm/m/n/10 indicates an er-ror from the []\T1/pcr/m/n/10 "L-BFGS-B" []\T1
/ptm/m/n/10 method; see com-po-nent
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Overfull \hbox (15.18042pt too wide) in paragraph at lines 19313--19313
[] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[]
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Overfull \hbox (9.78043pt too wide) in paragraph at lines 19356--19356
[] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem",
axes = FALSE)[]
Overfull \hbox (123.1803pt too wide) in paragraph at lines 19374--19374
[]\T1/pcr/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b
ut NM may be ok and "unavoidable",[]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 19377--19377
[]\T1/pcr/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[]
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Overfull \hbox (36.78088pt too wide) in paragraph at lines 19397--19397
[]\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max
(interval),
Overfull \hbox (36.78088pt too wide) in paragraph at lines 19400--19400
[]\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max
(interval),[]
Underfull \hbox (badness 2564) in paragraph at lines 19435--19446
[]\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 f []\T1/ptm/m/n/10 is never eva
l-u-ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m
/n/10 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/
10 tol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1082) in paragraph at lines 19435--19446
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately
[]\T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) []\T1/ptm/m/n/10 and $\OML
/cmm/m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa
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[]\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x -
1)), 10), 10)[]
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Overfull \hbox (9.78043pt too wide) in paragraph at lines 19728--19728
[]\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp =
1, lty = 1:6,[]
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Underfull \hbox (badness 1337) in paragraph at lines 19839--19842
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
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Overfull \hbox (0.78088pt too wide) in paragraph at lines 20157--20157
[] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd =
1.5),[]
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Overfull \hbox (24.78088pt too wide) in paragraph at lines 20244--20244
[] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist
vs Leverage* " * h[ii] / (1 - h[ii]))),[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 20246--20246
[] \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else
points,[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20248--20248
[] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[]
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Underfull \hbox (badness 10000) in paragraph at lines 20308--20314
\T1/pcr/m/n/10 "bottomleft", legend = "Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s di
stance", lty = cook.lty,
Underfull \hbox (badness 10000) in paragraph at lines 20308--20314
\T1/pcr/m/n/10 col = cook.col, text.col = cook.col, bty = "n", x.intersp
Underfull \hbox (badness 10000) in paragraph at lines 20316--20322
[]\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment []\T
1/pcr/m/n/10 iter []\T1/ptm/m/n/10 in
Underfull \hbox (badness 10000) in paragraph at lines 20327--20330
[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 1 or 2, to be used in []\T1/pcr/m
/n/10 ylim <-
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[]\T1/pcr/m/n/9 nlmod <- nls(y ~ Const + A * exp(B * x), start=list(Const=100
, A=10, B=1))[]
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Overfull \hbox (0.78088pt too wide) in paragraph at lines 20725--20725
[] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
...)[]
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Underfull \hbox (badness 1194) in paragraph at lines 20735--20738
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
of the con-fi-dence
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Underfull \hbox (badness 1107) in paragraph at lines 20793--20795
[]\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate []
\T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . De-faults to
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20848--20848
[]\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[]
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Overfull \hbox (31.3804pt too wide) in paragraph at lines 20855--20855
[]\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty =
1, y.intersp = 1)[]
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[]\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[]
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[] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no
cancellation[]
[1664]
Underfull \hbox (badness 7740) in paragraph at lines 21140--21142
[]\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Exact Poisson test" [
]\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 "Comparison of
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Overfull \hbox (6.78088pt too wide) in paragraph at lines 21188--21188
[]\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple =
FALSE)
Underfull \hbox (badness 10000) in paragraph at lines 21244--21246
[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 poly(*, simple=TRUE)[]\T1/ptm/m/n/10 , []
\T1/pcr/m/n/10 polym(*, coefs=<non-NULL>)[]\T1/ptm/m/n/10 , and
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 21281--21281
[] \T1/pcr/m/n/9 zm <- zapsmall(polym ( 1:4, c(1, 4:6), degree = 3)) # or
just poly():[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 21286--21286
[]\T1/pcr/m/n/9 ## poly(<matrix>, df) --- used to fail till July 14 (vive la F
rance!), 2017:[]
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[] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tolerance = 1e-15)) # e
xactly equal typically[]
[1680]
Underfull \hbox (badness 6859) in paragraph at lines 22207--22214
[][][]\T1/pcr/m/n/10 predict.glm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 p
redict.lm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.loess[][][][]\T1
/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.nls[][][][]\T1/ptm/m/n/10 , [][][]\T
1/pcr/m/n/10 predict.poly[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 22218--22224
[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][][]\T1/pcr/m/n/10 predict.ar[
][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.Arima[][][][]\T1/ptm/m/n/1
0 , [][][]\T1/pcr/m/n/10 predict.arima0[][][][]\T1/ptm/m/n/10 ,
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Overfull \hbox (54.78088pt too wide) in paragraph at lines 22506--22506
[] \T1/pcr/m/n/10 rankdeficient = c("warnif", "simple", "non-estim", "N
A", "NAwarn"),[]
Underfull \hbox (badness 10000) in paragraph at lines 22532--22535
[]\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string
spec-i-fy-ing what should hap-pen in the
Underfull \hbox (badness 10000) in paragraph at lines 22532--22535
\T1/ptm/m/n/10 case of a rank de-fi-cient model, i.e., when []\T1/pcr/m/n/10 ob
ject$rank <
[1686]
Underfull \hbox (badness 5832) in paragraph at lines 22537--22542
\T1/ptm/m/n/10 cases, i.e., vec-tors not in the same pre-dic-tor sub-space as t
he
Underfull \hbox (badness 8151) in paragraph at lines 22537--22542
\T1/ptm/m/n/10 orig-i-nal data (with tol-er-ance []\T1/pcr/m/n/10 tol[]\T1/ptm/
m/n/10 ). In that case, the non-
Underfull \hbox (badness 1184) in paragraph at lines 22537--22542
\T1/ptm/m/n/10 estimable in-dices are also re-turned as at-tribute []\T1/pcr/m/
n/10 "non-estim" []\T1/ptm/m/n/10 (see
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Overfull \hbox (48.78088pt too wide) in paragraph at lines 23005--23005
[] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign
= TRUE, ...)[]
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Overfull \hbox (0.78088pt too wide) in paragraph at lines 23289--23289
[] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x
)) &&[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 23290--23290
[] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr("
, "p-v"),[]
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Underfull \hbox (badness 1337) in paragraph at lines 23694--23700
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
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[1709]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 24006--24006
[]\T1/pcr/m/n/9 with(d, qqplot(Female, Male, pch = 19, xlim = c(-31, 31), ylim
= c(-31, 31),[]
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[1711]
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Underfull \hbox (badness 10000) in paragraph at lines 24338--24340
[]\T1/ptm/m/n/10 Wicklin, R. (2017) Sam-ple quan-tiles: A com-par-i-son of 9 de
f-i-ni-tions;
Underfull \hbox (badness 10000) in paragraph at lines 24338--24340
\T1/ptm/m/n/10 SAS Blog. [][]$\T1/pcr/m/n/10 https : / / blogs . sas . com / co
ntent / iml / 2017 / 05 / 24 /
Underfull \hbox (badness 10000) in paragraph at lines 24341--24342
[]\T1/ptm/m/n/10 Wikipedia: [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . or
g / wiki / Quantile # Estimating _
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[1715]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 24452--24452
[] \T1/pcr/m/n/10 method = c("non.compact", "row.compact", "col.compact"
, "compact"),[]
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Underfull \hbox (badness 1028) in paragraph at lines 24510--24513
[]\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for []\T
1/pcr/m/n/10 write() []\T1/ptm/m/n/10 and
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[1718]
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[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
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[]\T1/ptm/m/n/10 This, as [][][]\T1/pcr/m/n/10 reorder[][][]()[]\T1/ptm/m/n/10
, is a spe-cial case of sim-ply call-ing [][][]\T1/pcr/m/n/10 factor[][][](x, l
evels =
[1720]
Underfull \hbox (badness 7099) in paragraph at lines 24744--24746
[]\T1/ptm/m/n/10 This, as [][][]\T1/pcr/m/n/10 relevel[][][]()[]\T1/ptm/m/n/10
, is a spe-cial case of sim-ply call-ing [][][]\T1/pcr/m/n/10 factor[][][](x, l
evels =
Overfull \hbox (31.3804pt too wide) in paragraph at lines 24779--24779
[]\T1/pcr/m/n/9 bymedianR <- with(InsectSprays, reorder(spray, count, median,
decreasing=TRUE))[]
[1721]
[1722]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24855--24855
[]\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd,
10:1, mean)")[]
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[1724]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 24972--24972
[]\T1/pcr/m/n/10 # varying = ___, # list / matrix / vector (use with
care)[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 24973--24973
[]\T1/pcr/m/n/10 # v.names = ___, # vector of variable names in long
format[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 24974--24974
[]\T1/pcr/m/n/10 # timevar, times, # name / values of constructed time
variable[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 24975--24975
[]\T1/pcr/m/n/10 # idvar, ids) # name / values of constructed id v
ariable[]
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[1726]
Underfull \hbox (badness 10000) in paragraph at lines 25132--25137
[][][]\T1/pcr/m/n/10 stack[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 aperm[]
[][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 relist[][][] []\T1/ptm/m/n/10 for r
e-shap-ing the re-sult of [][][]\T1/pcr/m/n/10 unlist[][][][]\T1/ptm/m/n/10 . [
][][]\T1/pcr/m/n/10 xtabs[][][] []\T1/ptm/m/n/10 and
Underfull \hbox (badness 2495) in paragraph at lines 25132--25137
[][][]\T1/pcr/m/n/10 as.data.frame.table[][][] []\T1/ptm/m/n/10 for cre-at-ing
con-tin-gency ta-bles and con-vert-ing them back to
Overfull \hbox (15.18042pt too wide) in paragraph at lines 25145--25145
[]\T1/pcr/m/n/9 ## long to wide (direction = "wide") requires idvar and timeva
r at a minimum[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25146--25146
[]\T1/pcr/m/n/9 reshape(Indometh, direction = "wide", idvar = "Subject", timev
ar = "time")[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 25165--25165
[]\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[]
[1727]
[1728]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 25270--25270
[] \T1/pcr/m/n/10 na.action = c("+Big_alternate", "-Big_alternate", "na.
omit", "fail"),[]
Underfull \hbox (badness 1033) in paragraph at lines 25313--25319
\T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10
where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/
m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where
[1729]
Underfull \hbox (badness 10000) in paragraph at lines 25334--25337
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult []\T1/pcr/m/n/10 y = r
unmed(x, k) []\T1/ptm/m/n/10 sim-ply has []\T1/pcr/m/n/10 y[j] =
[1730]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 25412--25412
[]\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 25438--25438
[]\T1/pcr/m/n/9 ## An example with initial NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s -
used to fail badly (notably for "Turlach"):[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 25450--25450
[]\T1/pcr/m/n/9 matplot(y = cbind(x15, rT15), type = "b", ylim = c(1,9), pch=1
:5, xlab = NA,[]
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Underfull \vbox (badness 10000) has occurred while \output is active
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[1738]
Underfull \hbox (badness 6268) in paragraph at lines 25909--25914
[][][]\T1/pcr/m/n/10 SSasympOrig[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 S
Sbiexp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSfol[][][][]\T1/ptm/m/n/10
, [][][]\T1/pcr/m/n/10 SSfpl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSgo
mpertz[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSlogis[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 SSmicmen[][][][]\T1/ptm/m/n/10 ,
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[1740]
[1741]
Underfull \hbox (badness 1867) in paragraph at lines 26119--26121
[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods.
Passed to
Underfull \hbox (badness 10000) in paragraph at lines 26135--26139
[]\T1/ptm/m/n/10 where []\T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallba
ck = use.fallback) []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 PP
Underfull \hbox (badness 10000) in paragraph at lines 26135--26139
\T1/pcr/m/n/10 <- sum(!is.na([][]coef[][][](object))) []\T1/ptm/m/n/10 -- where
in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was
[1742]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 26177--26177
[]\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr
om summary(lm1)[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 26184--26184
[]\T1/pcr/m/n/9 stopifnot(all.equal(sigma(fm.DN1), summary(fm.DN1)$sigma, tole
rance=1e-15))[]
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[1744]
[1745]
Underfull \hbox (badness 2495) in paragraph at lines 26366--26375
[]\T1/ptm/m/n/10 For an in-verse gaus-sian GLM the model as-sumed is $\OML/cmm/
m/it/10 IG\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^V[]; ^^Uw[]\OT1/cmr/m/n/10 )$ \T1
/ptm/m/n/10 (see [][]$\T1/pcr/m/n/10 https : / / en .
[1746]
[1747]
Underfull \hbox (badness 2197) in paragraph at lines 26512--26515
[]\T1/pcr/m/n/10 psmirnov []\T1/ptm/m/n/10 gives the dis-tri-bu-tion func-tion,
[]\T1/pcr/m/n/10 qsmirnov []\T1/ptm/m/n/10 gives the quan-tile func-tion, and
Overfull \hbox (24.78088pt too wide) in paragraph at lines 26532--26532
[] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
= FALSE)[]
Underfull \hbox (badness 1412) in paragraph at lines 26539--26541
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1748]
[1749]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 26624--26624
[]\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 26649--26649
[]\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda
= NULL, cv = FALSE,
Overfull \hbox (66.78088pt too wide) in paragraph at lines 26652--26652
[] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee
p.stuff = FALSE)[]
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[1751]
[1752]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 26877--26877
[] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / t
ol) ))[]
Underfull \hbox (badness 2547) in paragraph at lines 26881--26887
[]\T1/ptm/m/n/10 The de-fault []\T1/pcr/m/n/10 all.knots = FALSE []\T1/ptm/m/n/
10 and []\T1/pcr/m/n/10 nknots = .nknots.smspl[]\T1/ptm/m/n/10 , en-tails us-in
g only
[1753]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26928--26928
[]\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi
ng splines")[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 26949--26949
[]\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # =
= unique(cars$speed)[]
[1754]
[1755]
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Overfull \hbox (0.78088pt too wide) in paragraph at lines 27141--27141
[]\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail,
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[1758]
[1759]
[1760]
Underfull \hbox (badness 10000) in paragraph at lines 27406--27411
\T1/ptm/m/n/10 This makes the spec-tral den-sity a den-sity over the range []\T
1/pcr/m/n/10 (-frequency(x)/2,
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[1762]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 27520--27520
[] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[]
[1763]
[1764]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 27702--27702
[]\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi
* x) + rnorm(30)/10, 3)[]
[1765]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 27708--27708
[]\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean))
for when x has ties")[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 27717--27717
[]\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c
ol = 3, n = 1001)[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 27718--27718
[]\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c
ol = 4, n = 1001)[]
[1766]
Underfull \hbox (badness 2922) in paragraph at lines 27787--27792
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (9.78043pt too wide) in paragraph at lines 27824--27824
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim
= c(-.3, 5),[]
[1767]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 27827--27827
[] \T1/pcr/m/n/9 {f[phi](x) == phi[1] + (phi[2]-phi[1])*~e^
{-e^{phi[3]}*~x}}))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 27836--27836
[] \T1/pcr/m/n/9 c(0 , 1 ), 1, length = 0.08, angle = 25); text(0.
5, 1, quote(1))[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27837--27837
[] \T1/pcr/m/n/9 y0 <- 1 + 4*exp(-3/4) ; t.5 <- log(2) / exp(-3/4) ; AR2 <- 3
# (Asym + R0)/2[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 27841--27841
[] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi
[1]+phi[2],2), phi[1]),[]
[1768]
Underfull \hbox (badness 3240) in paragraph at lines 27895--27898
[][][]\T1/pcr/m/n/10 nls[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 selfStart
[][][][]\T1/ptm/m/n/10 ; []\T1/pcr/m/n/10 example(SSasympOff) []\T1/ptm/m/n/10
gives graph show-ing the []\T1/pcr/m/n/10 SSasympOff
Overfull \hbox (36.7804pt too wide) in paragraph at lines 27916--27916
[] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOff(xx, Asym = 5, lrc = log(
0.4), c0 = 3/4)) )[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27919--27919
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim
= c(-1, 8),[]
[1769]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28002--28002
[] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOrig(xx, Asym = 5, lrc = log
(log(2)))) )[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28006--28006
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim =
c(-1/4, 5),[]
[1770]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 28016--28016
[] \T1/pcr/m/n/9 axis(2, at = 5*c(1/2,1), labels= expression(frac(phi[1],2),
phi[1]), pos=0, las=1)[]
Overfull \hbox (106.98032pt too wide) in paragraph at lines 28021--28021
[] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
== frac(log(2), e^{phi[2]})}),[]
Underfull \hbox (badness 2922) in paragraph at lines 28057--28063
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 28079--28079
[]\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28095--28095
[] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 =
1.5 * exp(-x)"),[]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 28109--28109
[]\T1/pcr/m/n/9 ## Fails by default (scaleOffset=0) on most platforms {also af
ter increasing maxiter !}[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28111--28111
[] \T1/pcr/m/n/9 nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d
atN, trace=TRUE)[]
Overfull \hbox (128.58029pt too wide) in paragraph at lines 28117--28117
[] \T1/pcr/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol=
1e-11, nDcentral=TRUE), trace=TRUE)[]
[1772]
[1773]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 28228--28228
[]\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input))
[1774]
Underfull \hbox (badness 2922) in paragraph at lines 28290--28295
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
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Overfull \hbox (69.18036pt too wide) in paragraph at lines 28328--28328
[] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm
id", phi[4] == "scal")))[]
Underfull \hbox (badness 2922) in paragraph at lines 28377--28382
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1776]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28408--28408
[]\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = "
red", lwd=2)[]
Underfull \hbox (badness 2922) in paragraph at lines 28442--28447
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1777]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28467--28467
[]\T1/pcr/m/n/9 ## Initial values are in fact the converged one here, "Number
of iter...: 0" :[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 28471--28471
[]\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR
UE), trace = TRUE)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28491--28491
[] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3]
== "scal")))[]
[1778]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 28501--28501
[] \T1/pcr/m/n/9 segments(c(2,2.6,2.6), c(0, 2.5,3.5), # NB. SSlogis(x =
xmid = 2) = 2.5[]
Underfull \hbox (badness 2922) in paragraph at lines 28536--28541
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28558--28558
[]\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
digits = 3)[]
[1779]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 28576--28576
[] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS
micmen model")[]
[1780]
Underfull \hbox (badness 6493) in paragraph at lines 28628--28633
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 x[]\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28656--28656
[]\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28658--28658
[]\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 28662--28662
[]\T1/pcr/m/n/9 plot(weight ~ Time, Chick.6, xlim = c(0, 21), main = "SSweibul
l() fit to Chick.6")[]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 28665--28665
[]\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f
m1)[["Drop"]]), lty = 3)[]
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[1783]
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[]\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.glm"[]\T1/ptm/m/
n/10 , usu-ally, a re-sult of a call to
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[1797]
Underfull \hbox (badness 2237) in paragraph at lines 29725--29727
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1
/pcr/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if
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[]\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.nls"[]\T1/ptm/m/
n/10 , usu-ally the re-sult of a call to
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[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1
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[]\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t
race = FALSE)
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[]\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m
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[]\T1/pcr/m/n/9 symnum(ii, cutpoints = 2*(0:4), symbols = c(".", "-", "+", "$
"), show.max = TRUE)[]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
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[]\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200,
main = t.tit,[]
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[] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com
mon",[]
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[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
resid-u-als, when
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[]\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[]
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[]\T1/ptm/m/n/10 There are meth-ods for classes []\T1/pcr/m/n/10 "aovlist"[]\T1
/ptm/m/n/10 , []\T1/pcr/m/n/10 "terms"[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 "
formula" []\T1/ptm/m/n/10 (see
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[]\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out =
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[]\T1/pcr/m/n/10 toeplitz2(x, nrow = length(x) +1 - ncol, ncol = length(x) +1
- nrow)[]
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[]\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 toeplitz(x, *)[]\T1/ptm/m/n/10 : the firs
t col-umn of the Toeplitz ma-trix; for
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[]\T1/pcr/m/n/9 # Matrix of character (could also have logical, raw, complex .
.) {also warning}:[]
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[] \T1/pcr/m/n/9 colnames(W) <- paste0(",", if(n <= 9) 1:n else c(1:9, lette
rs[seq_len(n-9)]))[]
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[]\T1/pcr/m/n/9 y.hat <- W. %*% y # y.hat := smoothed(y) ("mass preserving" ->
longer than y)[]
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[]\T1/pcr/m/n/9 plot(x,y, type="b", xlim=c(1,m)); curve(f(x), 1,n, col="gray",
lty=2, add=TRUE)[]
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[] \T1/pcr/m/n/10 class = if(nseries > 1) c("mts", "ts", "matrix", "array")
else "ts",[]
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[]\T1/pcr/m/n/10 is.mts(x) []\T1/ptm/m/n/10 tests if an ob-ject []\T1/pcr/m/n/1
0 x []\T1/ptm/m/n/10 is a mul-ti-vari-ate time se-ries, i.e., ful-fills []\T1/p
cr/m/n/10 is.ts(x)[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 utils:: methods(class = "ts") # all functions with methods ava
ilable for "ts"[]
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[]\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
FALSE)
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[]\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
FALSE)[]
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[] \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con
v = FALSE,[]
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[] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace
= 0)[]
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[]\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature
s: --------------[]
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[]\T1/pcr/m/n/9 ## where as \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 simply first enlarges the search interval:[]
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[]\T1/pcr/m/n/9 wilcox.test( 4:2, 3:1, paired=TRUE) # Warning: canno
t compute exact p-value with ties[]
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[]\T1/pcr/m/n/9 wilcox.test((4:2)/10, (3:1)/10, paired=TRUE, digits.rank = 9)
# same ties as (4:2, 3:1)[]
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[] \T1/pcr/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps
= getOption("ts.eps"), ...)[]
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[]\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE,
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[] \T1/pcr/m/n/10 exclude = if(!addNA) c(NA, NaN), drop.unused.levels = F
ALSE)[]
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[1853]) (./stats4-pkg.tex
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Chapter 11.
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[] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[]
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[]\T1/pcr/m/n/9 ## Boundary case: This works, but fails if limits are set clos
er to 0 and 1[]
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Chapter 12.
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[]\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all.names = TRUE) # .Tcl.args put a ca
llback ref in here[]
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[]\T1/pcr/m/n/10 tcl []\T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-i
ng any Tk or Tcl com-mand by sim-ply run-ning
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[]\T1/pcr/m/n/9 eval.txt <- function() eval(str2lang(tclvalue(tkget(txt.w, "0.
0", "end"))))[]
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[][][]\T1/pcr/m/n/10 select.list[][][] []\T1/ptm/m/n/10 (a text ver-sion ex-cep
t on Win-dows and the ma-cOS GUI), [][][]\T1/pcr/m/n/10 menu[][][] []\T1/ptm/m/
n/10 (whose
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Chapter 13.
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[]\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
new methods.[]
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[]\T1/pcr/m/n/10 assertWarning() []\T1/ptm/m/n/10 as-serts that a warn-ing will
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[]\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
ing warning)[]
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[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
o ren-der each of the 12
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\T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][][]\T1/pcr/m/n
/10 bibentry[][][] []\T1/ptm/m/n/10 as well as sev-eral other rou-
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\T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named []\T1/pcr/m/n
/10 formatArticle[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 formatBook[]\T1/ptm/m/n/10
,
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[]\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta
ngle = TRUE,
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[]\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gin
e to use. Over-rides any
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\T1/ptm/m/n/10 If given, vi-gnette source files are by de-fault looked for in s
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diff \T1/ptm/m/n/10 or \T1/pcr/m/n/10 \dontshow\T1/ptm/m/n/10 , and \T1/pcr/m/n
/10 \title \T1/ptm/m/n/10 re-placed by \T1/pcr/m/n/10 \section \T1/ptm/m/n/10 o
r
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[]\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", "
xz"),[]
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[]\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co
mpress == "none")[]
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[] \T1/pcr/m/n/10 outputs = FALSE, sources = FALS
E, ...)[]
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[]\T1/pcr/m/n/10 check_packages_in_dir_details(dir, logs = NULL, drop_ok = TRU
E, ...)[]
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[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v
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[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-
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[]\T1/pcr/m/n/10 check_packages_in_dir []\T1/ptm/m/n/10 re-turns an ob-ject in-
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[]\T1/pcr/m/n/10 codocClasses []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 codocData [
]\T1/ptm/m/n/10 re-turn ob-jects of class []\T1/pcr/m/n/10 "codocClasses" []\T1
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[]\T1/pcr/m/n/10 CRAN_package_db() []\T1/ptm/m/n/10 re-turns a data frame with
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' meta-data for the cu
r-rent pack-ages in the CRAN pack-age repos-i-
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\T1/ptm/m/n/10 tory, in-clud-ing in par-tic-u-lar the De-scrip-tion and Main-ta
iner in-for-ma-tion not pro-vided by
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[]\T1/ptm/m/n/10 Functions []\T1/pcr/m/n/10 CRAN_current_db()[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 CRAN_aliases_db()[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 CRAN_rdx
refs_db()[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 CRAN_authors_db() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 CRAN_a
rchive_db() []\T1/ptm/m/n/10 (also used by []\T1/pcr/m/n/10 R CMD check[]\T1/pt
m/m/n/10 )
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T1/pcr/m/n/10 R_CRAN_WEB[]\T1/ptm/m/n/10 . The mir-ror to be used is re-ported
by
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[] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En
hances"))[]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
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\T1/pcr/m/n/10 "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string []\T1/pcr/m/n/1
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[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 loadPkgRdMacros []\T1/ptm/m/n/10 func-tio
n first looks for an []\T1/pcr/m/n/10 "RdMacros" []\T1/ptm/m/n/10 en-try in the
pack-age
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[]\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user
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\T1/ptm/m/n/10 tion set-tings also for com-pi-la-tions not us-ing \T1/phv/m/n/1
0 R\T1/ptm/m/n/10 's mech-a-nisms (in par-tic-u-lar, cus-tom com-
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\T1/ptm/m/n/10 pi-la-tions in sub-di-rec-to-ries of `\T1/pcr/m/n/10 src\T1/ptm/
m/n/10 '), e.g., by adding con-fig-ure code call-ing \T1/phv/m/n/10 R \T1/ptm/m
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[]\T1/pcr/m/n/10 matchConcordance []\T1/ptm/m/n/10 con-verts from out-put lo-ca
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[]\T1/ptm/m/n/10 The de-fault method of []\T1/pcr/m/n/10 as.Rconcordance []\T1/
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[]\T1/pcr/m/n/10 followConcordance []\T1/ptm/m/n/10 is used when a file is tran
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\T1/ptm/m/n/10 trans-for-ma-tion records a con-cor-dance in the file which is r
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[]\T1/pcr/m/n/10 package_dependencies(packages = NULL, db = NULL, which = "str
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\T1/pcr/m/n/10 "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string []\T1/pcr/m/n/1
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[]\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster"
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[] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations
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[1934]
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[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion 3.2.0, User-d
efined macros may be given in a sep-a-rate file us-ing
[1935]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3259--3259
[] \T1/pcr/m/n/10 stylesheet = file.path(R.home("doc"), "html", "R-nav
.css"),[]
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[] \T1/pcr/m/n/10 hooks = list(pkg_href = function(pkg) sprintf("%s.ht
ml", pkg)),[]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 3267--3267
[] \T1/pcr/m/n/10 mathjax_config = file.path(R.home("doc"), "html", "m
athjax-config.js"),[]
[1936]
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[1938]
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[]\T1/pcr/m/n/10 checkDocFiles (package, dir, lib.loc = NULL, chkInternal =
NULL)
[1939]
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[]\T1/pcr/m/n/10 checkRdContents (package, dir, lib.loc = NULL, chkInternal =
NULL)[]
[1940]
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[] \T1/pcr/m/n/10 fragment = FALSE, ..., writeEncoding = outputEncodin
g != "UTF-8",[]
[1943]
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[]\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-
tor of links, as re-turned by
[1944]
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[1948]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 4153--4153
[] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro
s", "system.Rd"))[]
Underfull \hbox (badness 5417) in paragraph at lines 4191--4201
[]\T1/ptm/m/n/10 By de-fault, the tags \T1/pcr/m/n/10 \S3method\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 \S4method\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \command\T1/ptm/m/n/10
, \T1/pcr/m/n/10 \docType\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \email\T1/ptm/m/n/10
,
[1949]
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Underfull \hbox (badness 4108) in paragraph at lines 4462--4469
[]\T1/ptm/m/n/10 This func-tion starts the in-ter-nal HTTP server, which runs o
n the loop-back in-ter-face
[1954]
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[] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett
es"),[]
[1955]
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[]\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter
net", "all"),[]
Underfull \hbox (badness 10000) in paragraph at lines 4591--4593
[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
[1956]
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[]\T1/pcr/m/n/9 (prio <- sapply(as.vector(pNms), packageDescription, fields =
"Priority"))[]
[1957]
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[1959]
[1960]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4909--4909
[]\T1/pcr/m/n/9 toTitleCase("ensemble tool for predictions from species distri
bution models")[]
Overfull \hbox (128.58029pt too wide) in paragraph at lines 4913--4913
[]\T1/pcr/m/n/9 toTitleCase("a small fox is jumping") # "a Small Fox is .."
(the \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 a\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 may cha
nge)% i.e. BUG[]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 4917--4917
[]\T1/pcr/m/n/9 toTitleCase("asking -- \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 is a smal
l fox jumping?\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ") # ".. -- Is a Small ..." (fi
ne)[]
[1961]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5000--5000
[] \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry
run),[]
[1962]
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Underfull \hbox (badness 10000) in paragraph at lines 5184--5187
[]\T1/ptm/m/n/10 optional char-ac-ter strings for the `[]\T1/pcr/m/n/10 Copyrig
ht[]\T1/ptm/m/n/10 ' and
Underfull \hbox (badness 6859) in paragraph at lines 5200--5205
[]\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory []\T1/pcr/m/n/10 po []\T1/
ptm/m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\
T1/ptm/m/n/10 ' are up-dated from
Underfull \hbox (badness 1184) in paragraph at lines 5208--5214
[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po
/\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T
he
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t
he pack-age are ex-am-ined to cre-ate a file
[1965]
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[]\T1/pcr/m/n/9 parse_URI_reference(c("foo://example.com:8042/over/there?name=
ferret#nose",[]
[1967]
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[]\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 vignetteEngine[][][][]\T1/ptm/m/n/10
, such as []\T1/pcr/m/n/10 "utils::Sweave" []\T1/ptm/m/n/10 or
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5542--5542
[] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F
ALSE,[]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 5543--5543
[] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr
ess = "xz",[]
Underfull \hbox (badness 3240) in paragraph at lines 5556--5559
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T
1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ',
Underfull \hbox (badness 1742) in paragraph at lines 5560--5570
[]\T1/pcr/m/n/10 "Package"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Version"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "Priority"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Depe
nds"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Imports"[]\T1/ptm/m/n/10 ,
[1970]
Underfull \hbox (badness 1127) in paragraph at lines 5598--5604
[]\T1/pcr/m/n/10 write_PACKAGES []\T1/ptm/m/n/10 scans the named di-rec-tory fo
r R pack-ages, ex-tracts in-for-ma-tion from
Underfull \hbox (badness 1635) in paragraph at lines 5598--5604
\T1/ptm/m/n/10 each pack-age's `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file
, and writes this in-for-ma-tion into the `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/1
0 ',
Underfull \hbox (badness 1571) in paragraph at lines 5626--5630
[]\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down-
load speed and time spent by
[1971]
Underfull \hbox (badness 2772) in paragraph at lines 5652--5657
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 PACKAGES.gz\T1/ptm/m/n/10 ' files. See [][][
]\T1/pcr/m/n/10 update_PACKAGES[][][] []\T1/ptm/m/n/10 for ef-fi-ciently up-dat
-ing ex-ist-ing
[1972]
[1973]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5790--5790
[] \T1/pcr/m/n/9 " stop(errorCondition(gettext(\TS1/pcr/m/n/9 '\T1/pcr/m/n
/9 needs Deep Thought\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ), class=\TS1/pcr/m/n/9 '\T1
/pcr/m/n/9 myError\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ))",[]
[1974]) (./utils-pkg.tex
Chapter 14.
Underfull \hbox (badness 1072) in paragraph at lines 47--52
[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[]
\T1/pcr/m/n/10 insertions[]\T1/ptm/m/n/10 ',
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[]\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with
these names[]
[1979]
[1980]
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\T1/ptm/m/n/10 are []\T1/pcr/m/n/10 c("vertical", "horizontal", "cascade", "min
imize",
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[]\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 list[][][] []\T1/ptm/m/n/10 of win-dow
han-dles, by de-fault pro-duced by
[1981]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 450--450
[]\T1/pcr/m/n/9 # This default is useful only in SDI mode: it will tile any F
irefox window[]
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[]\T1/pcr/m/n/9 .arrangeWindowsDefaults <- list(c("R", "all"), pattern = c("",
"Firefox"))[]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 469--469
[] \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No
", "Cancel"))),[]
[1982]
[1983]
[1984]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 691--691
[]\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l
ist(),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 692--692
[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 693--693
[]\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l
ist(),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 694--694
[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
[1985]
Underfull \hbox (badness 10000) in paragraph at lines 728--734
[]\T1/ptm/m/n/10 Functions []\T1/pcr/m/n/10 aspell_package_Rd_files[]\T1/ptm/m/
n/10 , []\T1/pcr/m/n/10 aspell_package_vignettes[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 4416) in paragraph at lines 728--734
[]\T1/pcr/m/n/10 aspell_package_R_files []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 a
spell_package_C_files []\T1/ptm/m/n/10 per-form spell check-
[1986]
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[] \T1/pcr/m/n/10 fields = getOption("available_packages_fie
lds"),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 802--802
[] \T1/pcr/m/n/10 str2logical(Sys.getenv("R_PACKAGES_CAC
HE_USER_DIR",[]
Underfull \hbox (badness 10000) in paragraph at lines 842--845
[][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 in-di-cat-ing if caching sh
ould hap-pen in \T1/ptm/b/n/10 tools\T1/ptm/m/n/10 '
[1987]
Underfull \hbox (badness 1552) in paragraph at lines 936--942
[]\T1/ptm/m/n/10 A char-ac-ter ma-trix with one row per pack-age, row names the
pack-age names and col-
[1988]
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[]\T1/pcr/m/n/9 db <- available.packages(repos = findCRANmirror("web"), filter
s = "duplicates")[]
[1989]
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[]\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
NULL,
[1990]
[1991]
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[][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 in-di-cat-ing if Bib-TeX co
de should be given ad-di-tion-ally;
Underfull \hbox (badness 5533) in paragraph at lines 1139--1145
\T1/ptm/m/n/10 cur-rently ap-plies only to []\T1/pcr/m/n/10 style = "citation"[
]\T1/ptm/m/n/10 . The de-fault for
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\T1/ptm/m/n/10 the []\T1/pcr/m/n/10 print() []\T1/ptm/m/n/10 method de-pends on
the num-ber of (bib) en-tries and
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\T1/ptm/m/n/10 For ex-am-ple, to see no Bib-TeX at all, you can change the de-f
ault by
Underfull \hbox (badness 10000) in paragraph at lines 1148--1150
[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1992]
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[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org
/ wiki / Digital _ Object _
[1993]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1349--1349
[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
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Underfull \hbox (badness 1859) in paragraph at lines 1758--1767
[]\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b
e quite large the com-
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\T1/ptm/m/n/10 mand []\T1/pcr/m/n/10 data.frame(x, y, z, monday, tuesday) []\T1
/ptm/m/n/10 never re-turns. Do not re-port that
[2000]
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[] \T1/pcr/m/n/9 data = infert, family = b
inomial())))[]
[2002]
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[] \T1/pcr/m/n/10 md5sum = FALSE, digest = NULL, full.names = length(path)
> 1,[]
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[]\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[]
[2003]
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[]\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[]
[2004]
Underfull \hbox (badness 2277) in paragraph at lines 2113--2118
[]\T1/pcr/m/n/10 charClass []\T1/ptm/m/n/10 was added in \T1/phv/m/n/10 R \T1/p
tm/m/n/10 4.1.0. A less di-rect way to ex-am-ine char-ac-ter classes
[2005]
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[]\T1/pcr/m/n/9 cl <- c("alnum", "alpha", "blank", "digit", "graph", "punct",
"upper", "xdigit")[]
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[]\T1/pcr/m/n/9 X <- as.data.frame(X); row.names(X) <- sQuote(intToUtf8(x, mul
tiple = TRUE))[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2155--2155
[]\T1/pcr/m/n/9 ## How many printable characters are there? (Around 280,000 in
Unicode 13.)[]
[2006]
[2007]
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[]\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
NULL,
[2008]
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[]\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
NULL,
[2009]
[2010]
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[]\T1/ptm/m/n/10 If the ob-ject re-turned by []\T1/pcr/m/n/10 citation() []\T1/
ptm/m/n/10 con-tains only one ref-er-ence, the as-so-ci-ated print
Underfull \hbox (badness 1400) in paragraph at lines 2481--2488
\T1/ptm/m/n/10 method shows both a text ver-sion and a Bib-TeX en-try for it. I
f a pack-age has more
[2011]
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[]\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
NULL,[]
[2012]
[2013]
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[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
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[]\T1/pcr/m/n/10 citEntry(entry, textVersion = NULL, header = NULL, footer = N
ULL, ...)
[2014]
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[][][]\T1/pcr/m/n/10 citation[][][] []\T1/ptm/m/n/10 for more in-for-ma-tion ab
out cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file
s;
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard
}) has been already used, duplicate ignored
<to be read again>
\relax
l.2758 ... the Clipboard in MS Windows}{clipboard}
[2015]
[2016]
Underfull \hbox (badness 10000) in paragraph at lines 2882--2884
[]\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/
phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see
[2017]
[2018]
[2019]
[2020]
Underfull \hbox (badness 10000) in paragraph at lines 3103--3105
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[2021]
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[]\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re
c-tory of the cur-rent work-ing di-rec-tory, set []\T1/pcr/m/n/10 package =
[2025]
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[]\T1/pcr/m/n/9 try(data(package = "rpart"), silent = TRUE) # list the data se
ts in the rpart package[]
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[]\T1/pcr/m/n/9 data(USArrests, "VADeaths") # load the data sets \TS1/pcr/m
/n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9
'\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[]
[2026]
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[]\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class []\
T1/pcr/m/n/10 R_dataentry[]\T1/ptm/m/n/10 . Re-sources
[2027]
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[] \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf
orm$r_arch, "stats.dll"))[]
[2033]
[2034]
Underfull \hbox (badness 4779) in paragraph at lines 4068--4073
[]\T1/ptm/m/n/10 Support for method []\T1/pcr/m/n/10 "libcurl" []\T1/ptm/m/n/10
was op-tional on Win-dows prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0: use
Underfull \hbox (badness 1072) in paragraph at lines 4131--4135
[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
the []\T1/pcr/m/n/10 quiet []\T1/ptm/m/n/10 ar-gu-ment and the
[2035]
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[]\T1/ptm/m/n/10 For the []\T1/pcr/m/n/10 "libcurl" []\T1/ptm/m/n/10 and []\T1/
pcr/m/n/10 "curl" []\T1/ptm/m/n/10 meth-ods, prox-ies can be set \T1/ptm/m/it/1
0 via \T1/ptm/m/n/10 the en-vi-ron-
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\T1/ptm/m/n/10 ment vari-ables []\T1/pcr/m/n/10 http_proxy []\T1/ptm/m/n/10 or
[]\T1/pcr/m/n/10 ftp_proxy[]\T1/ptm/m/n/10 . See [][]$\T1/pcr/m/n/10 https : /
/ curl . se / libcurl / c /
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\T1/ptm/m/n/10 string con-tain-ing `[]\T1/pcr/m/n/10 "Schannel"[]\T1/ptm/m/n/10
'. If it does not, for ver-i-fi-ca-tion to be on the en-vi-ron-
[2036]
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\T1/ptm/m/n/10 able at the repos-i-to-ries, or []\T1/pcr/m/n/10 NULL []\T1/ptm/
m/n/10 which makes an in-ter-nal call to
Underfull \hbox (badness 10000) in paragraph at lines 4357--4359
[]\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][][]\T1/pcr/m/n/10 do
wnload.file[][][] []\T1/ptm/m/n/10 and
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[]\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c
har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of
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[] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[]
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\T1/ptm/m/n/10 is saved, then ini-tial-ized to a spec-i-fied state, the ex-am-p
le is run and
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\T1/ptm/m/n/10 the (saved) state is re-stored. []\T1/pcr/m/n/10 setRNG = TRUE [
]\T1/ptm/m/n/10 sets the same state as
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[]\T1/pcr/m/n/10 R CMD [][]check[][][] []\T1/ptm/m/n/10 does for run-ning a pac
k-age's ex-am-ples. This is cur-
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\T1/ptm/m/n/10 rently equiv-a-lent to []\T1/pcr/m/n/10 setRNG = {RNGkind("defau
lt", "default",
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[]\T1/ptm/m/n/10 logical (or []\T1/pcr/m/n/10 "default"[]\T1/ptm/m/n/10 ) in-di
-cat-ing if [][][]\T1/pcr/m/n/10 devAskNewPage[][][](ask = TRUE)
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[]\T1/ptm/m/n/10 An en-try in []\T1/pcr/m/n/10 getOption("repos") []\T1/ptm/m/n
/10 named `[]\T1/pcr/m/n/10 CRAN[]\T1/ptm/m/n/10 ' which is not the de-fault
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[]\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[]
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pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format})
has been already used, duplicate ignored
<to be read again>
\relax
l.5136 ...mat Unordered and Ordered Lists}{format}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format.1}
) has been already used, duplicate ignored
<to be read again>
\relax
l.5136 ...mat Unordered and Ordered Lists}{format}
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[]\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing
to ex-ter-nal GUIs or to the
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[]\T1/ptm/m/n/10 External pointer ob-jects are com-pared as ref-er-ence ob-ject
s, cor-re-spond-ing to call-ing
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[]\T1/pcr/m/n/10 ## NB: The methods for \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 data.f
rame\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 and \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 array\
TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 are identical to the \TS1/pcr/m/n/10 '\T1/pcr/
m/n/10 matrix\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 one[]
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[]\T1/pcr/m/n/10 tail(x, n = 6L, keepnums = TRUE, addrownums, ...) # exported
as tail.matrix()[]
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[] \T1/pcr/m/n/9 ## BUT if I use "useAttrib(.)", this is *not* ok, when n i
s of length 2:[]
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[] \T1/pcr/m/n/9 ## --- because [i,j]-indexing of data frames *also* drops
"other" attributes ..[]
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 6558--6558
[] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[]
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[]\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 https : / / www . r-[]
project . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also
[2072]
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[]\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words
'. `Key-
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\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are
listed in file
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[]\T1/pcr/m/n/9 help.search("linear models") # In case you forgot how to fit
linear models[]
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[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-
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\T1/ptm/m/n/10 dex, `\T1/ptm/m/sl/10 R_DOC_DIR\T1/pcr/m/n/10 /html/packages.htm
l\T1/ptm/m/n/10 ', which can be re-made by
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion
to search. See
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Underfull \hbox (badness 5175) in paragraph at lines 6949--6952
[]\T1/pcr/m/n/10 hsearch_db() []\T1/ptm/m/n/10 builds and caches the help searc
h database for sub-se-quent use by
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[]\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion `
Lock-ing' in the help for
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[]\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 means to use []\T1/pcr/m/n/10 c("Depends
", "Imports", "LinkingTo",
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\T1/pcr/m/n/10 "Suggests") []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pkgs []\T1/ptm
/m/n/10 and []\T1/pcr/m/n/10 c("Depends", "Imports",
Underfull \hbox (badness 1270) in paragraph at lines 7276--7283
\T1/pcr/m/n/10 "LinkingTo") []\T1/ptm/m/n/10 for added de-pen-den-cies: this in
-stalls all the pack-ages
Underfull \hbox (badness 1270) in paragraph at lines 7291--7301
\T1/ptm/m/n/10 for the `[]\T1/pcr/m/n/10 --configure-args[]\T1/ptm/m/n/10 ' fla
g in the call to []\T1/pcr/m/n/10 R CMD INSTALL[]\T1/ptm/m/n/10 . If
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Underfull \hbox (badness 1975) in paragraph at lines 7334--7338
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
be passed to []\T1/pcr/m/n/10 R
Underfull \hbox (badness 4913) in paragraph at lines 7334--7338
\T1/pcr/m/n/10 CMD INSTALL []\T1/ptm/m/n/10 for a source pack-age in-stall. E.g
., []\T1/pcr/m/n/10 c("--html",
Underfull \hbox (badness 10000) in paragraph at lines 7334--7338
\T1/pcr/m/n/10 "--no-multiarch", "--no-test-load") []\T1/ptm/m/n/10 or, for ma-
cOS,
Underfull \hbox (badness 1424) in paragraph at lines 7343--7346
[]\T1/ptm/m/n/10 logical: if true, re-duce the amount of out-put. This is \T1/p
tm/m/it/10 not \T1/ptm/m/n/10 passed to
Underfull \hbox (badness 10000) in paragraph at lines 7356--7360
[]\T1/ptm/m/n/10 further ar-gu-ments to be passed to [][][]\T1/pcr/m/n/10 downl
oad.file[][][][]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is []\T1/pcr/m/n
/10 "both" []\T1/ptm/m/n/10 which means `use bi-nary if avail-
Underfull \hbox (badness 5175) in paragraph at lines 7424--7431
\T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there
are source pack-ages
Underfull \hbox (badness 1342) in paragraph at lines 7424--7431
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by
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[]\T1/ptm/m/n/10 Using pack-ages with []\T1/pcr/m/n/10 type = "source" []\T1/pt
m/m/n/10 al-ways works pro-vided the pack-age con-tains no
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Underfull \hbox (badness 1314) in paragraph at lines 7511--7518
[]\T1/pcr/m/n/10 install.packages []\T1/ptm/m/n/10 needs to be able to com-pute
all the de-pen-den-cies of []\T1/pcr/m/n/10 pkgs []\T1/ptm/m/n/10 from
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Underfull \hbox (badness 10000) in paragraph at lines 7594--7599
[][][]\T1/pcr/m/n/10 update.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 download.pac
kages[][][][]\T1/ptm/m/n/10 ,
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[] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[]
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[] \T1/pcr/m/n/10 str2logical(Sys.getenv("R_PACKAGES_CAC
HE_USER_DIR",[]
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[][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 in-di-cat-ing if caching sh
ould hap-pen in \T1/ptm/b/n/10 tools\T1/ptm/m/n/10 '
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each
pack-age's
Underfull \hbox (badness 1983) in paragraph at lines 7674--7677
[]\T1/pcr/m/n/10 installed.packages []\T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10
DESCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along
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[]\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
= "License")[]
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[]\T1/pcr/m/n/9 ## Keep packages that come with R (priority="high") and all ot
hers separate![]
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Underfull \hbox (badness 4132) in paragraph at lines 7852--7854
[]\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion
of []\T1/pcr/m/n/10 libtool []\T1/ptm/m/n/10 in-stalled at
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[]\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h
ave defined?[]
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[]\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE)
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[]\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/
phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see
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[] \T1/pcr/m/n/10 methods(generic.function, class, all.names = FALSE, dropPa
th = FALSE)[]
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[] \T1/pcr/m/n/10 all.names = FALSE, dropPa
th = FALSE, useEnv = FALSE)[]
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[]\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if
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[]\T1/ptm/m/n/10 typically the re-sult of []\T1/pcr/m/n/10 methods(..)[]\T1/ptm
/m/n/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of S3 class
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[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
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[]\T1/pcr/m/n/9 db4 <- news(Version == "4.0.0" & grepl("^BUG", Category) & gre
pl("PR#", Text),[]
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[]\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri
x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[]
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[]\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[]
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[]\T1/pcr/m/n/10 "B"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "KiB"[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 "MiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "GiB"[]\T1/ptm/m/n/1
0 , []\T1/pcr/m/n/10 "TiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "PiB"[]\T1/ptm/m/
n/10 ,
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[]\T1/ptm/m/n/10 For all stan-dards, []\T1/pcr/m/n/10 units = "auto" []\T1/ptm/
m/n/10 is also al-lowed. If []\T1/pcr/m/n/10 standard =
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[]\T1/ptm/m/n/10 optionally a [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/
n/10 string with an en-cod-ing for an op-tional
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[] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica
tion", "Built"),[]
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[] \T1/pcr/m/n/10 tryFormats = c("%Y-%m-%d", "%Y/%m/%d", "%D", "%m/
%d/%y"),[]
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[] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f
ields=date.fields))[]
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[]\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 asDateBuilt()[]\T1/ptm/m/n/10 , a [][][]\
T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string as from
Underfull \hbox (badness 10000) in paragraph at lines 9106--9108
[]\T1/pcr/m/n/10 packageVersion() []\T1/ptm/m/n/10 is a con-ve-nience short-cut
, al-low-ing things like []\T1/pcr/m/n/10 if
Underfull \hbox (badness 1259) in paragraph at lines 9114--9119
[]\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the
given pack-age is found and can suc-cess-fully be read,
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[] \T1/pcr/m/n/9 identical(pu, packageDate("stats"))) # as "utils" an
d "stats" are[]
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[] \T1/pcr/m/n/9 # both \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 base R\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and "Built" at same time[]
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[]\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 "Status"[]\T1/ptm/m/n/10 , a fac-tor wit
h lev-els []\T1/pcr/m/n/10 c("ok", "upgrade",
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[]\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 "Status"[]\T1/ptm/m/n/10 , a fac-tor wit
h lev-els []\T1/pcr/m/n/10 c("installed", "not
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[] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[]
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[] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<",
">"),[]
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[] \T1/pcr/m/n/9 "S original, <http://statwww.epfl.ch/davison/BMA/libr
ary.html>"),[]
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[]\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for
more dis-cus-sion of the
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the name of the help topic;
de-faults to
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[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[]
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[]\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[]
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[]\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23
456 98 76 54[]
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[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
"no.loss"),[]
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[] \T1/pcr/m/n/10 row.names, col.names, as.is = !stringsAsFactors, t
ryLogical = TRUE,[]
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[] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[]
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[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[]
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[]\T1/ptm/m/n/10 Using []\T1/pcr/m/n/10 row.names = NULL []\T1/ptm/m/n/10 force
s row num-ber-ing. Miss-ing or []\T1/pcr/m/n/10 NULL
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[]\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 de-ter-m
in-ing if columns con-sist-ing en-tirely of []\T1/pcr/m/n/10 "F"[]\T1/ptm/m/n/1
0 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 "FALSE"[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 "TRUE" []\T1/pt
m/m/n/10 should be con-verted to [][][]\T1/pcr/m/n/10 logical[][][][]\T1/ptm/m/
n/10 ; passed to
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[]\T1/pcr/m/n/10 readRegistry(key, hive = c("HLM", "HCR", "HCU", "HU", "HCC",
"HPD"),
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[] \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64-
bit"))[]
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[]\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are
Underfull \hbox (badness 10000) in paragraph at lines 11417--11422
\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 HKEY_LOCAL_MACHINE[]\T1/ptm/m/n/10 , []\T1/
pcr/m/n/10 HKEY_CLASSES_ROOT[]\T1/ptm/m/n/10 .
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[]\T1/pcr/m/n/10 HKEY_CURRENT_USER[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 HKEY_USER
S[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 HKEY_CURRENT_CONFIG
[2141]
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[] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0)))
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[]\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2024). Ro-man nu-mer-als. Wikipedia
, The Free En-cy-clo-pe-dia.
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[][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / w / index . php ? title
= Roman _ numerals & oldid =
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[]\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:7))) # + NA with a warni
ng for the last.[]
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[]\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in
{1,2,..,4999} :[]
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[]\T1/pcr/m/n/10 4. | \-base:::tryCatchOne(expr, names, parentenv, handler
s[[1L]])[]
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[]\T1/pcr/m/n/10 5. | \-base:::doTryCatch(return(expr), name, parentenv,
handler)[]
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[]\T1/ptm/m/n/10 The chap-ter on ``Tidy-ing and pro-fil-ing R code'' in `Writ-i
ng R Ex-ten-sions':
[2153]
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[]\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
= 0)
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[]\T1/ptm/m/n/10 If `[]\T1/pcr/m/n/10 --default-packages[]\T1/ptm/m/n/10 ' is n
ot used, then []\T1/pcr/m/n/10 Rscript []\T1/ptm/m/n/10 checks the en-vi-ron-me
nt vari-
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\T1/ptm/m/n/10 able []\T1/pcr/m/n/10 R_SCRIPT_DEFAULT_PACKAGES[]\T1/ptm/m/n/10
. If this is set, then it takes prece-dence over
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[]\T1/pcr/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr
aphics,stats -e \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 sessionInfo()\TS1/pcr/m/n/9 '[]
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[] \T1/pcr/m/n/10 restrict = c("functions", "descriptions", "news",
"Rfunctions",[]
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[] \T1/pcr/m/n/10 "Rmanuals", "READMEs", "views", "vig
nettes"),[]
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[] \T1/pcr/m/n/10 sortby = c("score", "date:late", "date:early", "s
ubject",[]
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[] \T1/pcr/m/n/10 "subject:descending", "size", "size:de
scending"),[]
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\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 score[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 date:
late []\T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first,
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\T1/ptm/m/n/10 der, []\T1/pcr/m/n/10 subject:descending []\T1/ptm/m/n/10 for re
-verse al-pha-bet-i-cal or-der, []\T1/pcr/m/n/10 size []\T1/ptm/m/n/10 or
[2158]
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[]\T1/pcr/m/n/9 fullquery <- RSiteSearch("lattice", restrict = c("vignettes","
Rfunctions"))[]
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[]\T1/ptm/m/n/10 Character string spec-i-fy-ing whether emacs style ([]\T1/pcr/
m/n/10 "etags"[]\T1/ptm/m/n/10 ) or vi style
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p
tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software /
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[] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F
ALSE, ...)[]
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[]\T1/ptm/m/n/10 The de-fault for []\T1/pcr/m/n/10 stylepath []\T1/ptm/m/n/10 i
s now taken from the en-vi-ron-ment vari-able
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[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
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[]\T1/ptm/m/n/10 The use of fancy quotes (see [][][]\T1/pcr/m/n/10 sQuote[][][]
[]\T1/ptm/m/n/10 ) can cause prob-lems when set-ting \T1/phv/m/n/10 R \T1/ptm/m
/n/10 out-put in
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[] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[]
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[]\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func-
tions can be ex-e-cuted. If
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[]\T1/ptm/m/n/10 The file `\T1/pcr/m/n/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ures
the R GUI ([]\T1/pcr/m/n/10 Rgui[]\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows
and
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[]\T1/ptm/m/n/10 At the time of writ-ing `\T1/pcr/m/n/10 Rdevga\T1/ptm/m/n/10 '
con-fig-ured the map-ping of font num-bers to fonts, and
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[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
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[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
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[]\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at
end of report[]
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[]\T1/ptm/m/n/10 Repository `[]\T1/pcr/m/n/10 CRAN[]\T1/ptm/m/n/10 ' is treated
spe-cially: the value is taken from the cur-rent set-ting of
[2173]
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[]\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf
fix))
[2174]
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[]\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t
o the Win-dows API call
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[]\T1/pcr/m/n/10 getSrcFilename []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 getSrcDir
ectory []\T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file-
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Overfull \hbox (42.78088pt too wide) in paragraph at lines 14080--14080
[] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
TRUE, ...))[]
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[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
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[][][]\T1/pcr/m/n/10 options[][][]("width")[]\T1/ptm/m/n/10 ; note that this ha
s only a weak ef-fect, un-less
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[]\T1/ptm/m/n/10 (see [][][]\T1/pcr/m/n/10 options[][][][]\T1/ptm/m/n/10 ) whic
h de-faults to []\T1/pcr/m/n/10 "no" []\T1/ptm/m/n/10 for back com-pat-i-bil-it
y rea-sons;
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[]\T1/ptm/m/n/10 numeric or []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 as by de-fau
lt, de-ter-min-ing the []\T1/pcr/m/n/10 nlines []\T1/ptm/m/n/10 ar-gu-ment to
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[]\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
of binary numbers[]
[2182]
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[]\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo
ng" non-ASCII:[]
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[]\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of 2 in order to se
e 1 (in UTF-8!):[]
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[]\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N)))
# "1 is 1" here[]
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[]\T1/ptm/m/n/10 Options other than []\T1/pcr/m/n/10 memory = "none" []\T1/ptm/
m/n/10 ap-ply only to files pro-duced by
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[]\T1/ptm/m/n/10 The chap-ter on `Tidy-ing and pro-fil-ing R code' in `Writ-ing
R Ex-ten-sions':
[2186]
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[]\T1/ptm/m/n/10 further ar-gu-ments passed to the driver's setup func-tion. Se
e
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[][][]\T1/pcr/m/n/10 RweaveLatexSetup[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/
m/n/10 RtangleSetup[][][][]\T1/ptm/m/n/10 , re-spec-tively, for the ar-gu-
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 syntax = NULL []\T1/ptm/m/n/10 (the de-fau
lt) then the avail-able syn-tax ob-jects are con-sulted in
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\T1/ptm/m/n/10 turn, and se-lected if their []\T1/pcr/m/n/10 extension []\T1/pt
m/m/n/10 com-po-nent matches (as a reg-exp) the file
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\T1/ptm/m/n/10 name. Ob-jects []\T1/pcr/m/n/10 SweaveSyntaxNoweb []\T1/ptm/m/n/
10 (with []\T1/pcr/m/n/10 extension = "[.][rsRS]nw$"[]\T1/ptm/m/n/10 ) and
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\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `[]\T1/pcr/m/n/10 -h[]\T1/ptm/m/
n/10 ' (fol-low sym-bolic links, also `[]\T1/pcr/m/n/10 -L[]\T1/ptm/m/n/10 ' on
some plat-forms),
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\T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 --acls[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 --
exclude-backups[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 --exclude-vcs[]\T1/ptm/m/n
/10 ' (and sim-i-lar) and on Win-dows
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[]\T1/ptm/m/n/10 A con-ve-nient and ro-bust way to set op-tions for GNU []\T1/p
cr/m/n/10 tar []\T1/ptm/m/n/10 is via en-vi-ron-ment vari-able
[2191]
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[]\T1/ptm/m/n/10 When ar-gu-ment []\T1/pcr/m/n/10 tar []\T1/ptm/m/n/10 is set t
o the com-mand []\T1/pcr/m/n/10 tar []\T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment
vari-able
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f
ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / pubs .
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\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _ 92 _
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[] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
...),[]
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[] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
...),[]
Underfull \hbox (badness 4660) in paragraph at lines 15546--15550
\T1/ptm/m/n/10 able at the repos-i-to-ries, or []\T1/pcr/m/n/10 NULL []\T1/ptm/
m/n/10 which makes an in-ter-nal call to
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[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][][]\T1/pcr/m/n/10 ins
talled.packages[][][](lib.loc =
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[]\T1/ptm/m/n/10 Arguments such as []\T1/pcr/m/n/10 destdir []\T1/ptm/m/n/10 an
d []\T1/pcr/m/n/10 dependencies []\T1/ptm/m/n/10 to be
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\T1/ptm/m/n/10 passed to [][][]\T1/pcr/m/n/10 install.packages[][][] []\T1/ptm/
m/n/10 and []\T1/pcr/m/n/10 ignore_repo_cache[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 15566--15571
[]\T1/pcr/m/n/10 max_repo_cache_age []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 noCac
he []\T1/ptm/m/n/10 to [][][]\T1/pcr/m/n/10 available.packages[][][]
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[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
in-stall. See
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Underfull \hbox (badness 10000) in paragraph at lines 15602--15607
[]\T1/pcr/m/n/10 available = NULL []\T1/ptm/m/n/10 make a call to []\T1/pcr/m/n
/10 available.packages(contriburl =
Underfull \hbox (badness 1226) in paragraph at lines 15602--15607
\T1/pcr/m/n/10 contriburl, method = method) []\T1/ptm/m/n/10 and hence by de-fa
ult fil-ters on \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion, OS type
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[]\T1/ptm/m/n/10 Take care when us-ing []\T1/pcr/m/n/10 dependencies []\T1/ptm/
m/n/10 (passed to [][][]\T1/pcr/m/n/10 install.packages[][][][]\T1/ptm/m/n/10 )
with
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[][][]\T1/pcr/m/n/10 install.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n
/10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 download.pa
ckages[][][][]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 ## Not run: url.show("https://www.stats.ox.ac.uk/pub/datasets/
csb/ch3a.txt")
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[][][]\T1/pcr/m/n/10 browseVignettes[][][] []\T1/ptm/m/n/10 for an HTML-based v
i-gnette browser; [][][]\T1/pcr/m/n/10 RShowDoc[][][]("\T1/ptm/m/sl/10 basename
\T1/pcr/m/n/10 ",
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[]\T1/pcr/m/n/9 ## Note that \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 package = *\TS1/pcr
/m/n/9 ' \T1/pcr/m/n/9 is much faster in the case of many installed packages:[]
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[] \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d
ata = DAT)))[]
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[] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal),
data = DD)))[]
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[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i
s se-lected, or
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[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 winMenuDel []\T1/ptm/m/n/10 func-tion wil
l delete a menu and all of its items and sub-menus.
[2212]
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[]\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
" ",
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[]\T1/ptm/m/n/10 arguments to []\T1/pcr/m/n/10 write.table[]\T1/ptm/m/n/10 : []
\T1/pcr/m/n/10 append[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 col.names[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 sep[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 dec []\T1/ptm/m/n
/10 and
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[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion e.g. []\T1/pcr/m/n/10 file =
[2215]
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[2217])
[2218]
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[2220] (./KernSmooth-pkg.tex
Chapter 15.
[2221]
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[]\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE)
[2222]
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Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518
[]\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
= 0.05,
[2227]
[2228]
[2229]
[2230]) (./MASS-pkg.tex
Chapter 16.
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[]\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b
eav2$hours/24))[]
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pdfTeX warning (ext4): destination with the same identifier (name{Rfn.confint.g
lm}) has been already used, duplicate ignored
<to be read again>
\relax
l.1477 ...{confint.glm}{confint-MASS}{confint.glm}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.confint.n
ls}) has been already used, duplicate ignored
<to be read again>
\relax
l.1478 ...{confint.nls}{confint-MASS}{confint.nls}
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[]\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq",
"F"),[]
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[]\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq",
"F"),[]
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[]\T1/ptm/m/n/10 further ar-gu-ments for []\T1/pcr/m/n/10 plot []\T1/ptm/m/n/10
and graph-i-cal pa-ram-e-ters. Note that
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[]\T1/pcr/m/n/10 "gamma"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "geometric"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "log-normal"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lo
gnormal"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 "logistic"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "negative binomi
al"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "normal"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n
/10 "Poisson"[]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
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[] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[]
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[]\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
"exponential")[]
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[]\T1/ptm/m/n/10 The va-ri-ety of bar-ley ([]\T1/pcr/m/n/10 "manchuria"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "svansota"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "velv
et"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "trebi" []\T1/ptm/m/n/10 and
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[] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
...)[]
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[]\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model
= FALSE,
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[]\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE)
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[]\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/
10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log")
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\relax
l.6085 ...sical N, P, K Factorial Experiment}{npk}
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[] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[]
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[] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[]
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[] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[]
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[]\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea
s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c
mr/m/n/10 ) =
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[]\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[]
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[]\T1/ptm/m/n/10 the di-men-sion of the space to be used. If this is less than
[]\T1/pcr/m/n/10 min(p,
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[]\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[]
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[] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[]
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l.7513 ... for Profiling glm Objects}{profile.glm}
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[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
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[] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
NULL)[]
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[]\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if []\T1/pcr/m
/n/10 NA[]\T1/ptm/m/n/10 s are found. The
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[]\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[]
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[]\T1/ptm/m/n/10 ``Fold your arms! Which is on top'' (Fac-tor, with lev-els []\
T1/pcr/m/n/10 "R on L"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "L on R"[]\T1/ptm/m/n
/10 ,
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[]\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els []\T1/pcr/m/n/
10 "Heavy"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Regul" []\T1/ptm/m/n/10 (reg-u-l
arly),
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[]\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub
le.eps^0.25)
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[]\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[]
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[]\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[]
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[]\T1/ptm/m/n/10 The orig-i-nal data are avail-able at [][]$\T1/pcr/m/n/10 http
s : / / lib . stat . cmu . edu / datasets / 1993 .
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Chapter 17.
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[]\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec
t to change, and if you
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\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
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[]\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o
wn code. Please con-tact us
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[]\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm
/m/n/10 ob-jects; here, when the first is
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\T1/ptm/m/n/10 an []\T1/pcr/m/n/10 "[][]abIndex[][][]" []\T1/ptm/m/n/10 vec-tor
, these ar-gu-ments will be con-cate-nated to a new
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.all.equal
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l.182 ...{all.equal}{all.equal-methods}{all.equal}
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[]\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing
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[]\T1/ptm/m/n/10 There are more meth-ods, no-tably also for []\T1/pcr/m/n/10 "[
][]sparseVector[][][]"[]\T1/ptm/m/n/10 's, see
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[]\T1/ptm/m/n/10 optional ar-gu-ments passed to the de-fault method for generic
func-tion
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[] \T1/pcr/m/n/9 band(sm5, -1, 1)# "dsyMatrix": symmetric band preserves sym
metry property[]
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[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class
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[][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/
m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc
r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse
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[]\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[]
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[]\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[]
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[]\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20, 1), rpois(20, 3))[
c(1:3, 2:3, 3:2)],[]
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[]\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Fast version of Matrix :: .bd
iag() -- for the case of *many* (k x k) matrices:[]
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[]\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(<mat1>, <mat
2>, ....., <mat_N>) where each mat_j is a k x k \TS1/pcr/m/n/9 '\T1/pcr/m/n/9
matrix\TS1/pcr/m/n/9 '[]
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[]\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @return a sparse (N*k x N*k)
matrix of class \code{"\linkS4class{dgCMatrix}"}.[]
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[] \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 i :\TS1/pcr/m/n/9 ' \
T1/pcr/m/n/9 maybe there\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s a faster way (w/o matri
x indexing), but elegant?[]
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[] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len(
N), each=k)]),[]
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[]\T1/pcr/m/n/9 L. <- L; L.[1:2,1] <- TRUE; L.@x[1:2] <- FALSE; L. # has "zero
s" to drop0()[]
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[]\T1/pcr/m/n/10 new("pBunchKaufman", ...)[]\T1/ptm/m/n/10 , but they are more
typ-i-cally ob-tained as the value of
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[]\T1/pcr/m/n/10 signature(from = "pBunchKaufman", to = "dtpMatrix")[]\T1/ptm/m
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[]\T1/pcr/m/n/10 signature(from = "p?BunchKaufman", logarithm =
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[]\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m
atrix"), ...)[]
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[]\T1/ptm/m/n/10 An ob-ject rep-re-sent-ing the fac-tor-iza-tion, in-her-it-ing
from vir-tual class
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[]\T1/pcr/m/n/9 stopifnot(all.equal(as(A, "matrix"), as(Reduce(\TS1/cmtt/m/n/9
`\T1/pcr/m/n/9 %*%\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 , e.bk.A), "matrix")))[]
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l.1185 ... on cbind2/rbind2}{cbind2.Rdash.methods}
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l.1186 \aliasA{cbind2}{cbind2-methods}{cbind2}
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[]\T1/ptm/m/n/10 Our class def-i-ni-tion help pages men-tion-ing []\T1/pcr/m/n/
10 cbind2() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 rbind2() []\T1/ptm/m/n/10 met
h-ods:
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[]\T1/ptm/m/n/10 The im-ple-men-ta-tion of class []\T1/pcr/m/n/10 CHMfactor []\
T1/ptm/m/n/10 is based on CHOLMOD's C-level
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[]\T1/pcr/m/n/10 signature(from = "CHMfactor", logarithm = "logical")[]\T1/ptm/
m/n/10 : be-
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[]\T1/pcr/m/n/10 signature(update = ., C = ., object = "CHMfactor")[]\T1/ptm/m/
n/10 : see
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[]\T1/ptm/m/n/10 The CHOLMOD source code; see [][]$\T1/pcr/m/n/10 https : / / g
ithub . com / DrTimothyAldenDavis /
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\T1/pcr/m/n/10 SuiteSparse$[][]\T1/ptm/m/n/10 , no-tably the header file `\T1/p
cr/m/n/10 CHOLMOD/Include/cholmod.h\T1/ptm/m/n/10 ' defin-ing
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[]\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m
atrix"), ...)[]
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[] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(list(
NULL), dn[2L]),[]
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[] \T1/pcr/m/n/9 ae2(A[ch.A@perm + 1L, ch.A@perm + 1L], with(e.ch.A, L1 %*%
D %*% L1.))[]
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[] \T1/pcr/m/n/9 ae2(A[ch.A@perm + 1L, ch.A@perm + 1L], with(E.ch.A, L %*%
L. ))[]
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[]\T1/pcr/m/n/9 u2 <- update(ch.A, t(M), mult = sqrt(2)) # updating with cross
prod(M), not M[]
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\T1/pcr/m/n/10 double / dpstrf . f$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 htt
ps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and
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[]\T1/ptm/m/n/10 The CHOLMOD source code; see [][]$\T1/pcr/m/n/10 https : / / g
ithub . com / DrTimothyAldenDavis /
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of length []\T1/pcr/m/n/10 n*n []\T1/ptm/m/
n/10 ([]\T1/pcr/m/n/10 Cholesky[]\T1/ptm/m/n/10 ) or []\T1/pcr/m/n/10 n*(n+1)/2
[]\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 pCholesky[]\T1/ptm/m/n/10 ), where
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[]\T1/ptm/m/n/10 Class [][][]\T1/pcr/m/n/10 CholeskyFactorization[][][][]\T1/pt
m/m/n/10 , di-rectly. Class [][][]\T1/pcr/m/n/10 MatrixFactorization[][][][]\T1
/ptm/m/n/10 , by class
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[]\T1/ptm/m/n/10 Objects can be gen-er-ated di-rectly by calls of the form []\T
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0 : re-turns a
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[]\T1/pcr/m/n/10 signature(from = "p?Cholesky", logarithm = "logical")[]\T1/ptm
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\T1/pcr/m/n/10 double / dpstrf . f$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 htt
ps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and
[2403]
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[]\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m
atrix"), ...)[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2121--2121
[] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(list(
NULL), dn[2L]),[]
[2404]
Underfull \hbox (badness 10000) in paragraph at lines 2252--2259
[]\T1/ptm/m/n/10 a [][]fi-nite[][][] num-ber. The ma-trix that is fac-tor-ized
is []\T1/pcr/m/n/10 A + Imult *
Underfull \hbox (badness 1946) in paragraph at lines 2252--2259
\T1/pcr/m/n/10 - diag(abs(A))) []\T1/ptm/m/n/10 en-sures that []\T1/pcr/m/n/10
A + Imult * diag(nrow(A)) []\T1/ptm/m/n/10 is di-
[2405]
Underfull \hbox (badness 10000) in paragraph at lines 2299--2312
[]\T1/ptm/m/n/10 An ob-ject rep-re-sent-ing the fac-tor-iza-tion, in-her-it-ing
from vir-tual class
Underfull \hbox (badness 10000) in paragraph at lines 2315--2319
\T1/pcr/m/n/10 double / dpstrf . f$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 htt
ps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and
Underfull \hbox (badness 1917) in paragraph at lines 2320--2324
[]\T1/ptm/m/n/10 The CHOLMOD source code; see [][]$\T1/pcr/m/n/10 https : / / g
ithub . com / DrTimothyAldenDavis /
Underfull \hbox (badness 8132) in paragraph at lines 2320--2324
\T1/pcr/m/n/10 SuiteSparse$[][]\T1/ptm/m/n/10 , no-tably the header file `\T1/p
cr/m/n/10 CHOLMOD/Include/cholmod.h\T1/ptm/m/n/10 ' defin-ing
[2406]
[2407]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2437--2437
[] \T1/pcr/m/n/9 list(simpl1 = Cholesky(A4, perm = TRUE, super = FALSE, L
DL = TRUE),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2438--2438
[] \T1/pcr/m/n/9 simpl0 = Cholesky(A4, perm = TRUE, super = FALSE, L
DL = FALSE),[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2439--2439
[] \T1/pcr/m/n/9 super0 = Cholesky(A4, perm = TRUE, super = TRUE
)),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2441--2441
[] \T1/pcr/m/n/9 list(simpl1 = Cholesky(A4, perm = FALSE, super = FALSE, L
DL = TRUE),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2442--2442
[] \T1/pcr/m/n/9 simpl0 = Cholesky(A4, perm = FALSE, super = FALSE, L
DL = FALSE),[]
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[] \T1/pcr/m/n/9 super0 = Cholesky(A4, perm = FALSE, super = TRUE
)))[]
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[]\T1/pcr/m/n/9 rapply2 <- function(object, f, ...) rapply(object, f, , , how
= "list", ...)[]
Underfull \vbox (badness 10000) has occurred while \output is active
[2408]
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[] \T1/pcr/m/n/9 x = c(1, 6, 38, 10, 60, 103, -4, 6, -32, -247, -2, -
16, -128, -2, -67))[]
Underfull \vbox (badness 10000) has occurred while \output is active
[2409]
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[] \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4), j=c(2:4,1), x = 2,
dimnames=dns))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2614--2614
[] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
dimnames=dns))[]
[2410]
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[] \T1/pcr/m/n/9 a. <- sparseMatrix(i=4:1, j=1:4, dimnames=list(n4, n4), repr
="T") # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[]
[2411]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colMeans}
) has been already used, duplicate ignored
<to be read again>
\relax
l.2696 ...asA{colMeans}{colSums-methods}{colMeans}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colSums})
has been already used, duplicate ignored
<to be read again>
\relax
l.2704 \aliasA{colSums}{colSums-methods}{colSums}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowMeans}
) has been already used, duplicate ignored
<to be read again>
\relax
l.2711 ...asA{rowMeans}{colSums-methods}{rowMeans}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowSums})
has been already used, duplicate ignored
<to be read again>
\relax
l.2719 \aliasA{rowSums}{colSums-methods}{rowSums}
Underfull \hbox (badness 2922) in paragraph at lines 2771--2775
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i
n-her-it-ing from
Underfull \hbox (badness 1728) in paragraph at lines 2771--2775
\T1/ptm/m/n/10 class [][][]\T1/pcr/m/n/10 sparseVector[][][][]\T1/ptm/m/n/10 .
Only ap-pli-ca-ble when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 is in-her-it-ing fr
om a
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[][][]\T1/pcr/m/n/10 dimnames[][][](x) []\T1/ptm/m/n/10 are only kept (as [][][
]\T1/pcr/m/n/10 names[][][](v)[]\T1/ptm/m/n/10 ) when the re-sult-ing []\T1/pcr
/m/n/10 v []\T1/ptm/m/n/10 is [][][]\T1/pcr/m/n/10 numeric[][][][]\T1/ptm/m/n/1
0 , since
[2412]
[2413]
Underfull \hbox (badness 3547) in paragraph at lines 2888--2891
[]\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10
, the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when
[2414]
[2415]
[2416]
[2417]
[2418]
Underfull \hbox (badness 10000) in paragraph at lines 3290--3293
[]\T1/pcr/m/n/10 signature(from = "denseLU", logarithm = "logical")[]\T1/ptm/m/
n/10 : com-
[2419]
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[]\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m
atrix"), ...)[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 3352--3352
[] \T1/pcr/m/n/9 new( "pMatrix", Dim = c(n, n), Dimnames = c(dn[
1L], list(NULL)),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3355--3355
[] \T1/pcr/m/n/9 new("dtrMatrix", Dim = c(n, n), Dimnames = list(
NULL, NULL),[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 3358--3358
[] \T1/pcr/m/n/9 new("dtrMatrix", Dim = c(n, n), Dimnames = c(lis
t(NULL), dn[2L]),[]
[2420]
Underfull \hbox (badness 7379) in paragraph at lines 3486--3488
[]\T1/pcr/m/n/10 signature(x = "dgCMatrix")[]\T1/ptm/m/n/10 : com-putes the LU
de-com-po-si-tion of a square
[2421]
[2422]
[2423]
Underfull \hbox (badness 4846) in paragraph at lines 3707--3711
[]\T1/ptm/m/n/10 Note that both []\T1/pcr/m/n/10 new(.) []\T1/ptm/m/n/10 and []
[][]\T1/pcr/m/n/10 spMatrix[][][] []\T1/ptm/m/n/10 con-struc-tors for []\T1/pcr
/m/n/10 "dgTMatrix" []\T1/ptm/m/n/10 (and other
Underfull \hbox (badness 2717) in paragraph at lines 3712--3716
[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can be stored in
more than one pos-si-ble
[2424]
Underfull \hbox (badness 5231) in paragraph at lines 3757--3762
[]\T1/ptm/m/n/10 Construct a for-mally di-ag-o-nal [][][]\T1/pcr/m/n/10 Matrix[
][][][]\T1/ptm/m/n/10 , i.e., an ob-ject in-her-it-ing from vir-tual class
Overfull \hbox (84.78088pt too wide) in paragraph at lines 3768--3768
[]\T1/pcr/m/n/10 .sparseDiagonal(n, x = NULL, uplo = "U", shape = "t", unitri
= TRUE, kind, cols)[]
[2425]
Underfull \hbox (badness 10000) in paragraph at lines 3824--3827
[]\T1/pcr/m/n/10 .trDiagonal() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 .symDiagon
al() []\T1/ptm/m/n/10 are sim-ple wrap-pers, for
Underfull \hbox (badness 6792) in paragraph at lines 3824--3827
[]\T1/pcr/m/n/10 .sparseDiagonal(shape = "t") []\T1/ptm/m/n/10 and []\T1/pcr/m/
n/10 .sparseDiagonal(shape = "s")[]\T1/ptm/m/n/10 , re-spec-
[2426]
Underfull \hbox (badness 3646) in paragraph at lines 3901--3904
[]\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 dimnames[][][][]\T1/ptm/m/n/10 , a []
[][]\T1/pcr/m/n/10 list[][][][]\T1/ptm/m/n/10 , see the [][][]\T1/pcr/m/n/10 Ma
trix[][][] []\T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally
Underfull \hbox (badness 6542) in paragraph at lines 3936--3940
[]\T1/pcr/m/n/10 signature(x = "diagonalMatrix")[]\T1/ptm/m/n/10 : all these gr
oup meth-ods re-turn a
Underfull \hbox (badness 4518) in paragraph at lines 3945--3951
[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")[]\T1/ptm/m/n/10
: the re-sult is from class
[2427]
Underfull \hbox (badness 10000) in paragraph at lines 3952--3956
[]\T1/pcr/m/n/10 (object = "diagonalMatrix")[]\T1/ptm/m/n/10 : Re-turns an ob-j
ect of S3 class
Underfull \hbox (badness 2318) in paragraph at lines 3962--3966
[][][]\T1/pcr/m/n/10 Diagonal[][][]() []\T1/ptm/m/n/10 as con-struc-tor of thes
e ma-tri-ces, and [][][]\T1/pcr/m/n/10 isDiagonal[][][][]\T1/ptm/m/n/10 . [][][
]\T1/pcr/m/n/10 ddiMatrix[][][] []\T1/ptm/m/n/10 and
[2428]
[2429]
[2430]
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[]\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")[]\T1/ptm/m/n/10 :
this group con-tains
[2431]
[2432]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 4360--4360
[]\T1/pcr/m/n/9 stopifnot(all.equal(S9p0, S9p))# same as as default, but diffe
rent from the random one[]
[2433]
Underfull \hbox (badness 2469) in paragraph at lines 4474--4477
[]\T1/pcr/m/n/10 signature(x = "dpoMatrix")[]\T1/ptm/m/n/10 : Re-turns the [][]
[]\T1/pcr/m/n/10 determinant[][][] []\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 x[]\T1/
ptm/m/n/10 , via
[2434]
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[]\T1/ptm/m/n/10 Currently the va-lid-ity meth-ods for these classes such as
Underfull \hbox (badness 2020) in paragraph at lines 4497--4502
[][][]\T1/pcr/m/n/10 getValidity[][][](getClass("dpoMatrix")) []\T1/ptm/m/n/10
for ef-fi-ciency rea-sons only check the di-
Underfull \hbox (badness 1748) in paragraph at lines 4503--4512
\T1/pcr/m/n/10 error=identity), "error") []\T1/ptm/m/n/10 . In-deed, when \T1/p
tm/m/it/10 co-erc-ing \T1/ptm/m/n/10 to these classes, a ver-sion
Underfull \hbox (badness 1590) in paragraph at lines 4503--4512
\T1/ptm/m/n/10 of [][][]\T1/pcr/m/n/10 Cholesky[][][]() []\T1/ptm/m/n/10 or [][
][]\T1/pcr/m/n/10 chol[][][]() []\T1/ptm/m/n/10 is typ-i-cally used, e.g., see
[]\T1/pcr/m/n/10 selectMethod("coerce",
Underfull \hbox (badness 6675) in paragraph at lines 4559--4566
[]\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 Matrix[][][][]\T1/ptm/m/n/10 , typ-i-ca
lly in-her-it-ing from vir-tual class [][][]\T1/pcr/m/n/10 sparseMatrix[][][][]
\T1/ptm/m/n/10 .
Underfull \hbox (badness 6493) in paragraph at lines 4559--4566
[][][]\T1/pcr/m/n/10 denseMatrix[][][] []\T1/ptm/m/n/10 and tra-di-tional vec-t
ors and ma-tri-ces are co-erced to
[2435]
Underfull \hbox (badness 10000) in paragraph at lines 4574--4582
[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing if the re-sult must in-herit from vi
r-tual class
Underfull \hbox (badness 1365) in paragraph at lines 4574--4582
[][][]\T1/pcr/m/n/10 CsparseMatrix[][][][]\T1/ptm/m/n/10 . If []\T1/pcr/m/n/10
FALSE []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 in-her-its from
[][][]\T1/pcr/m/n/10 RsparseMatrix[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4597--4600
[]\T1/ptm/m/n/10 Function [][][]\T1/pcr/m/n/10 sparseMatrix[][][][]\T1/ptm/m/n/
10 , for con-struct-ing ob-jects in-her-it-ing from vir-tual class
[2436]
Underfull \hbox (badness 10000) in paragraph at lines 4641--4645
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10
new("dsCMatrix", ...) []\T1/ptm/m/n/10 or
Underfull \hbox (badness 2103) in paragraph at lines 4641--4645
[]\T1/pcr/m/n/10 new("dsTMatrix", ...)[]\T1/ptm/m/n/10 , or au-to-mat-i-cally v
ia e.g., []\T1/pcr/m/n/10 as(*, "symmetricMatrix")[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1571) in paragraph at lines 4691--4694
[]\T1/pcr/m/n/10 signature(x = "dsCMatrix", pivot = "logical")[]\T1/ptm/m/n/10
: Re-turns (and stores) the
[2437]
[2438]
Underfull \hbox (badness 1221) in paragraph at lines 4834--4837
[]\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "dMatrix"[]\T1/ptm/m/n/10 , by class []
\T1/pcr/m/n/10 "dsparseMatrix"[]\T1/ptm/m/n/10 ; class []\T1/pcr/m/n/10 "sparse
Matrix"[]\T1/ptm/m/n/10 , by classes
Underfull \hbox (badness 1400) in paragraph at lines 4844--4847
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")[]\T1/ptm/m/n/10
: if []\T1/pcr/m/n/10 uplo ==
[2439]
Underfull \hbox (badness 10000) in paragraph at lines 4896--4898
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10
new("dsyMatrix", ...) []\T1/ptm/m/n/10 or
Underfull \hbox (badness 1365) in paragraph at lines 4932--4935
[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")[]\T1/ptm/m/n/10
, or []\T1/pcr/m/n/10 x = "dsyMatrix"
[2440]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4978--4978
[]\T1/pcr/m/n/9 stopifnot(all(S1 == S2)) # equal "seen as matrix", but differ
internally :[]
[2441]
[2442]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5084--5084
[]\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim
= c(5L, 5L),[]
Underfull \hbox (badness 3635) in paragraph at lines 5139--5143
[]\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ddenseMatrix"[]\T1/ptm/m/n/10 , di-rec
tly. Class []\T1/pcr/m/n/10 "triangularMatrix"[]\T1/ptm/m/n/10 , di-rectly. Cla
ss
Underfull \hbox (badness 10000) in paragraph at lines 5148--5151
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")[]\T1/ptm/m/n/10 :
Ma-trix mul-ti-pli-ca-tion;
Underfull \hbox (badness 10000) in paragraph at lines 5151--5155
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")[]\T1/ptm/m/n
/10 : the
[2443]
[2444]
[2445]
[2446]
Underfull \hbox (badness 10000) in paragraph at lines 5399--5401
[]\T1/ptm/m/n/10 a ma-trix fac-tor-iza-tion, typ-i-cally in-her-it-ing from vir
-tual class
Overfull \hbox (29.27832pt too wide) in paragraph at lines 5418--5418
[] \T1/pcr/m/n/10 all.equal(as(x, "matrix"), as(Reduce(\TS1/cmtt/m/n/10 `\T
1/pcr/m/n/10 %*%\TS1/cmtt/m/n/10 `\T1/pcr/m/n/10 , expand2(y)), "matrix"))
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[] []
[2447]
Underfull \hbox (badness 7064) in paragraph at lines 5477--5494
[]\T1/pcr/m/n/10 signature(x = "p?BunchKaufman")[]\T1/ptm/m/n/10 : ex-pands the
fac-tor-iza-tion $\OML/cmm/m/it/10 A \OT1/cmr/m/n/10 =
Underfull \hbox (badness 3000) in paragraph at lines 5506--5513
[]\T1/pcr/m/n/10 signature(x = "denseLU")[]\T1/ptm/m/n/10 : ex-pands the fac-to
r-iza-tion $\OML/cmm/m/it/10 A \OT1/cmr/m/n/10 = \OML/cmm/m/it/10 P[]LU$ \T1/pt
m/m/n/10 as
Underfull \hbox (badness 2735) in paragraph at lines 5522--5529
[]\T1/pcr/m/n/10 signature(x = "CHMfactor")[]\T1/ptm/m/n/10 : as []\T1/pcr/m/n/
10 expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/pcr/m/n/10 list(P, L)[]\T1/p
tm/m/n/10 .
Underfull \hbox (badness 1337) in paragraph at lines 5529--5544
[]\T1/pcr/m/n/10 signature(x = "sparseLU")[]\T1/ptm/m/n/10 : as []\T1/pcr/m/n/1
0 expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/pcr/m/n/10 list(P, L, U,
Underfull \hbox (badness 2680) in paragraph at lines 5529--5544
\T1/pcr/m/n/10 Q)[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 expand(x)[["Q"]] []\T1/ptm
/m/n/10 and []\T1/pcr/m/n/10 expand2(x)[["P2."]] []\T1/ptm/m/n/10 rep-re-sent t
he same per-
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\T1/ptm/m/n/10 mu-ta-tion ma-trix $\OML/cmm/m/it/10 P[]$ \T1/ptm/m/n/10 but hav
e op-po-site []\T1/pcr/m/n/10 margin []\T1/ptm/m/n/10 slots and in-verted []\T1
/pcr/m/n/10 perm []\T1/ptm/m/n/10 slots.
Underfull \hbox (badness 2073) in paragraph at lines 5544--5549
[]\T1/pcr/m/n/10 signature(x = "denseLU")[]\T1/ptm/m/n/10 : as []\T1/pcr/m/n/10
expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/pcr/m/n/10 list(L, U, P)[]\T1/
ptm/m/n/10 .
[2448]
[2449]
[2450]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5752--5752
[]\T1/pcr/m/n/9 str(pores <- readMM(system.file("external/pores_1.mtx", packag
e = "Matrix")))[]
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[]\T1/pcr/m/n/9 str(utm <- readHB(system.file("external/utm300.rua" , packag
e = "Matrix")))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5754--5754
[]\T1/pcr/m/n/9 str(lundA <- readMM(system.file("external/lund_a.mtx" , packag
e = "Matrix")))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5755--5755
[]\T1/pcr/m/n/9 str(lundA <- readHB(system.file("external/lund_a.rsa" , packag
e = "Matrix")))[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5756--5756
[]\T1/pcr/m/n/9 ## https://math.nist.gov/MatrixMarket/data/Harwell-Boeing/coun
terx/counterx.htm[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5757--5757
[]\T1/pcr/m/n/9 str(jgl <- readMM(system.file("external/jgl009.mtx" , packag
e = "Matrix")))[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5763--5763
[]\T1/pcr/m/n/9 u. <- url("https://www.cise.ufl.edu/research/sparse/RB/Boeing/
msc00726.tar.gz")[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5768--5768
[]\T1/pcr/m/n/9 ## Store as MatrixMarket (".mtx") file, here inside temporary
dir./folder:[]
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[]\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of
the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[]
[2451]
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[]\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume
nts to sparseMatrix():[]
[2452]
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[] \T1/pcr/m/n/9 all.equal(facmul(x, nm, y, trans = TRUE, left = TRUE),
crossprod(L, y))[]
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[] \T1/pcr/m/n/9 all.equal(facmul(x, nm, y, trans = TRUE, left = FALSE), t
crossprod(y, L))[]
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[]\T1/pcr/m/n/10 .diag2dense(from, kind = ".", shape = "t", packed = FALSE, up
lo = "U")[]
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[]\T1/pcr/m/n/10 .m2dense(from, class = ".ge", uplo = "U", diag = "N", trans =
FALSE)[]
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[]\T1/pcr/m/n/10 .diag2sparse(from, kind = ".", shape = "t", repr = "C", uplo
= "U")[]
[2453]
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[]\T1/pcr/m/n/10 .m2sparse(from, class = ".gC", uplo = "U", diag = "N", trans
= FALSE)[]
Underfull \hbox (badness 10000) in paragraph at lines 6000--6002
[]\T1/ptm/m/n/10 a string in []\T1/pcr/m/n/10 c("trace", "sumLog", "prod", "min
", "max",
[2454]
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[][]\T1/pcr/m/n/10 .solve.dgC.*(a, b)[]\T1/ptm/b/n/10 : []\T1/pcr/m/n/10 .solv
e.dgC.lu(a, b) []\T1/ptm/m/n/10 needs a square ma-trix []\T1/pcr/m/n/10 a[]\T1/
ptm/m/n/10 .
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[]\T1/pcr/m/n/10 .solve.dgC.qr(a, b) []\T1/ptm/m/n/10 needs a ``long'' ma-trix
[]\T1/pcr/m/n/10 a[]\T1/ptm/m/n/10 , with []\T1/pcr/m/n/10 nrow(a) >= ncol(a)[]
\T1/ptm/m/n/10 .
[2455]
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[][]\T1/pcr/m/n/10 .updateCHMfactor(object, parent, mult)[]\T1/ptm/b/n/10 : []
\T1/pcr/m/n/10 .updateCHMfactor []\T1/ptm/m/n/10 up-
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\T1/ptm/m/n/10 dates []\T1/pcr/m/n/10 object []\T1/ptm/m/n/10 with the re-sult
of Cholesky fac-tor-iz-ing []\T1/pcr/m/n/10 F(parent) + mult[1] *
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\T1/pcr/m/n/10 diag(nrow(parent))[]\T1/ptm/m/n/10 , i.e., []\T1/pcr/m/n/10 F(pa
rent) []\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 mult[1] []\T1/ptm/m/n/10 times the
iden-tity ma-trix,
[2456]
[2457]
[2458]
[2459]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.image}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.6399 \aliasA{image}{image-methods}{image}
[2460]
[2461]
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[]\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][
][]\T1/pcr/m/n/10 dgTMatrix[][][] []\T1/ptm/m/n/10 class. Use
Overfull \hbox (47.58038pt too wide) in paragraph at lines 6514--6514
[]\T1/pcr/m/n/9 stopifnot(!is.null(leg <- imgC$legend), is.list(leg$right)) #
failed for 2 days ..[]
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[]\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col
/row) indices:[]
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[] \T1/pcr/m/n/9 I2 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE,
border.col=NA)[]
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[] \T1/pcr/m/n/9 I3 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd
=2, border.col=NA)[]
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[]\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor
der.col = adjustcolor("skyblue", 1/2))[]
[2462]
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[]\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a
nti-aliasing[]
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[] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[]
[2463]
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[]\T1/pcr/m/n/10 signature(x = "indMatrix", y = "Matrix") []\T1/ptm/m/n/10 and
oth-ers listed by
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[]\T1/pcr/m/n/10 showMethods("%*%", classes = "indMatrix")[]\T1/ptm/m/n/10 : ma
-trix prod-ucts im-ple-mented
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[]\T1/pcr/m/n/10 signature(from = "numeric", to = "indMatrix")[]\T1/ptm/m/n/10
: sup-port-ing typ-i-cal
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[]\T1/pcr/m/n/10 signature(from = "list", to = "indMatrix")[]\T1/ptm/m/n/10 : s
up-port-ing []\T1/pcr/m/n/10 indMatrix
[2464]
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[]\T1/pcr/m/n/10 signature(x = "indMatrix")[]\T1/ptm/m/n/10 : row and
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[]\T1/pcr/m/n/10 signature(X = "indMatrix", Y = "indMatrix")[]\T1/ptm/m/n/10 :
Kro-necker prod-uct of
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[]\T1/ptm/m/n/10 Fabian Scheipl at `\T1/pcr/m/n/10 uni-muenchen.de\T1/ptm/m/n/1
0 ', build-ing on the ex-ist-ing class [][][]\T1/pcr/m/n/10 pMatrix[][][] []\T1
/ptm/m/n/10 af-ter
Underfull \hbox (badness 1253) in paragraph at lines 6717--6726
\T1/ptm/m/n/10 a nice hike's con-ver-sa-tion with Mar-tin Maech-ler. Meth-ods f
or [][][]\T1/pcr/m/n/10 crossprod[][][](x, y) []\T1/ptm/m/n/10 and
[2465]
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[]\T1/ptm/m/n/10 an in-te-ger off-set, in-di-cat-ing that the re-sult should be
a per-mu-ta-tion of
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[]\T1/pcr/m/n/10 invertPerm(p) []\T1/ptm/m/n/10 re-turns an in-te-ger vec-tor o
f length []\T1/pcr/m/n/10 length(p) []\T1/ptm/m/n/10 such that
Underfull \hbox (badness 4441) in paragraph at lines 6837--6841
[]\T1/pcr/m/n/10 p[invertPerm(p)] []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 invertP
erm(p)[p] []\T1/ptm/m/n/10 are both []\T1/pcr/m/n/10 seq_along(p)[]\T1/ptm/m/n/
10 , i.e., the
[2466]
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[]\T1/pcr/m/n/9 ## Product of transpositions (1 2)(2 1)(4 3)(6 8)(10 1) = (3 4
)(6 8)(1 10)[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.anyNA}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.6888 \aliasA{anyNA}{is.na-methods}{anyNA}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.finite
}) has been already used, duplicate ignored
<to be read again>
\relax
l.6895 ...asA{is.finite}{is.na-methods}{is.finite}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.infini
te}) has been already used, duplicate ignored
<to be read again>
\relax
l.6903 ...is.infinite}{is.na-methods}{is.infinite}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.na}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.6911 \aliasA{is.na}{is.na-methods}{is.na}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.nan})
has been already used, duplicate ignored
<to be read again>
\relax
l.6918 \aliasA{is.nan}{is.na-methods}{is.nan}
[2467]
[2468]
[2469]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.isSymmetr
ic}) has been already used, duplicate ignored
<to be read again>
\relax
l.7077 ...etric}{isSymmetric-methods}{isSymmetric}
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[]\T1/pcr/m/n/10 isSymmetric(object, checkDN = TRUE, tol = 100 * .Machine$doub
le.eps, tol1 = 8 * tol, ...)[]
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[]\T1/pcr/m/n/10 isSymmetric(object, checkDN = TRUE, tol = 100 * .Machine$doub
le.eps, ...)[]
[2470]
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[]\T1/pcr/m/n/9 isSymmetric(as(M, "generalMatrix")) # still symmetric, even if
not "formally"[]
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[]\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs = TRUE) # includes S3 g
eneric from base[]
[2471]
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[]\T1/pcr/m/n/9 isTriangular(as(M, "generalMatrix")) # still triangular, even
if not "formally"[]
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[]\T1/pcr/m/n/10 KhatriRao(X, Y = X, FUN = "*", sparseY = TRUE, make.dimnames
= FALSE)
[2472]
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[]\T1/pcr/m/n/9 stopifnot(all(K1 <- KhatriRao(nd, zm) == 0), identical(dim(K1)
, c(12L, 4L)),[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7372--7372
[] \T1/pcr/m/n/9 all(K2 <- KhatriRao(zm, nd) == 0), identical(dim(K2)
, c(12L, 4L)))[]
[2473]
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[] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), d
imnames(Kmd)))[]
[2474]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.kronecker
}) has been already used, duplicate ignored
<to be read again>
\relax
l.7453 ...kronecker}{kronecker-methods}{kronecker}
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[]\T1/pcr/m/n/10 ldenseMatrix []\T1/ptm/m/n/10 is the vir-tual class of all den
se \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2475]
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[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-call
y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2476
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.*,ndiMatr
ix,Matrix.Rdash.method}) has been already used, duplicate ignored
<argument> ...shipout:D \box_use:N \l_shipout_box
\__shipout_drop_firstpage_...
l.7691 C
lass \code{"\LinkA{sparseMatrix}{sparseMatrix.Rdash.class}"}, by cla...
]
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[]\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ldenseMatrix"[]\T1/ptm/m/n/10 , di-rec
tly. Class []\T1/pcr/m/n/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/
10 "ldenseMatrix"[]\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "denseMatrix"[]\T1/ptm/m/n/10 , by class
[]\T1/pcr/m/n/10 "ldenseMatrix"[]\T1/ptm/m/n/10 . Class []\T1/pcr/m/n/10 "Matri
x"[]\T1/ptm/m/n/10 , by class
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[]\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n
/10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/
10 ); use, e.g.,
[2477]
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[]\T1/pcr/m/n/10 lsTMatrix[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 ltTMatrix[]\T
1/ptm/m/n/10 ) or in com-pressed column-oriented form (class
Underfull \hbox (badness 1242) in paragraph at lines 7804--7814
[][][]\T1/pcr/m/n/10 CsparseMatrix[][][][]\T1/ptm/m/n/10 , sub-classes []\T1/pc
r/m/n/10 lgCMatrix[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lsCMatrix[]\T1/ptm/m/n/10
, and []\T1/pcr/m/n/10 ltCMatrix[]\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\
T1/ptm/m/n/10 --in
[2478]
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[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cal
ly equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2479]
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[]\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n
/10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/
10 ; use, e.g.,
[2480]
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[]\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n
/10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/
10 ; use, e.g.,
[2481]
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[2483]
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[]\T1/ptm/m/n/10 vector of all non-zero en-tries of []\T1/pcr/m/n/10 x[]\T1/ptm
/m/n/10 ; ex-ists \T1/ptm/b/n/10 only \T1/ptm/m/n/10 when []\T1/pcr/m/n/10 as(x
,
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[]\T1/pcr/m/n/10 mat2triplet() []\T1/ptm/m/n/10 is con-cep-tu-ally the \T1/ptm/
m/it/10 in-verse \T1/ptm/m/n/10 func-tion of [][][]\T1/pcr/m/n/10 spMatrix[][][
] []\T1/ptm/m/n/10 and (one case of)
[2484]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rpcent.*
.Rpcent.}) has been already used, duplicate ignored
<to be read again>
\relax
l.8313 ...*\%}{matmult-methods}{.Rpcent.*.Rpcent.}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.crossprod
}) has been already used, duplicate ignored
<to be read again>
\relax
l.8387 ...A{crossprod}{matmult-methods}{crossprod}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tcrosspro
d}) has been already used, duplicate ignored
<to be read again>
\relax
l.8463 ...tcrossprod}{matmult-methods}{tcrossprod}
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\T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][][]\T1/
pcr/m/n/10 t[][][](.)[]\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn
[2485]
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[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")[]\T1/ptm/m/n/10 :
Ma-trix mul-ti-pli-ca-tion;
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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and
other sig-na-tures (use
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[]\T1/pcr/m/n/10 showMethods("%*%", class="dtrMatrix")[]\T1/ptm/m/n/10 ): ma-tr
ix mul-ti-pli-ca-tion. Mul-ti-
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\T1/ptm/m/n/10 sig-na-tures, use []\T1/pcr/m/n/10 showMethods("crossprod", clas
s = "dgeMatrix")[]\T1/ptm/m/n/10 , ma-trix
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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and
other sig-na-
[2486]
[2487]
[2488]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det}) has
been already used, duplicate ignored
<to be read again>
\relax
l.8859 \aliasA{det}{Matrix-class}{det}
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[]\T1/pcr/m/n/10 signature(x = "Matrix", value = "list")[]\T1/ptm/m/n/10 : set
the []\T1/pcr/m/n/10 dimnames []\T1/ptm/m/n/10 to a
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[2489]
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[]\T1/pcr/m/n/10 signature(from = "ANY", to = "Matrix")[]\T1/ptm/m/n/10 : This
re-lies on a cor-rect
[2490]
[2491]
Underfull \hbox (badness 10000) in paragraph at lines 9128--9132
[]\T1/pcr/m/n/10 CholeskyFactorization[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Bunch
KaufmanFactorization[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 signature(x = "MatrixFactorization", logarithm =
Underfull \hbox (badness 10000) in paragraph at lines 9168--9171
[]\T1/pcr/m/n/10 signature(obj = "MatrixFactorization")[]\T1/ptm/m/n/10 : re-tu
rns []\T1/pcr/m/n/10 obj []\T1/ptm/m/n/10 with
Underfull \hbox (badness 3019) in paragraph at lines 9177--9180
[]\T1/ptm/m/n/10 Classes ex-tend-ing []\T1/pcr/m/n/10 CholeskyFactorization[]\T
1/ptm/m/n/10 , namely [][][]\T1/pcr/m/n/10 Cholesky[][][][]\T1/ptm/m/n/10 , [][
][]\T1/pcr/m/n/10 pCholesky[][][][]\T1/ptm/m/n/10 , and
[2492]
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[]\T1/ptm/m/n/10 Classes ex-tend-ing []\T1/pcr/m/n/10 BunchKaufmanFactorization
[]\T1/ptm/m/n/10 , namely [][][]\T1/pcr/m/n/10 BunchKaufman[][][] []\T1/ptm/m/n
/10 and
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[]\T1/ptm/m/n/10 Generic func-tions [][][]\T1/pcr/m/n/10 expand1[][][] []\T1/pt
m/m/n/10 and [][][]\T1/pcr/m/n/10 expand2[][][] []\T1/ptm/m/n/10 for con-struct
-ing ma-trix fac-tors from
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[]\T1/pcr/m/n/10 ndenseMatrix []\T1/ptm/m/n/10 is the vir-tual class of all den
se \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
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[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-call
y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2493]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if []\T1/pcr/m/n/10 X <- (X + t(X))/2 []
\T1/ptm/m/n/10 should be done, af-ter []\T1/pcr/m/n/10 X <-
[2494]
[2495]
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[] \T1/pcr/m/n/9 all.equal(n.A.m, unname(as.matrix(n.A$mat)), tolerance = 1e
-15)# seen rel.d.= 1.46e-16[]
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[]\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a
ll in this example[]
[2496]
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[]\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ndenseMatrix"[]\T1/ptm/m/n/10 , di-rec
tly. Class []\T1/pcr/m/n/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/
10 "ndenseMatrix"[]\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 9510--9515
\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "denseMatrix"[]\T1/ptm/m/n/10 , by class
[]\T1/pcr/m/n/10 "ndenseMatrix"[]\T1/ptm/m/n/10 . Class []\T1/pcr/m/n/10 "Matri
x"[]\T1/ptm/m/n/10 , by class
Underfull \hbox (badness 10000) in paragraph at lines 9518--9521
[]\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n
/10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/
10 ); use, e.g.,
[2497]
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[]\T1/pcr/m/n/10 signature(from = "matrix", to = "nMatrix")[]\T1/ptm/m/n/10 : N
ote that these co-er-cions
[2498]
Underfull \hbox (badness 1867) in paragraph at lines 9699--9701
[]\T1/ptm/m/n/10 fast sim-
[2499]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.norm}) ha
s been already used, duplicate ignored
<to be read again>
\relax
l.9741 \aliasA{norm}{norm-methods}{norm}
[2500]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9836--9836
[]\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x) ## 8 x 10
"dgCMatrix"[]
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[]\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
"dsCMatrix"[]
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[]\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
"dtCMatrix"[]
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[]\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][][]\T1/pcr/m/n
/10 TsparseMatrix[][][][]\T1/ptm/m/n/10 , sub-classes []\T1/pcr/m/n/10 ngTMatri
x[]\T1/ptm/m/n/10 ,
[2501]
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[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cal
ly equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2502]
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[]\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n
/10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/
10 ; use, e.g.,
[2503]
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[]\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n
/10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/
10 ; use, e.g.,
[2504]
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[]\T1/ptm/m/n/10 typically a []\T1/pcr/m/n/10 "packedMatrix"[]\T1/ptm/m/n/10 ,
though
[2505]
[2506]
[2507]
Underfull \hbox (badness 10000) in paragraph at lines 10386--10389
[]\T1/pcr/m/n/10 signature(x = "pMatrix", y = "Matrix") []\T1/ptm/m/n/10 and ot
h-ers listed by
Underfull \hbox (badness 8189) in paragraph at lines 10386--10389
[]\T1/pcr/m/n/10 showMethods("%*%", classes = "pMatrix")[]\T1/ptm/m/n/10 : ma-t
rix prod-ucts im-ple-mented
Underfull \hbox (badness 10000) in paragraph at lines 10389--10393
[]\T1/pcr/m/n/10 signature(from = "numeric", to = "pMatrix")[]\T1/ptm/m/n/10 :
sup-port-ing typ-i-cal
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[]\T1/pcr/m/n/10 signature(a = "pMatrix", b = "missing")[]\T1/ptm/m/n/10 : the
in-verse per-mu-ta-tion ma-trix,
[2508]
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[] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD
iag = TRUE,[]
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[]\T1/pcr/m/n/10 printSpMatrix(x, digits = NULL, maxp = max(100L, getOption("m
ax.print")),[]
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[] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[]
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[]\T1/pcr/m/n/10 printSpMatrix2(x, digits = NULL, maxp = max(100L, getOption("
max.print")),[]
[2509]
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[] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[]
Underfull \hbox (badness 3989) in paragraph at lines 10502--10512
[]\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of []
\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 should
Underfull \hbox (badness 10000) in paragraph at lines 10502--10512
\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2510]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr}) has
been already used, duplicate ignored
<to be read again>
\relax
l.10604 \aliasA{qr}{qr-methods}{qr}
[2511]
[2512]
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[] \T1/pcr/m/n/9 all.equal(qr.coef(qr.A1, b), drop(solve(crossprod(A1), cro
ssprod(A1, b))))[]
[2513]
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[] \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 qr.coef\TS1/pcr/m/n/9 ' \
T1/pcr/m/n/9 computes unique least squares solution of "nearby" problem[]
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[] \T1/pcr/m/n/9 ## Z x = b for some full rank Z ~ A, currently without war
ning {FIXME} ![]
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[]\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m
atrix"), ...)[]
Underfull \vbox (badness 10000) has occurred while \output is active
[2514]
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[]\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of [][][]\T1/pcr/m/n/10
qr[][][](x, tol,
Underfull \hbox (badness 10000) in paragraph at lines 10865--10868
[]\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense []\T1/pcr/m/n/10 x[]\
T1/ptm/m/n/10 , it cor-re-sponds to
[2515]
[2516]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 10962--10962
[]\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/
n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale
free"[]
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[]\T1/pcr/m/n/9 sapply(meths, function(.m.) rankMatrix(M15, method = .m., tol
= 1e-7)) # all 14[]
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[]\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L))) # war
ning+ ~1.5 sec (2013)[]
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[]\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con
siderably faster![]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.11005 \aliasA{rcond}{rcond-methods}{rcond}
[2517]
[2518]
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[]\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
have full rank[]
[2519]
[2520]
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\T1/ptm/m/n/10 dices, if not []\T1/pcr/m/n/10 symmetric [][]sample.int[][][](nr
ow*ncol, nnz)[]\T1/ptm/m/n/10 , then---if []\T1/pcr/m/n/10 rand.x []\T1/ptm/m/n
/10 is not
[2521]
[2522]
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[]\T1/ptm/m/n/10 Class [][][]\T1/pcr/m/n/10 SchurFactorization[][][][]\T1/ptm/m
/n/10 , di-rectly. Class [][][]\T1/pcr/m/n/10 MatrixFactorization[][][][]\T1/pt
m/m/n/10 , by class
[2523]
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[]\T1/pcr/m/n/10 signature(from = "Schur", logarithm = "logical")[]\T1/ptm/m/n/
10 : com-putes
[2524]
[2525]
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[] \T1/pcr/m/n/9 all.equal(e1, e3[order(Mod(e3), decreasing = TRUE)], toler
ance = 1e-13)[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solve}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.11633 \aliasA{solve}{solve-methods}{solve}
[2526]
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[]\T1/pcr/m/n/10 solve(a, b, system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "
D", "P", "Pt"), ...)[]
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[]\T1/ptm/m/n/10 a vec-tor, [][][]\T1/pcr/m/n/10 sparseVector[][][][]\T1/ptm/m/
n/10 , ma-trix, or [][][]\T1/pcr/m/n/10 Matrix[][][] []\T1/ptm/m/n/10 sat-is-fy
-ing []\T1/pcr/m/n/10 NROW(b) ==
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[]\T1/ptm/m/n/10 Methods for dense []\T1/pcr/m/n/10 a []\T1/ptm/m/n/10 are buil
t on 14 LA-PACK rou-tines: class []\T1/pcr/m/n/10 d..Matrix[]\T1/ptm/m/n/10 , w
here
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[]\T1/ptm/m/n/10 Methods for sparse []\T1/pcr/m/n/10 a []\T1/ptm/m/n/10 are bui
lt on CXS-parse rou-tines []\T1/pcr/m/n/10 cs_lsolve[]\T1/ptm/m/n/10 , []\T1/pc
r/m/n/10 cs_usolve[]\T1/ptm/m/n/10 , and
[2527]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 11892--11892
[]\T1/pcr/m/n/9 image(ia0 <- solve(a, tol = 0)) # checker board, dense [but re
ally, a is singular!][]
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[] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on
[FIXME ??] only[]
[2528]
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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, from a for-mu
la and data frame
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[] \T1/pcr/m/n/10 drop.unused.levels = TRUE, repr = c("C", "R", "T"), giveC
sparse)[]
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[] \T1/pcr/m/n/10 drop.unused.levels = TRUE, repr = c("C", "R", "T"), giveC
sparse,[]
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[]\T1/ptm/m/n/10 a data frame cre-ated with [][][]\T1/pcr/m/n/10 model.frame[][
][][]\T1/ptm/m/n/10 . If an-other sort of ob-ject,
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[]\T1/ptm/m/n/10 character string or []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or
(co-er-ca-ble to)
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[]\T1/pcr/m/n/10 "[][]sparseMatrix[][][]"[]\T1/ptm/m/n/10 , spec-i-fy-ing the c
on-trasts to be ap-plied to the
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[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for
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[]\T1/pcr/m/n/10 sparse.model.matrix []\T1/ptm/m/n/10 has been changed to []\T1
/pcr/m/n/10 FALSE[]\T1/ptm/m/n/10 , 2010-07, for
[2529]
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[][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/
m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc
r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse
Underfull \hbox (badness 3291) in paragraph at lines 12008--12013
[]\T1/pcr/m/n/10 model.Matrix(sparse = TRUE) []\T1/ptm/m/n/10 from pack-age [][
]\T1/ptm/b/n/10 Ma-trix-Mod-els[][] \T1/ptm/m/n/10 may be nowa-days be
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\T1/ptm/m/n/10 prefer-able to []\T1/pcr/m/n/10 sparse.model.matrix[]\T1/ptm/m/n
/10 , as []\T1/pcr/m/n/10 model.Matrix []\T1/ptm/m/n/10 re-turns an ob-ject of
class
[2530]
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[] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M)
== c(0, 0),[]
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[] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M)
== c(3, 0),[]
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[] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
== c(0,12),[]
[2531]
Underfull \hbox (badness 2961) in paragraph at lines 12125--12128
[]\T1/pcr/m/n/10 signature(from = "sparseLU", logarithm = "logical")[]\T1/ptm/m
/n/10 : com-
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[]\T1/pcr/m/n/9 A <- as(readMM(system.file("external", "pores_1.mtx", package
= "Matrix")),[]
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[]\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m
atrix"), ...)[]
[2532]
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[] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(dn[1L
], list(NULL)),[]
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[] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(list(
NULL), dn[2L]),[]
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[]\T1/ptm/m/n/10 This in-ter-face is rec-om-mended over di-rect con-struc-tion
via calls such as
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[] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 =
TRUE,[]
[2533]
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\T1/ptm/m/n/10 of the sparse ma-trix re-sult, i.e., spec-i-fy-ing one of the vi
r-tual classes
[2534]
Underfull \hbox (badness 10000) in paragraph at lines 12348--12351
[]\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][][]\T1/pcr/m/n/10 xtabs[][][
](*, sparse=TRUE)[]\T1/ptm/m/n/10 , for sparse ta-bles and
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[]\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x)) ## 8 x 10
"dgCMatrix"[]
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[]\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
"dsCMatrix"[]
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[]\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
"dtCMatrix"[]
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[]\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims
= c(10,20)))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12374--12374
[]\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[]
[2535]
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[]\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
if necessary:[]
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[]\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x =
1:6, dimnames = dn)[]
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[]\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep
resentations.[]
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[] \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack
age = "SparseM"))) {[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12429--12429
[] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
X@dimension)[]
[2536]
Underfull \hbox (badness 6842) in paragraph at lines 12519--12522
[]\T1/pcr/m/n/10 (x = "sparseMatrix", logarithm=TRUE)[]\T1/ptm/m/n/10 : [][][]\
T1/pcr/m/n/10 determinant[][][]() []\T1/ptm/m/n/10 meth-ods
Underfull \hbox (badness 10000) in paragraph at lines 12554--12558
[][][]\T1/pcr/m/n/10 sparseMatrix[][][][]\T1/ptm/m/n/10 , and its ref-er-ences,
such as [][][]\T1/pcr/m/n/10 xtabs[][][](*, sparse=TRUE)[]\T1/ptm/m/n/10 , or
[2537]
[2538]
Underfull \hbox (badness 2961) in paragraph at lines 12738--12741
[]\T1/pcr/m/n/10 signature(from = "sparseQR", logarithm = "logical")[]\T1/ptm/m
/n/10 : com-
[2539]
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[]\T1/ptm/m/n/10 The many aux-il-iary func-tions for QR fac-tor-iza-tions: [][]
[]\T1/pcr/m/n/10 qr.Q[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 qr.R[][][][]
\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 qr.X[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc
r/m/n/10 qr.coef[][][][]\T1/ptm/m/n/10 ,
[2540]
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[]\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m
atrix"), ...)[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 12864--12864
[] \T1/pcr/m/n/9 new("pMatrix", Dim = c(m, m), Dimnames = c(dn[1L
], list(NULL)),[]
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[] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(list(
NULL), dn[2L]),[]
Underfull \vbox (badness 10000) has occurred while \output is active
[2541]
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[] \T1/pcr/m/n/9 ae2(qrc <- qr.coef (qr.A, b), with(e.qr.A, solve(R1 %*% P
2., t(qrQ)) %*% b))[]
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[]\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case
a
[2542]
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[]\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class []\T1/pcr/m/
n/10 "sparseVector" []\T1/ptm/m/n/10 has the five ac-
Underfull \hbox (badness 3679) in paragraph at lines 13044--13050
\T1/ptm/m/n/10 tual daugh-ter classes []\T1/pcr/m/n/10 "dsparseVector"[]\T1/ptm
/m/n/10 , []\T1/pcr/m/n/10 "isparseVector"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "
lsparseVector"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") []\T1/ptm/m/
n/10 co-erces sparse
[2543]
Underfull \hbox (badness 10000) in paragraph at lines 13123--13128
[]\T1/pcr/m/n/10 (x = "nsparseVector")[]\T1/ptm/m/n/10 : re-turn [][][]\T1/pcr/
m/n/10 logical[][][] []\T1/ptm/m/n/10 or
Underfull \hbox (badness 10000) in paragraph at lines 13141--13143
[][][]\T1/pcr/m/n/10 sparseVector[][][]() []\T1/ptm/m/n/10 for friendly con-str
uc-tion of sparse vec-tors (apart from []\T1/pcr/m/n/10 as(*,
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[2545]
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[]\T1/pcr/m/n/10 spMatrix(nrow, ncol, i = integer(0L), j = integer(0L), x = do
uble(0L))
Underfull \hbox (badness 2310) in paragraph at lines 13264--13270
[][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) []\T1/ptm/m/n/10 for the more
usual con-struc-tor of such ma-tri-ces. Then,
[2546]
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}) has been already used, duplicate ignored
<to be read again>
\relax
l.13316 ...\Rdash{}}{subassign-methods}{[<.Rdash.}
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[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
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een already used, duplicate ignored
<to be read again>
\relax
l.13450 \aliasA{[}{subscript-methods}{[}
[2548]
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\T1/ptm/m/n/10 Classes [][][]\T1/pcr/m/n/10 triangularMatrix[][][][]\T1/ptm/m/n
/10 , and, e.g., [][][]\T1/pcr/m/n/10 dsyMatrix[][][] []\T1/ptm/m/n/10 for nu-m
eric \T1/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or
[2549]
Underfull \hbox (badness 2057) in paragraph at lines 13661--13663
[]\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe
r-ent ma-trix classes, use e.g.,
Underfull \hbox (badness 6396) in paragraph at lines 13670--13674
[]\T1/pcr/m/n/10 symmpart(x) []\T1/ptm/m/n/10 re-turns a sym-met-ric ma-trix, i
n-her-it-ing from [][][]\T1/pcr/m/n/10 symmetricMatrix[][][] []\T1/ptm/m/n/10 o
r
[2550]
Underfull \hbox (badness 7722) in paragraph at lines 13675--13680
[]\T1/pcr/m/n/10 skewpart(x) []\T1/ptm/m/n/10 re-turns a skew-symmetric ma-trix
, in-her-it-ing from [][][]\T1/pcr/m/n/10 generalMatrix[][][][]\T1/ptm/m/n/10 ,
[2551]
Underfull \hbox (badness 6641) in paragraph at lines 13752--13755
[]\T1/ptm/m/n/10 Currently, [][][]\T1/pcr/m/n/10 Schur[][][][]\T1/ptm/m/n/10 ,
[][][]\T1/pcr/m/n/10 isSymmetric[][][] []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 as
() []\T1/ptm/m/n/10 (i.e. [][][]\T1/pcr/m/n/10 coerce[][][][]\T1/ptm/m/n/10 ) h
ave meth-ods with
Underfull \hbox (badness 5133) in paragraph at lines 13788--13792
[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 "TsparseMatrix" []\T1/ptm/m/n/10 class is
the vir-tual class of all sparse ma-tri-ces coded in
Underfull \hbox (badness 2818) in paragraph at lines 13788--13792
\T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c
re-ated from it. See
[2552]
[2553]
Underfull \hbox (badness 1668) in paragraph at lines 13915--13918
[][][]\T1/pcr/m/n/10 pack[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 unpac
k[][][][]\T1/ptm/m/n/10 ; its vir-tual "com-ple-ment" []\T1/pcr/m/n/10 "[][]pac
kedMatrix[][][]"[]\T1/ptm/m/n/10 ; its proper sub-classes
[2554]
Underfull \hbox (badness 10000) in paragraph at lines 14026--14032
[]\T1/ptm/m/n/10 GAL lat-tice file `\T1/pcr/m/n/10 usc_q.GAL\T1/ptm/m/n/10 ' (r
e-trieved in 2008 from
[2555]
[2556]
[2557]) (./boot-pkg.tex
[2558]
Chapter 18.
[2559]
[2560]
[2561]
[2562]
[2563]
[2564]
[2565]
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[]\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"),
[2566]
Underfull \hbox (badness 1325) in paragraph at lines 570--577
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r
e-quired. Pos-si-ble
Underfull \hbox (badness 1275) in paragraph at lines 585--590
[]\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m
ulti-sample prob-
[2567]
[2568]
[2569]
Underfull \hbox (badness 1881) in paragraph at lines 826--828
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
Underfull \hbox (badness 6493) in paragraph at lines 853--857
[][][]\T1/pcr/m/n/10 boot.array[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 bo
ot.ci[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 censboot[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 empinf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 j
ack.after.boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 tilt.boot[][][][]\T
1/ptm/m/n/10 ,
[2570]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 887--887
[]\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt,
data = nuke)[]
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[2571]
[2572]
[2573]
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[]\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari-
ance of the
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\T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i
n-ter-vals. If it
Underfull \hbox (badness 2343) in paragraph at lines 1084--1093
\T1/ptm/m/n/10 is not sup-plied and []\T1/pcr/m/n/10 length(index) []\T1/ptm/m/
n/10 is 2 then []\T1/pcr/m/n/10 var.t0 []\T1/ptm/m/n/10 de-faults to
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[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2574]
[2575]
[2576]
[2577]
Underfull \hbox (badness 1571) in paragraph at lines 1445--1447
[]\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An
al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis-
[2578]
[2579]
[2580]
[2581]
[2582]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1738--1738
[]\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2),
[2583]
[2584]
[2585]
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[2586]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 2013--2013
[]\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
+ strata(ulcer),[]
[2587]
Underfull \hbox (badness 6268) in paragraph at lines 2084--2086
[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2588]
[2589]
[2590]
Underfull \hbox (badness 1565) in paragraph at lines 2338--2343
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori
g-i-nal data set
[2591]
Underfull \hbox (badness 4595) in paragraph at lines 2363--2368
\T1/ptm/m/n/10 are passed un-changed ev-ery time []\T1/pcr/m/n/10 boot.out$stat
istic []\T1/ptm/m/n/10 is called.
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[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
Underfull \hbox (badness 2057) in paragraph at lines 2440--2441
[][][]\T1/pcr/m/n/10 boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 empinf[]
[][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 k3.linear[][][][]\T1/ptm/m/n/10 , [
][][]\T1/pcr/m/n/10 linear.approx[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
saddle.distn[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 smooth.spline[][][][]
\T1/ptm/m/n/10 ,
[2592]
[2593]
Underfull \hbox (badness 1077) in paragraph at lines 2536--2540
[]\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of []\T1/pcr/m
/n/10 n/((n-1)*(n-2)) []\T1/ptm/m/n/10 where []\T1/pcr/m/n/10 n []\T1/ptm/m/n/1
0 is the sam-ple
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\T1/ptm/m/n/10 size, if []\T1/pcr/m/n/10 unbiased []\T1/ptm/m/n/10 is []\T1/pcr
/m/n/10 FALSE []\T1/ptm/m/n/10 then a mul-ti-plier of []\T1/pcr/m/n/10 1/n []\T
1/ptm/m/n/10 is used. This is mul-ti-plied by
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[2595]
[2596]
[2597]
[2598]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2895--2895
[]\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t
= 25,
Overfull \hbox (18.78088pt too wide) in paragraph at lines 2897--2897
[]\T1/pcr/m/n/10 EL.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t
= 25,[]
[2599]
[2600]
[2601]
Underfull \hbox (badness 3861) in paragraph at lines 3105--3108
[][][]\T1/pcr/m/n/10 boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 boot.arr
ay[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 boot.ci[][][][]\T1/ptm/m/n/10 ,
[][][]\T1/pcr/m/n/10 control[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 jack
.after.boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 linear.approx[][][][]\
T1/ptm/m/n/10 ,
[2602]
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[]\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat))
[2603]
[2604]
[2605]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3378--3378
[]\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling
[2606]
[2607]
[2608]
[2609]
[2610]
[2611]
[2612]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3838--3838
[] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
= NULL)[]
[2613]
[2614]
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[]\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
grav.z0[3])[]
[2615]
[2616]
[2617]
[2618]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4259--4259
[]\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz
e data as in
[2619]
[2620]
Underfull \hbox (badness 10000) in paragraph at lines 4362--4364
[]\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o
f
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\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 t0 []\T1/ptm/m/n/10 is sup-plied but nei-the
r []\T1/pcr/m/n/10 t []\T1/ptm/m/n/10 nor []\T1/pcr/m/n/10 L []\T1/ptm/m/n/10 a
re sup-plied then []\T1/pcr/m/n/10 t0 []\T1/ptm/m/n/10 is set to
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[2622]
[2623]
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[2625]
[2626]
[2627]
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[2629]
Underfull \hbox (badness 3000) in paragraph at lines 4959--4962
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put
of a call to
[2630]
[2631]
[2632]
[2633]
Underfull \hbox (badness 2293) in paragraph at lines 5238--5241
[]\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the
boot-strap
Underfull \hbox (badness 1668) in paragraph at lines 5238--5241
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2634]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5317--5317
[]\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[]
[2635]
[2636]
[2637]
[2638]
[2639]
[2640]
[2641]
[2642]
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[]\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][]
[2643]
Underfull \hbox (badness 1127) in paragraph at lines 5988--6006
[]\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less
than []\T1/pcr/m/n/10 min(alpha)/10[]\T1/ptm/m/n/10 , then
[2644]
Underfull \hbox (badness 2837) in paragraph at lines 6021--6024
[]\T1/ptm/m/n/10 The re-turned value is an ob-ject of class []\T1/pcr/m/n/10 "s
addle.distn"[]\T1/ptm/m/n/10 . See the help file for
[2645]
[2646]
[2647]
[2648]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6306--6306
[]\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and
Wright (1991).
[2649]
[2650]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6495--6495
[]\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6497--6497
[]\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t
ilting was used[]
[2651]
[2652]
[2653]
Underfull \hbox (badness 1596) in paragraph at lines 6742--6746
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m
ent ex-pected by
[2654]
[2655]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6902--6902
[] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
c(0.05, 0.95),[]
[2656]
[2657]
[2658]
[2659]
[2660]
[2661]
[2662]
[2663]) (./class-pkg.tex
[2664]
Chapter 19.
[2665]
[2666]
[2667]
[2668]
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[2671]
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[] \T1/pcr/m/n/9 alpha = list(seq(0.05, 0, length.out = 1e4), seq(0.02, 0,
length.out = 1e5)),[]
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[] \T1/pcr/m/n/9 radii = list(seq(8, 1, length.out = 1e4), seq(4, 1, length
.out = 1e5)))[]
[2679]
[2680]) (./cluster-pkg.tex
Chapter 20.
[2681]
[2682]
[2683]
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[] \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met
hod = 0.5)[iC]) ,[]
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[] \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method=
c(.5,.5,0, -.5))[iC]),[]
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[] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
c(.5,.5,0, +.5))[iC]))[]
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[2685]
[2686] [2687]
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[] \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot
= axes,[]
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[] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
...)[]
[2688]
[2689]
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[] \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c
orrect.d = TRUE)[]
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[2691]
[2692]
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[][][]\T1/pcr/m/n/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-en
ces; [][][]\T1/pcr/m/n/10 clara.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 pam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 partition.object[][][][]\
T1/ptm/m/n/10 ,
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[] \T1/pcr/m/n/9 cl[,i] <- clara(xclara, nCl, medoids.x = FALSE, rngR = TRUE
)$clustering[]
[2693]
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[]\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[]
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[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2694]
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[] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code
=3), ...)[]
[2695]
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[]\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is
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[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
2012,
[2696]
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[]\T1/ptm/m/n/10 Per Broberg (2006). SAGx: Sta-tis-ti-cal Anal-y-sis of the Gen
eChip. R pack-age ver-
[2697]
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[] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[]
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[]\T1/pcr/m/n/9 ## You can manually set it before running this : doExtras <
- TRUE # or FALSE[]
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[] \T1/pcr/m/n/9 gskmn <- clusGap(x, FUNcluster = kmeans, nstart = 20, K.max
= 8, B = 60)[]
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[] \T1/pcr/m/n/9 plot(gskmn, main = "clusGap(., FUNcluster = kmeans, n.start=
20, B= 60)")[]
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[2698]
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[]\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap(<iid_rnorm_p=3>) ==> k = 1 clust
er is optimal")[]
Underfull \hbox (badness 4144) in paragraph at lines 1205--1209
[]\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 does not have a []\T1
/pcr/m/n/10 diss []\T1/ptm/m/n/10 nor a []\T1/pcr/m/n/10 data []\T1/ptm/m/n/10
com-po-nent, e.g., for
[2699]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1281--1281
[] \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1,
cex.txt = cex,[]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 1287--1287
[] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[]
[2700]
[2701]
[2702]
Underfull \hbox (badness 10000) in paragraph at lines 1474--1477
Underfull \hbox (badness 10000) in paragraph at lines 1488--1492
[][][]\T1/pcr/m/n/10 princomp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cmds
cale[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pam[][][][]\T1/ptm/m/n/10 , [
][][]\T1/pcr/m/n/10 clara[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 daisy[][
][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 par[][][][]\T1/ptm/m/n/10 , [][][]\T
1/pcr/m/n/10 identify[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cov.mve[][][
][]\T1/ptm/m/n/10 ,
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1512--1512
[]\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a
nd label ellipses[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1522--1522
[] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[]
[2703]
Underfull \hbox (badness 5741) in paragraph at lines 1562--1565
[]\T1/pcr/m/n/10 coefHier() []\T1/ptm/m/n/10 di-rectly in-ter-faces to the un-d
er-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only
[2704]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1631--1631
[] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa
rnType,[]
[2705]
Underfull \hbox (badness 1552) in paragraph at lines 1680--1682
[]\T1/ptm/b/n/10 A\T1/ptm/m/n/10 symmetric bi-nary vari-able, aka []\T1/pcr/m/n
/10 "A" []\T1/ptm/m/n/10 in re-sult []\T1/pcr/m/n/10 Types[]\T1/ptm/m/n/10 , se
e
Underfull \hbox (badness 1629) in paragraph at lines 1694--1698
[]\T1/ptm/b/n/10 I\T1/ptm/m/n/10 nterval scaled -- the \T1/ptm/b/n/10 de-fault
\T1/ptm/m/n/10 for all nu-meric
Underfull \hbox (badness 3746) in paragraph at lines 1694--1698
\T1/ptm/m/n/10 (incl []\T1/pcr/m/n/10 integer[]\T1/ptm/m/n/10 ) columns of []\T
1/pcr/m/n/10 x[]\T1/ptm/m/n/10 , aka []\T1/pcr/m/n/10 "I" []\T1/ptm/m/n/10 in r
e-sult []\T1/pcr/m/n/10 Types[]\T1/ptm/m/n/10 , see
[2706]
Underfull \hbox (badness 1540) in paragraph at lines 1769--1777
\T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh
ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1
0 w[]^^N[]$\T1/ptm/m/n/10 , where $\OML/cmm/m/it/10 w[]$[]\T1/pcr/m/n/10 =
[2707]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1856--1856
[]\T1/pcr/m/n/9 ## Example 2 in reference, extended --- different ways of "m
ixed" / "gower":[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1860--1860
[]\T1/pcr/m/n/9 summary(d0 <- daisy(flower)) # -> the first 3 {0,1} treate
d as *N*ominal[]
Overfull \hbox (90.78033pt too wide) in paragraph at lines 1861--1861
[]\T1/pcr/m/n/9 summary(dS123 <- daisy(flower, type = list(symm = 1:3))) # fi
rst 3 treated as *S*ymmetric[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1862--1862
[]\T1/pcr/m/n/9 stopifnot(dS123 == d0) # i.e., *S*ymmetric <==> *N*ominal {fo
r 2-level factor}[]
Overfull \hbox (106.98032pt too wide) in paragraph at lines 1866--1866
[]\T1/pcr/m/n/9 summary(dA123 <- daisy(flowerN)) # .. all 3 logicals treated *
A*symmetric binary (w/ warning)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1868--1868
[]\T1/pcr/m/n/9 summary(dA13 <- daisy(flower, type = list(asymm = c(1, 3), ord
ratio = 7)))[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1875--1875
[]\T1/pcr/m/n/9 Nflow[,1:3] <- lapply(flower[,1:3], function(f) as.integer(as.
character(f)))[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1876--1876
[]\T1/pcr/m/n/9 summary(dN <- daisy(Nflow)) # w/ warning: treated binary .. 1:
3 as interval[]
Overfull \hbox (117.7803pt too wide) in paragraph at lines 1877--1877
[]\T1/pcr/m/n/9 ## Still, using Euclidean/Manhattan distance for {0-1} *is* id
entical to treating them as "N" :[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 1893--1893
[]\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE,
[2708]
[2709]
[2710]
[2711]
[2712]
Underfull \hbox (badness 10000) in paragraph at lines 2212--2215
Underfull \hbox (badness 3179) in paragraph at lines 2223--2229
[][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] []\T1/ptm/m/n/10 which is also the
[][][]\T1/pcr/m/n/10 predict[][][] []\T1/ptm/m/n/10 method for []\T1/pcr/m/n/1
0 ellipsoid []\T1/ptm/m/n/10 ob-jects.
[2713]
[2714]
Underfull \hbox (badness 10000) in paragraph at lines 2380--2383
[][][]\T1/pcr/m/n/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-en
ces; [][][]\T1/pcr/m/n/10 fanny.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 partition.object[][][][]\T1/ptm/m/n/10 ,
[2715]
Underfull \hbox (badness 1292) in paragraph at lines 2448--2451
[]\T1/ptm/m/n/10 named vec-tor with []\T1/pcr/m/n/10 iterations[]\T1/ptm/m/n/10
, the num-ber of it-er-a-tions needed and
[2716]
Underfull \hbox (badness 6675) in paragraph at lines 2457--2459
[]\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl
us-ter-ing, see
Underfull \hbox (badness 10000) in paragraph at lines 2480--2483
[][][]\T1/pcr/m/n/10 fanny[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.f
anny[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 dissimilarity.object[][][][]\
T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 partition.object[][][][]\T1/ptm/m/n/10 ,
[2717]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2555--2555
[] \T1/pcr/m/n/9 "4" = "red", "5" = "blue")[levels(f
lowerN$color)][]
Overfull \hbox (90.78033pt too wide) in paragraph at lines 2556--2556
[]\T1/pcr/m/n/9 levels(flowerN$soil) <- c("1" = "dry", "2" = "normal", "3" =
"wet")[levels(flowerN$soil)][]
[2718]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 2619--2619
[]\T1/pcr/m/n/10 medoids(x, clustering, diss = inherits(x, "dist"), USE.NAMES
= FALSE, ...)
[2719]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 2666--2666
[] \T1/pcr/m/n/9 stopifnot(length(cl.k) == nrow(votes.repub), 1 <= cl.k, cl.k
<= k, table(cl.k) >= 2)[]
[2720]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2771--2771
[]\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to
\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/
9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[]
[2721]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 2850--2850
[] \T1/pcr/m/n/10 variant = c("original", "o_1", "o_2", "f_3", "f_4", "f_5"
, "faster"),[]
[2722]
[2723]
[2724]
[2725]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 3078--3078
[]\T1/pcr/m/n/9 ## use obs. 1 & 16 as starting medoids -- same result (for see
d above, *and* typically) :[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3080--3080
[]\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 3083--3083
[]\T1/pcr/m/n/9 keep_nms <- setdiff(names(pamx), c("call", "objective"))# .$ob
jective["build"] differ[]
[2726]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3187--3187
[]\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[]
[2727]
[2728]
[2729]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3381--3381
[] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3382--3382
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2730]
Underfull \hbox (badness 10000) in paragraph at lines 3449--3452
[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via []\T1/pcr/m
/n/10 pltree() []\T1/ptm/m/n/10 is pro-vided by []\T1/pcr/m/n/10 dg <-
[2731]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3499--3499
[] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3500--3500
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2732]
[2733]
[2734]
Underfull \hbox (badness 10000) in paragraph at lines 3685--3688
[]\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 does not have a []\T1
/pcr/m/n/10 diss []\T1/ptm/m/n/10 com-po-nent as for [][][]\T1/pcr/m/n/10 pam[]
[][](*,
Underfull \hbox (badness 1448) in paragraph at lines 3685--3688
\T1/pcr/m/n/10 keep.diss=FALSE)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 dist []\T1/p
tm/m/n/10 must be the dis-sim-i-lar-ity if a clus-plot is
[2735]
Underfull \hbox (badness 10000) in paragraph at lines 3748--3753
[][][]\T1/pcr/m/n/10 partition.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n
/10 clusplot.partition[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 clusplot.de
fault[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pam[][][][]\T1/ptm/m/n/10 ,
[2736]
Underfull \hbox (badness 1748) in paragraph at lines 3810--3815
\T1/ptm/m/n/10 dis-patches to [][][]\T1/pcr/m/n/10 plot.hclust[][][](..)[]\T1/p
tm/m/n/10 . If more flex-i-ble plots are needed, con-sider []\T1/pcr/m/n/10 xx
<-
Underfull \hbox (badness 6268) in paragraph at lines 3822--3825
[][][]\T1/pcr/m/n/10 agnes[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 agnes.o
bject[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 diana[][][][]\T1/ptm/m/n/10
, [][][]\T1/pcr/m/n/10 diana.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/1
0 hclust[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 par[][][][]\T1/ptm/m/n/10
, [][][]\T1/pcr/m/n/10 plot.agnes[][][][]\T1/ptm/m/n/10 ,
[2737]
Underfull \hbox (badness 10000) in paragraph at lines 3883--3885
[]\T1/ptm/m/n/10 Available as `\T1/pcr/m/n/10 pluton.dat\T1/ptm/m/n/10 ' from t
he archive of the Uni-ver-sity of Antwer-pen,
[2738]
[2739]
Underfull \hbox (badness 10000) in paragraph at lines 4002--4005
[][][]\T1/pcr/m/n/10 summary.agnes[][][] []\T1/ptm/m/n/10 pro-duc-ing more out-
put; [][][]\T1/pcr/m/n/10 agnes[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 ag
nes.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/
n/10 ,
[2740]
Underfull \hbox (badness 10000) in paragraph at lines 4033--4036
[][][]\T1/pcr/m/n/10 summary.clara[][][] []\T1/ptm/m/n/10 pro-duc-ing more out-
put; [][][]\T1/pcr/m/n/10 clara[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cl
ara.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/
n/10 ,
[2741]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 4086--4086
[] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
TRUE, ...)[]
Underfull \hbox (badness 2035) in paragraph at lines 4097--4099
[]\T1/ptm/m/n/10 a []\T1/pcr/m/n/10 dissimilarity []\T1/ptm/m/n/10 ob-ject or a
[]\T1/pcr/m/n/10 summary.dissimilarity []\T1/ptm/m/n/10 one for
[2742]
[2743]
[2744]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4290--4290
[] \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w
idth "* s[i]),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 4292--4292
[] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
= TRUE, ...)[]
[2745]
[2746]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4434--4434
[]\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus
ter-wise coloring[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4443--4443
[] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
do.n.k=FALSE)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4445--4445
[] \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma
in")); frame()[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 4448--4448
[]\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol
denrod4", "gray20")[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4450--4450
[] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
do.n.k=FALSE,[]
[2747]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4457--4457
[]\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro
wnames == indices[]
[2748]
[2749]
[2750]
[2751]
[2752]
[2753]
Underfull \hbox (badness 10000) in paragraph at lines 4828--4834
[]\T1/ptm/m/n/10 Our ver-sion of the []\T1/pcr/m/n/10 xclara []\T1/ptm/m/n/10 i
s slightly more rounded than the one from
Underfull \hbox (badness 10000) in paragraph at lines 4844--4846
[]\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file
`\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side
Overfull \hbox (52.98038pt too wide) in paragraph at lines 4857--4857
[]\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10
01:2000}, {2001:3000}
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4859--4859
[]\T1/pcr/m/n/9 p.ID <- c(78, 1411, 2535) ## PAM\TS1/pcr/m/n/9 '\T1/pcr/m/n/9
s medoid indices == pam(xclara, 3)$id.med[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4869--4869
[] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o
bservations:[]
[2754]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4873--4873
[] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? -
- Robust range:[]
[2755]) (./codetools-pkg.tex
[2756]
Chapter 21.
Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16
[] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
= FALSE,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17
[] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun =
!all,[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18
[] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[]
[2757]
Underfull \hbox (badness 10000) in paragraph at lines 65--70
[]\T1/pcr/m/n/10 checkUsageEnv []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 checkUsage
Package []\T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply
[2758]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 118--118
[]\T1/pcr/m/n/10 makeConstantFolder(..., leaf, handler, call, exit, isLocal, f
oldable,[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 121--121
[]\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[]
[2759]
[2760]
[2761]) (./foreign-pkg.tex
[2762]
Chapter 22.
Underfull \hbox (badness 10000) in paragraph at lines 33--37
[]\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o
ut of a Data
Underfull \hbox (badness 10000) in paragraph at lines 33--37
\T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able as [][]$\T1/p
cr/m/n/10 https : / / support .
Underfull \hbox (badness 10000) in paragraph at lines 33--37
\T1/pcr/m/n/10 sas . com / content / dam / SAS / support / en / technical-[]pap
ers /
Overfull \hbox (74.28088pt too wide) in paragraph at lines 33--37
\T1/pcr/m/n/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[]s
et-[]in-[]sas-[]transport-[]xport-[]format .
[2763]
Underfull \hbox (badness 1231) in paragraph at lines 67--70
[]\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr
om, or a
[2764]
[2765]
Underfull \hbox (badness 3601) in paragraph at lines 234--242
[]\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude []\T1/pcr/m
/n/10 "datalabel"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "time.stamp"[]\T1/ptm/m/n/
10 ,
[2766]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 292--292
[]\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
FALSE,
[2767]
[2768]
[2769]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 458--458
[] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame,[]
[2770]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 459--459
[] \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen
d", "no"),[]
Underfull \hbox (badness 2846) in paragraph at lines 502--511
[]\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif-
fer-ent lev-
Underfull \hbox (badness 3746) in paragraph at lines 502--511
\T1/ptm/m/n/10 els. For []\T1/pcr/m/n/10 "append" []\T1/ptm/m/n/10 (the de-faul
t), the first orig-i-nal value la-bel is
Underfull \hbox (badness 2269) in paragraph at lines 502--511
\T1/ptm/m/n/10 kept while fur-ther du-pli-cated la-bels are re-named to []\T1/p
cr/m/n/10 paste0(label,
Underfull \hbox (badness 10000) in paragraph at lines 512--515
[]\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with
du-
Underfull \hbox (badness 10000) in paragraph at lines 512--515
\T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault []\T1/pcr/m/n/10 "_dup
licated_"[]\T1/ptm/m/n/10 ) if
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[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 https : / / learn . microsoft . com /
en-[]us / windows / win32 / intl /
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[]\T1/ptm/m/n/10 There may be at-tributes []\T1/pcr/m/n/10 "label.table" []\T1/
ptm/m/n/10 and []\T1/pcr/m/n/10 "variable.labels"[]\T1/ptm/m/n/10 . At-tribute
[2772]
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[]\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg
ument settings.[]
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[]\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to
R factor labels) are uncomplete,[]
[2773]
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[]\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ
ate variables[]
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[]\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt
h=w), "\n"))[]
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[]\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste,
collapse="")[]
[2774]
[2775]
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[]\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[]
[2776]
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[]\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o
ut of a Data
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\T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able at [][]$\T1/p
cr/m/n/10 https : / / support .
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\T1/pcr/m/n/10 sas . com / content / dam / SAS / support / en / technical-[]pap
ers /
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\T1/pcr/m/n/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[]s
et-[]in-[]sas-[]transport-[]xport-[]format .
[2777]
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[] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv)
[2778]
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[]\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x)))
[2779]
[2780]
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[][][]$\T1/pcr/m/n/10 https : / / www . clicketyclick . dk / databases / xbase
/ format / data _ types .
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[] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric",
"codes"))[]
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[2782]
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[]\T1/ptm/m/n/10 The work for this func-tion is done by []\T1/pcr/m/n/10 foreig
n:::writeForeignStata[]\T1/ptm/m/n/10 ,
[2783]
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[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 package="SPSS"[]\T1/ptm/m/n/10 , as a sid
e ef-fect, the dec-i-mal in-di-ca-tor is al-ways set by []\T1/pcr/m/n/10 SET
[2784]) (./lattice-pkg.tex
Chapter 23.
[2785]
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\T1/ptm/m/n/10 pro-vide a holis-tic in-tro-duc-tion to the Trel-lis paradigm: [
][]$\T1/pcr/m/n/10 http : / / web . archive . org /
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\T1/pcr/m/n/10 web / 20081020164041 / http : / / cm . bell-[]labs . com / cm /
ms / departments / sia /
[2786]
[2787]
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[] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.xyplot"),[]
[2788]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul
t.dotplot"),[]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.barchart"),[]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.stripplot"),[]
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[] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[]
Underfull \vbox (badness 10000) has occurred while \output is active
[2789]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.bwplot"),[]
[2790]
[2791]
[2792]
Underfull \hbox (badness 1221) in paragraph at lines 655--658
[]\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as
ar-gu-ments to
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[2794]
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[2796]
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[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of
fac-tors will be
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\T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a
use-ful lay-out.
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[2798]
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[]\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 y []\T1/ptm/m/n/10 sho
uld be num-bers be-tween 0 and 1, giv-ing co-or-di-nates
[2799]
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[]\T1/ptm/m/n/10 Logical flag, whether leg-end should have a
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[]\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to
[2800]
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[2802]
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[]\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][][]\T1/pcr/m/
n/10 plot.trellis[][][][]\T1/ptm/m/n/10 ,
[2803]
Underfull \hbox (badness 10000) in paragraph at lines 1563--1580
[][][]\T1/pcr/m/n/10 panel.dotplot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
panel.stripplot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.superpose[]
[][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.loess[][][][]\T1/ptm/m/n/10 ,
[2804]
Underfull \vbox (badness 10000) has occurred while \output is active
[2805]
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[] \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar
dSprays$rowpos))),[]
[2806]
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[]\T1/ptm/m/n/10 additional ar-gu-ments passed to [][][]\T1/pcr/m/n/10 xyplot[]
[][][]\T1/ptm/m/n/10 , which may pass them on to
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[]\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p
assed to
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[]\T1/ptm/m/n/10 style set-tings be-yond the stan-dard []\T1/pcr/m/n/10 col[]\T
1/ptm/m/n/10 , []\T1/pcr/m/n/10 lty[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lwd[]\T1
/ptm/m/n/10 , etc; see
[2807]
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[]\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix
An-drews
[2808]
[2809]
[2810]
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[] \T1/pcr/m/n/10 auto.key = lattice.getOption("default.args")$auto
.key,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2058--2058
[] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[]
Underfull \vbox (badness 10000) has occurred while \output is active
[2811]
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[]\T1/ptm/m/n/10 When []\T1/pcr/m/n/10 breaks []\T1/ptm/m/n/10 is un-spec-i-fie
d, the value of
Underfull \hbox (badness 1320) in paragraph at lines 2137--2140
[]\T1/pcr/m/n/10 lattice.getOption("histogram.breaks") []\T1/ptm/m/n/10 is firs
t checked. If
[2812]
[2813]
[2814]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2342--2342
[] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 2346--2346
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.qqmath"),[]
[2815]
[2816]
[2817]
[2818]
[2819]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 2702--2702
[] \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev
elplot.raster")[]
[2820]
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[] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl
ot"),[]
Underfull \vbox (badness 10000) has occurred while \output is active
[2821]
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[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when []\T1/
pcr/m/n/10 x []\T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 2813--2818
[]\T1/pcr/m/n/10 row.values []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 column.values
[]\T1/ptm/m/n/10 must have the same lengths as
[2822]
[2823]
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[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be
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\T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][][]\T1/pcr/m/n/10 grid.ra
ster[][][][]\T1/ptm/m/n/10 . See also
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[]\T1/ptm/m/n/10 Logical flag, passed to [][][]\T1/pcr/m/n/10 rasterGrob[][][]
[]\T1/ptm/m/n/10 when
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[]\T1/pcr/m/n/10 allow.multiple[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 outer[]\T1/p
tm/m/n/10 , []\T1/pcr/m/n/10 prepanel[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 scales
[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 strip[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 gr
oups[]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti
ons should be used,
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\T1/ptm/m/n/10 both for the false color im-age and the color key (if present).
Ef-
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\T1/ptm/m/n/10 fec-tively, set-ting this to []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n
/10 changes the de-fault panel func-tion from
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[]\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for
the de-fault panel func-tion
[2824]
[2825]
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[] \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite
= TRUE),[]
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[] \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite
= TRUE),[]
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[] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
= TRUE),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3139--3139
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[]
[2826]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[]
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[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when []\T1/
pcr/m/n/10 x []\T1/ptm/m/n/10 is a ma-trix.
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[]\T1/pcr/m/n/10 row.values []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 column.values
[]\T1/ptm/m/n/10 must have the same lengths as
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[]\T1/pcr/m/n/10 allow.multiple[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 outer[]\T1/p
tm/m/n/10 , []\T1/pcr/m/n/10 auto.key[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 prepan
el[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 strip[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10
groups[]\T1/ptm/m/n/10 ,
[2828]
[2829]
[2830]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.parallel}
) has been already used, duplicate ignored
<to be read again>
\relax
l.3506 \aliasA{parallel}{B\_08\_splom}{parallel}
[2831]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[]
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[2833]
[2834]
[2835]
[2836]
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[]\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x)))
[2837]
[2838]
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[]\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault
set-tings by
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\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2839]
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[] \T1/pcr/m/n/10 symbol = palette.colors(palette = "Okabe-Ito")
[c(6, 2, 4, 7, 3, 5, 8)],[]
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[] \T1/pcr/m/n/10 region = hcl.colors(14, palette = "YlGnBu", re
v = TRUE),[]
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[] \T1/pcr/m/n/10 reference = "gray90", bg = "transparent", fg = "
black",[]
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[] \T1/pcr/m/n/10 strip.bg = rep("gray95", 7), strip.fg = rep("gra
y70", 7),[]
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[]\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict
= FALSE)
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[]\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un-
spec-i-fied in
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[]\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i
s-sued when
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[]\T1/pcr/m/n/10 theme[]\T1/ptm/m/n/10 ). These are used to mod-ify the cur-ren
t set-tings (ob-tained by
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[]\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in []\T1/pcr/m/n/10 trell
is.settings []\T1/ptm/m/n/10 has not been fi-nal-ized,
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\T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca
n be ob-tained by
[2844]
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[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. []\T1/pcr/m/n/10 col []\T1/ptm/m/n/
10 is used for com-po-nents []\T1/pcr/m/n/10 "plot.symbol"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 "plot.line"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "plot.polygon"[
]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "superpose.symbol"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 "superpose.line"[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 "super
pose.polygon"[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 col.points
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[]\T1/ptm/m/n/10 over-rides []\T1/pcr/m/n/10 col[]\T1/ptm/m/n/10 , but is used
only for []\T1/pcr/m/n/10 "plot.symbol" []\T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/10 "superpose.symbol"[]\T1/ptm/m/n/10 . Sim-i-larly, []\T1/pcr/m/
n/10 col.line []\T1/ptm/m/n/10 over-rides []\T1/pcr/m/n/10 col []\T1/ptm/m/n/10
for
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[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents []\T1/pcr/m/n/10 pl
ot.symbol[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 plot.polygon[]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents []\T1/pcr/m/n/10
plot.polygon []\T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/10 auto.key[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 aspect[]\T1/ptm/m/
n/10 , []\T1/pcr/m/n/10 between[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 grid[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 skip[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 strip[]\T1/
ptm/m/n/10 , []\T1/pcr/m/n/10 xscale.components[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
= "Height")[]
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[2852]
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[]\T1/pcr/m/n/10 main[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 page[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 par.strip.text[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 prepanel[]\
T1/ptm/m/n/10 , []\T1/pcr/m/n/10 scales[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 skip
[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 strip[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 xscale.components[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 yscale.co
mponents[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 axis[]\T1/ptm/m/n/10 , []\T1/pcr/m/
n/10 par.settings[]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 trellis[]\T1/ptm/m/n/10 ,
by de-fault plot-ted by []\T1/pcr/m/n/10 print.trellis[]\T1/ptm/m/n/10 .
[2854]
[2855]
Underfull \hbox (badness 1442) in paragraph at lines 5232--5235
[]\T1/pcr/m/n/10 plot.shingle []\T1/ptm/m/n/10 dis-plays the ranges of shin-gle
s via rect-an-gles. []\T1/pcr/m/n/10 print.shingle []\T1/ptm/m/n/10 and
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[2857]
[2858]
[2859]
[2860]
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[][][]\T1/pcr/m/n/10 Lattice[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 draw.
key[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 trellis.par.get[][][][]\T1/ptm
/m/n/10 , and [][][]\T1/pcr/m/n/10 xyplot[][][][]\T1/ptm/m/n/10 , specif-i-call
y the en-try for
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[] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[]
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[] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[]
[2861]
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[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.
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[]\T1/pcr/m/n/10 horizontal=FALSE []\T1/ptm/m/n/10 is use-ful for strips on the
left of pan-els us-ing
[2862]
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[]\T1/pcr/m/n/10 strip.default []\T1/ptm/m/n/10 is called for its side-effect,
which is to draw a strip ap-pro-pri-ate for
[2863]
[2864]
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[]\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[]
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[]\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[]
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[]\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[]
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[]\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[]
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[] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[]
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[] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[]
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[] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[]
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[] \T1/pcr/m/n/10 prefix = pre
fix),[]
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[] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[]
[2865]
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[] \T1/pcr/m/n/10 prefix = pre
fix),[]
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[] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[]
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[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of
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[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
De-faults to
[2866]
Underfull \hbox (badness 2538) in paragraph at lines 6045--6049
\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 trellis.focus[]\T1/ptm/m/n/10 , the de-faul
t is []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 in in-ter-ac-tive mode, and
Underfull \hbox (badness 4205) in paragraph at lines 6056--6063
[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 panel.identify.qqmath[]\T1/ptm/m/n/10 , e
x-tra pa-ram-e-ters are passed on to
Underfull \hbox (badness 4792) in paragraph at lines 6056--6063
[]\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 trellis.switchFocus[]\T1/ptm/m/n/10 , the
se are used (in com-bi-na-tion with
[2867]
[2868]
Underfull \hbox (badness 10000) in paragraph at lines 6209--6213
[][][]\T1/pcr/m/n/10 identify[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Latt
ice[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.trellis[][][][]\T1/ptm/m
/n/10 , [][][]\T1/pcr/m/n/10 trellis.currentLayout[][][][]\T1/ptm/m/n/10 ,
[2869]
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[2871]
Underfull \hbox (badness 4242) in paragraph at lines 6356--6361
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2872]
[2873]
Underfull \hbox (badness 3601) in paragraph at lines 6472--6477
[]\T1/ptm/m/n/10 Creates Box and Whisker plot of []\T1/pcr/m/n/10 x []\T1/ptm/m
/n/10 for ev-ery level of []\T1/pcr/m/n/10 y []\T1/ptm/m/n/10 (or the other way
round
Underfull \hbox (badness 2486) in paragraph at lines 6472--6477
\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 horizontal=FALSE[]\T1/ptm/m/n/10 ). By de-fa
ult, the ac-tual box-plot statis-tics are cal-cu-lated us-ing
[2874]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 6558--6558
[] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[]
[2875]
[2876]
[2877]
Underfull \hbox (badness 10000) in paragraph at lines 6757--6761
[]\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The
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[]\T1/ptm/m/n/10 numeric, be-tween 0 and 1, giv-ing a min-i-mum sat-u-ra-tion i
n
[2878]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6858--6858
[] \T1/pcr/m/n/9 shade.colors.palette = makeShadePalette(hcl.colors(1
0, "Inferno"),[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6861--6861
[] \T1/pcr/m/n/9 shade.colors.palette = makeShadePalette(hcl.colors(1
0, "Dark Mint"),[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6864--6864
[] \T1/pcr/m/n/9 shade.colors.palette = makeShadePalette(hcl.colors(1
0, "Harmonic"),[]
[2879]
[2880]
[2881]
[2882]
[2883]
Underfull \hbox (badness 1320) in paragraph at lines 7225--7232
[]\T1/pcr/m/n/10 panel.levelplot.raster []\T1/ptm/m/n/10 is an al-ter-na-tive p
anel func-tion that uses the raster draw-
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\T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more
ef-fi-cient. When us-ing
[2884]
[2885]
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[] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels =
NULL,[]
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[]\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments
to
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[]\T1/pcr/m/n/10 diag.panel.splom []\T1/ptm/m/n/10 to know what ar-gu-ments thi
s func-tion is passed
[2886]
[2887]
Underfull \hbox (badness 10000) in paragraph at lines 7435--7438
\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 diag.panel []\T1/ptm/m/n/10 from []\T1/pcr/
m/n/10 panel.pairs[]\T1/ptm/m/n/10 . Cur-rently ig-nored by
Overfull \hbox (101.58032pt too wide) in paragraph at lines 7460--7460
[] \T1/pcr/m/n/9 function(i,j) hcl.colors(11)[i+j-1]) ## rainbow(
11, start=.12, end=.5)[i+j-1])[]
[2888]
[2889]
Underfull \hbox (badness 2012) in paragraph at lines 7601--7604
[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2890]
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[] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[]
[2891]
[2892]
Underfull \hbox (badness 1939) in paragraph at lines 7836--7844
[]\T1/pcr/m/n/10 "lm" []\T1/ptm/m/n/10 adds a lin-ear re-gres-sion line (same a
s [][][]\T1/pcr/m/n/10 panel.lmline[][][][]\T1/ptm/m/n/10 , ex-cept
Underfull \hbox (badness 1163) in paragraph at lines 7836--7844
\T1/ptm/m/n/10 for de-fault graph-i-cal pa-ram-e-ters). []\T1/pcr/m/n/10 "loess
" []\T1/ptm/m/n/10 adds a loess fit (same as
[2893]
Underfull \hbox (badness 2772) in paragraph at lines 7859--7862
[]\T1/ptm/m/n/10 Most gen-er-ally, []\T1/pcr/m/n/10 grid []\T1/ptm/m/n/10 can b
e a list of ar-gu-ments to be sup-plied to
[2894]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7930--7930
[] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
= c(1/6, 4/6)),[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7940--7940
[] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[]
[2895]
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[] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[]
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[] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ide
ntifier, name.type)[]
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[2896]
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[]\T1/pcr/m/n/10 col[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 alpha[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 lty[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lwd[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 fill[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pch[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 cex[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lineheight[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 font[]\T1/ptm/m/n/10 ,
[2897]
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[]\T1/pcr/m/n/9 xyplot(y ~ x, d, panel = panel.rect, col = 4, alpha = 0.5, wid
th = 0.1, height = 0.1)[]
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[]\T1/pcr/m/n/9 xyplot(y ~ x, d, panel = panel.polygon, col = 4, alpha = 0.5,
rule = "evenodd")[]
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[]\T1/pcr/m/n/9 ## Example adapted from https://journal.r-project.org/articles
/RJ-2012-017/[]
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[]\T1/pcr/m/n/9 xyplot(y ~ x, data = d, panel = panel.polygon, rule = "none",
col = "grey")[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8194--8194
[]\T1/pcr/m/n/9 xyplot(y ~ x, data = d, panel = panel.polypath, rule = "windin
g", col = "grey")[]
[2898]
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[]\T1/pcr/m/n/9 xyplot(y ~ x, data = d, panel = panel.polypath, rule = "evenod
d", col = "grey")[]
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[]\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[]
[2899]
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[]\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c
al pa-ram-e-ters for
[2900]
[2901]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 8439--8439
[] \T1/pcr/m/n/9 panel.superpose(x, y, ..., panel.groups = panel.ave
rage, grid = FALSE,[]
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[] \T1/pcr/m/n/9 args = list(mean = mean(x), sd
= sd(x)), ...)[]
[2902]
[2903]
[2904]
[2905]
[2906]
[2907]
Underfull \hbox (badness 10000) in paragraph at lines 8878--8881
[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to []\T1/pcr/m/n/10 panel.super
pose
Underfull \hbox (badness 10000) in paragraph at lines 8878--8881
[]\T1/ptm/m/n/10 from []\T1/pcr/m/n/10 panel.superpose.2[]\T1/ptm/m/n/10 , and
to []\T1/pcr/m/n/10 panel.groups []\T1/ptm/m/n/10 from
[2908]
[2909]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 9053--9053
[]\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9054--9054
[]\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[]
[2910]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 9066--9066
[]\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[]
Underfull \hbox (badness 3118) in paragraph at lines 9085--9088
[]\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. []\T1/pcr/m/n/10 type [
]\T1/ptm/m/n/10 has a dif-fer-ent mean-ing in
[2911]
Underfull \hbox (badness 1515) in paragraph at lines 9160--9164
[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2912]
[2913]
Underfull \hbox (badness 6316) in paragraph at lines 9266--9271
[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2914]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 9376--9376
[] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[]
[2915]
[2916]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9515--9515
[]\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[]
[2917]
Underfull \hbox (badness 1028) in paragraph at lines 9574--9578
\T1/pcr/m/n/10 condition []\T1/ptm/m/n/10 for 2-D, and []\T1/pcr/m/n/10 left, r
ight.x, right.y, left.name, right.x.name,
[2918]
[2919]
[2920]
[2921]
[2922]
[2923]
[2924]
Underfull \hbox (badness 7238) in paragraph at lines 10018--10022
[]\T1/ptm/m/n/10 Factor with lev-els []\T1/pcr/m/n/10 "Svansota"[]\T1/ptm/m/n/1
0 , []\T1/pcr/m/n/10 "No. 462"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Manchuria"[]
\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "No. 475"[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 10018--10022
[]\T1/pcr/m/n/10 "Velvet"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Peatland"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "Glabron"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "No. 4
57"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Wisconsin No. 38"[]\T1/ptm/m/n/10 ,
[2925]
[2926]
[2927]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma}
) has been already used, duplicate ignored
<to be read again>
\relax
l.10249 \aliasA{melanoma}{H\_melanoma}{melanoma}
[2928]
[2929]
[2930]
Underfull \hbox (badness 10000) in paragraph at lines 10411--10416
\T1/pcr/m/n/10 diseases[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Diabetes[]\T1/ptm/m/
n/10 , []\T1/pcr/m/n/10 Flu and pneumonia[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 He
art disease[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Lower
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10484--10484
[] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list(
columns = 2),[]
[2931]
[2932]) (./mgcv-pkg.tex
Chapter 24.
[2933]
[2934]
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[]\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,
Overfull \hbox (18.78088pt too wide) in paragraph at lines 163--163
[] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret
e=FALSE,[]
[2935]
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[] \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in
tercept=NULL,[]
Underfull \hbox (badness 1142) in paragraph at lines 185--189
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known
scale.
[2936]
[2937]
[2938]
[2939]
Underfull \hbox (badness 10000) in paragraph at lines 382--389
[][][]\T1/pcr/m/n/10 mgcv.parallel[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gamObject[][][][]\T1
/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/ptm/m/n/10 , [][][]\T1
/pcr/m/n/10 smooth.terms[][][][]\T1/ptm/m/n/10 ,
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[][][]\T1/pcr/m/n/10 linear.functional.terms[][][][]\T1/ptm/m/n/10 , [][][]\T1/
pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][] [][]predict.
gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10
,
Underfull \hbox (badness 10000) in paragraph at lines 382--389
[][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 g
am.side[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.selection[][][][]\T1/p
tm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][][]\T1/ptm
/m/n/10 ,
[2940]
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[]\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2
,bs=bs,k=k)+[]
[2941]
[2942]
[2943]
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[]\T1/ptm/m/n/10 The link func-tion: one of []\T1/pcr/m/n/10 "logit"[]\T1/ptm/m
/n/10 , []\T1/pcr/m/n/10 "probit"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cloglog"
[]\T1/ptm/m/n/10 and
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[]\T1/ptm/m/n/10 The MKL BLAS is mut-lithreaded by de-fault. Un-der linux set-t
ing en-vi-ron-ment vari-able
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[]\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe
n us-ing pe-nal-ized re-gres-sion
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[]\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro
-duc-tion with R (2nd edi-tion).
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[]\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$
q^.5),col=2)[]
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[]\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[]
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[] \T1/pcr/m/n/9 plot(b$y[oy],rs[oy,ii[1]],ylim=c(-3,3),type="l",ylab="scor
e residuals",[]
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[]\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor
+rx+obstruct[]
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[]\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in
d]),type="l",[]
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[] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind])
,lwd=2,col=i)[]
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[]\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights=
d,data=surv)[]
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[] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid),
initial = 0,[]
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[] \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][
nrow(um)] <- 1[]
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[]\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter
polate to te[]
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[]\T1/pcr/m/n/9 bd <- bam(y~s(x0)+ s(x1) + s(x1,fac,bs="sz",k=5)+s(x2,k=20),di
screte=TRUE)[]
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[]\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE)
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[]\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,[]
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[]\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][][]\T1/pcr/m/n
/10 formula.gam[][][] []\T1/ptm/m/n/10 and also
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known
scale.
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[]\T1/ptm/m/n/10 A list spec-i-fy-ing the neigh-bour-hood struc-ture for [][][]
\T1/pcr/m/n/10 NCV[][][][]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 a []\T1/ptm/m/n/10
is the vec-tor
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[]\T1/ptm/m/n/10 gives the points dropped for the neigh-bour-hood []\T1/pcr/m/n
/10 j[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 d []\T1/ptm/m/n/10 is the vec-tor
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\T1/ptm/m/n/10 of in-dices of points to pre-dict, with cor-re-spond-ing end-poi
nts []\T1/pcr/m/n/10 md[]\T1/ptm/m/n/10 . So
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\T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v
en-tion mech-a-nism de-scribed in
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[][][]\T1/pcr/m/n/10 mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
gamObject[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/pt
m/m/n/10 , [][][]\T1/pcr/m/n/10 smooth.terms[][][][]\T1/ptm/m/n/10 ,
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[][][]\T1/pcr/m/n/10 linear.functional.terms[][][][]\T1/ptm/m/n/10 , [][][]\T1/
pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][] [][]predict.
gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10
,
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[][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 g
am.side[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.selection[][][][]\T1/p
tm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][][]\T1/ptm
/m/n/10 ,
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[]\T1/pcr/m/n/10 gam.control(nthreads=1,ncv.threads=1,irls.reg=0.0,epsilon = 1
e-07,
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[] \T1/pcr/m/n/10 maxit = 200,mgcv.tol=1e-7,mgcv.half=15, trace = F
ALSE,[]
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[] \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco
l(x)),[]
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[] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol
(x)),[]
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[] \T1/pcr/m/n/10 pearson.extra=0,dev.extra=0,n.true=-1,Sl=NULL,nei=NU
LL,...)[]
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[]\T1/ptm/m/n/10 Random ef-fects can be added to []\T1/pcr/m/n/10 gam []\T1/ptm
/m/n/10 mod-els us-ing []\T1/pcr/m/n/10 s(...,bs="re") []\T1/ptm/m/n/10 terms (
see
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[]\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[]
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[]\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix
ed penalty, if
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[] \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i
d=1)+s(x1,id=1)+[]
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[]\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0,
d1b = 0,
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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[]\T1/ptm/m/n/10 In the event of []\T1/pcr/m/n/10 lme []\T1/ptm/m/n/10 con-ver-
gence fail-ures, con-sider mod-i-fy-ing
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[][][]\T1/pcr/m/n/10 magic[][][] []\T1/ptm/m/n/10 for an al-ter-na-tive for cor
-re-lated data, [][][]\T1/pcr/m/n/10 te[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m
/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.gam[][][][]\T1/ptm
/m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10 ,
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[][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 n
egbin[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 vis.gam[][][][]\T1/ptm/m/n/1
0 ,[][][]\T1/pcr/m/n/10 pdTens[][][][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 gamm4 [
]\T1/ptm/m/n/10 ( [][]$\T1/pcr/m/n/10 https : / / cran . r-[]project .
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[]\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see []
[][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 ar-gu-ment
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[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
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[]\T1/pcr/m/n/10 ginla(G,A=NULL,nk=16,nb=100,J=1,interactive=FALSE,integ=0,app
rox=0)
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[]\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by []\T1/pcr/m/n/10 gam(..
.,fit=FALSE) []\T1/ptm/m/n/10 or
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[] \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d
ata. A simple[]
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[] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j]
,lty=lty[j])[]
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[] \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo
r comparison[]
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[] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r
norm(100)*.4[]
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[]\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n
a.action,
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[]\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona
lize=FALSE)[]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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[]\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999,
all.derivs=FALSE)
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[]\T1/pcr/m/n/10 lp(c,A,b,C=NULL,d=NULL,Bi=NULL,maxit=max(1000, nrow(A) * 10),
phase1 = FALSE)
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[]\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
to rule the world.",[]
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[] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[]
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[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
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[]\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt
ion with bam...[]
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[]\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate
d covariates[]
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[] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]]
,na.rm=TRUE)[]
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[]\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: []\T1/pcr/m/n/10 Dim
.pdIndot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 coef.pdIdnot[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 corMatrix.pdIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 logDet.pd
Idnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdConstruct.pdIdnot[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 pdFactor.pdIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdMatrix.p
dIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 solve.pdIdnot[]\T1/ptm/m/n/10 , []\T1
/pcr/m/n/10 summary.pdIdnot[]\T1/ptm/m/n/10 .
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[]\T1/ptm/m/n/10 These func-tions ([]\T1/pcr/m/n/10 pdTens[]\T1/ptm/m/n/10 , []
\T1/pcr/m/n/10 pdConstruct.pdTens[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdFactor.p
dTens[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 pdMatrix.pdTens[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 coef.pdTens
[]\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 summary.pdTens[]\T1/ptm/m/n/10 ) would n
ot nor-mally be
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[]\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s
cale=-1,[]
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[] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi
ds=FALSE,[]
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[]\T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion
is some-times to clone the
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[] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,gc.level=0,...)[]
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[]\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 type=="terms" []\T1/ptm/m/n/10 or []\T1/pc
r/m/n/10 type="iterms" []\T1/ptm/m/n/10 then terms (smooth or para-
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[] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL
L,...)[]
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[]\T1/pcr/m/n/9 x1 <- seq(.2,.8,length=m1);x2 <- seq(.2,.8,length=m2) ## margi
nal grid points[]
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[]\T1/pcr/m/n/9 df <- data.frame(x0=rep(.5,n),x1=rep(x1,m2),x2=rep(x2,each=m1)
,x3=rep(0,n))[]
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[] \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s
mooth deriv i[]
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are
as for
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[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[3124]
[3125]
Underfull \hbox (badness 1205) in paragraph at lines 11124--11125
[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
Underfull \hbox (badness 2689) in paragraph at lines 11124--11125
\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are
as for
[3126]
Underfull \hbox (badness 10000) in paragraph at lines 11193--11196
[]\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from
Underfull \hbox (badness 2057) in paragraph at lines 11193--11196
[][][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][][]\T1/ptm/m/n/10 , al
-though el-e-ments []\T1/pcr/m/n/10 X []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 S [
]\T1/ptm/m/n/10 are not needed,
[3127]
[3128]
Underfull \hbox (badness 1253) in paragraph at lines 11323--11325
[]\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion
cri-te-rion re-ported is one of GCV,
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Underfull \hbox (badness 1946) in paragraph at lines 11576--11583
[]\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef-
fects in a GAM in the same
Underfull \hbox (badness 2221) in paragraph at lines 11576--11583
\T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre
s-sion terms. This method
Underfull \hbox (badness 2042) in paragraph at lines 11576--11583
\T1/ptm/m/n/10 can be used with [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10
by mak-ing use of []\T1/pcr/m/n/10 s(...,bs="re") []\T1/ptm/m/n/10 terms in a
model: see
Underfull \hbox (badness 2846) in paragraph at lines 11584--11587
[]\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the []\T1/pcr/m/n
/10 paraPen []\T1/ptm/m/n/10 ar-gu-ment to [][][]\T1/pcr/m/n/10 gam[][][] []\T1
/ptm/m/n/10 can be used:
Underfull \hbox (badness 5862) in paragraph at lines 11584--11587
\T1/ptm/m/n/10 see [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/ptm/m/n/10 . If s
mooth-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g.
[3134]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11650--11650
[]\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11660--11660
[]\T1/pcr/m/n/9 ## The effect of the new factor levels (or any interaction inv
olving them)[]
[3135]
Underfull \hbox (badness 10000) in paragraph at lines 11691--11694
[]\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of []\T1/pcr/m/n/
10 "deviance"[]\T1/ptm/m/n/10 ,
[3136]
[3137]
[3138]
[3139]
[3140]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 11993--11993
[]\T1/pcr/m/n/10 s(..., k=-1,fx=FALSE,bs="tp",m=NA,by=NA,xt=NULL,id=NULL,sp=NU
LL,pc=NULL)
[3141]
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[3143]
[3144]
[3145]
[3146]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12366--12366
[] \T1/pcr/m/n/9 true <- mu + (del * sigma) * sinh((1/del) * asinh(qnorm(qq))
+ (eps/del))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12380--12380
[]\T1/pcr/m/n/9 b <- gam(list(accel~s(times, k=20, bs = "ad"), ~s(times, k = 1
0), ~1, ~1),[]
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[3147]
[3148]
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[]\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to
model ma-trix X, or, if
Overfull \hbox (36.78088pt too wide) in paragraph at lines 12491--12491
[]\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE,
cov = TRUE,[]
[3149]
Underfull \hbox (badness 10000) in paragraph at lines 12508--12512
[]\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 inverse==TRUE []\T1/ptm/m/n/10 and []\T1/p
cr/m/n/10 both.sides==FALSE []\T1/ptm/m/n/10 then the re-
Underfull \hbox (badness 10000) in paragraph at lines 12548--12552
[]\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 inverse==TRUE []\T1/ptm/m/n/10 and []\T1/p
cr/m/n/10 both.sides==FALSE []\T1/ptm/m/n/10 then the re-
[3150]
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[]\T1/pcr/m/n/10 Sl.setup(G,cholesky=FALSE,no.repara=FALSE,sparse=FALSE,keepS=
FALSE)
[3151]
[3152]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 12695--12695
[] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$
vectors[,ind]))[]
Underfull \hbox (badness 1975) in paragraph at lines 12706--12711
[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[3153]
Underfull \hbox (badness 1803) in paragraph at lines 12783--12787
\T1/ptm/m/n/10 The last en-try will be the []\T1/pcr/m/n/10 by []\T1/ptm/m/n/10
vari-able, if []\T1/pcr/m/n/10 object$by []\T1/ptm/m/n/10 is not []\T1/pcr/m/n
/10 "NA"[]\T1/ptm/m/n/10 .
Underfull \hbox (badness 1502) in paragraph at lines 12795--12807
[]\T1/pcr/m/n/10 cs.smooth.spec []\T1/ptm/m/n/10 (cu-bic re-gres-sion splines w
ith shrinkage-to-zero); []\T1/pcr/m/n/10 cc.smooth.spec
[3154]
Underfull \hbox (badness 2401) in paragraph at lines 12812--12816
[]\T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able
. Plot meth-ods can be
Underfull \hbox (badness 2970) in paragraph at lines 12812--12816
\T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for []\T1/pc
r/m/n/10 mgcv:::plot.sos.smooth[]\T1/ptm/m/n/10 ,
[3155]
[3156]
[3157]
Underfull \hbox (badness 6876) in paragraph at lines 13007--13013
[][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use adap-tive smooths of on
e or two vari-ables, spec-i-fied via terms like
[3158]
Underfull \hbox (badness 10000) in paragraph at lines 13048--13049
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3159]
[3160]
Underfull \hbox (badness 10000) in paragraph at lines 13166--13167
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3161]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13220--13220
[] \T1/pcr/m/n/9 b <- gam(y~s(x0,bs=bs,m=c(4,2))+s(x1,bs=bs)+s(x2,k=15,bs=bs,
m=c(4,3,0))+[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13232--13232
[] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5,
1.5) (black)[]
[3162]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13244--13244
[] \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions
and intervals[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13249--13249
[] \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i
ntervals away[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13255--13255
[] \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w
ild and wide[]
Overfull \hbox (3.70428pt too wide) in paragraph at lines 13256--13256
[] \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/cmtt/m/n/9 `\T1
/pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[]
[3163]
Underfull \hbox (badness 10000) in paragraph at lines 13325--13327
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
Underfull \hbox (badness 10000) in paragraph at lines 13325--13327
\T1/ptm/m/n/10 term []\T1/pcr/m/n/10 s(...,bs="cr",...)[]\T1/ptm/m/n/10 , []\T1
/pcr/m/n/10 s(...,bs="cs",...) []\T1/ptm/m/n/10 or
[3164]
[3165]
Underfull \hbox (badness 10000) in paragraph at lines 13455--13456
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3166]
[3167]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13536--13536
[]\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data) ## first
deriv penalty[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13537--13537
[]\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi
ed 2nd deriv[]
[3168]
[3169]
Underfull \hbox (badness 10000) in paragraph at lines 13690--13691
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
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[3171]
[3172]
[3173]
[3174]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13940--13940
[]\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[]
[3175]
Underfull \hbox (badness 10000) in paragraph at lines 14001--14003
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3176]
[3177]
Underfull \hbox (badness 10000) in paragraph at lines 14160--14163
[]\T1/ptm/m/n/10 For the []\T1/pcr/m/n/10 smooth.construct []\T1/ptm/m/n/10 met
hod a smooth spec-i-fi-ca-tion ob-
Underfull \hbox (badness 3312) in paragraph at lines 14160--14163
\T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term []\T1/pcr/m/n/10 s(x,...,bs
="re",)[]\T1/ptm/m/n/10 . For the
Underfull \hbox (badness 7099) in paragraph at lines 14160--14163
[]\T1/pcr/m/n/10 predict.Matrix []\T1/ptm/m/n/10 method an ob-ject of class []\
T1/pcr/m/n/10 "random.effect"
[3178]
[3179]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 14246--14246
[]\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with
2 variances[]
[3180]
Underfull \hbox (badness 10000) in paragraph at lines 14291--14297
[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a
Underfull \hbox (badness 7832) in paragraph at lines 14291--14297
[]\T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) []\T1/ptm/m/n/10 term in a
[]\T1/pcr/m/n/10 gam []\T1/ptm/m/n/10 for-
[3181]
[3182]
[3183]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 14506--14506
[]\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[]
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Underfull \vbox (badness 10000) has occurred while \output is active
[3185]
Underfull \hbox (badness 10000) in paragraph at lines 14609--14617
[][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths on th
e sphere, via terms like
Underfull \hbox (badness 10000) in paragraph at lines 14635--14636
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
[3186]
[3187]
[3188]
Underfull \hbox (badness 7613) in paragraph at lines 14780--14783
[]\T1/ptm/m/n/10 method an ob-ject of class []\T1/pcr/m/n/10 "sz.interaction" [
]\T1/ptm/m/n/10 pro-duced by the
[3189]
Underfull \hbox (badness 1546) in paragraph at lines 14801--14802
[]\T1/ptm/m/n/10 The terms can have a smooth-ing pa-ram-e-ter per smooth, or a
sin-gle smooth-ing pa-ram-e-
Overfull \hbox (128.58029pt too wide) in paragraph at lines 14847--14847
[]\T1/pcr/m/n/9 b <- gam(y ~ s(x)+s(f1,x,bs="sz")+s(f2,x,bs="sz")+s(f1,f2,x,bs
="sz",id=1),data=dat,method="REML")[]
[3190]
[3191]
[3192]
Underfull \hbox (badness 3396) in paragraph at lines 14993--14996
[][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths of an
y num-ber of vari-ables, spec-i-fied via terms like
Underfull \hbox (badness 10000) in paragraph at lines 15038--15040
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
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[3197]
[3198]
Underfull \hbox (badness 10000) in paragraph at lines 15329--15331
[]\T1/pcr/m/n/10 bs="fs" []\T1/ptm/m/n/10 A spe-cial smoother class (see
[3199]
Underfull \hbox (badness 10000) in paragraph at lines 15363--15367
[][][]\T1/pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][][]\
T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 t2[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m
/n/10 tprs[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Duchon.spline[][][][]\T
1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cubic.regression.spline[][][][]\T1/ptm/m/n/
10 ,
Underfull \hbox (badness 10000) in paragraph at lines 15363--15367
[][][]\T1/pcr/m/n/10 p.spline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 d.sp
line[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 mrf[][][][]\T1/ptm/m/n/10 , [
][][]\T1/pcr/m/n/10 soap[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Spherical
.Spline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 adaptive.smooth[][][][]\T1
/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 15363--15367
[][][]\T1/pcr/m/n/10 user.defined.smooth[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/
m/n/10 smooth.construct.re.smooth.spec[][][][]\T1/ptm/m/n/10 ,
[3200]
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[3203]
[3204]
Underfull \hbox (badness 2158) in paragraph at lines 15652--15652
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[3205]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 15731--15731
[]\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[]
[3206]
[3207]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 15865--15865
[] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[]
[3208]
[3209]
Underfull \hbox (badness 4846) in paragraph at lines 15996--15999
[]\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or
es-ti-ma-tors if
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[3211]
[3212]
[3213]
[3214]
[3215]
[3216]
[3217]
[3218]
[3219]
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[3229]
Overfull \hbox (120.78088pt too wide) in paragraph at lines 17220--17220
[]\T1/pcr/m/n/10 vcov(object, sandwich=FALSE, freq = FALSE, dispersion = NULL,
unconditional=FALSE, ...)[]
[3230]
Underfull \hbox (badness 1715) in paragraph at lines 17242--17243
[]\T1/ptm/m/n/10 Basically, just ex-tracts []\T1/pcr/m/n/10 object$Ve[]\T1/ptm/
m/n/10 , []\T1/pcr/m/n/10 object$Vp []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 object
$Vc []\T1/ptm/m/n/10 (if avail-able) from a
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[3232]
[3233]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 17433--17433
[]\T1/pcr/m/n/10 XWXd(X,w,k,ks,ts,dt,v,qc,nthreads=1,drop=NULL,ar.stop=-1,ar.r
ow=-1,ar.w=-1,
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[]\T1/pcr/m/n/10 XWyd(X,w,y,k,ks,ts,dt,v,qc,drop=NULL,ar.stop=-1,ar.row=-1,ar.
w=-1,lt=NULL)[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17437--17437
[]\T1/pcr/m/n/10 diagXVXd(X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,rt=
NULL)[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 17438--17438
[]\T1/pcr/m/n/10 ijXVXd(i,j,X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,r
t=NULL)[]
[3234]
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[]\T1/ptm/m/n/10 Negative to ig-nore. Oth-er-wise sum rows
Underfull \hbox (badness 1668) in paragraph at lines 17458--17459
[]\T1/pcr/m/n/10 (ar.stop[i-1]+1):ar.stop[i] []\T1/ptm/m/n/10 of the rows se-le
cted by []\T1/pcr/m/n/10 ar.row
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[3236]
[3237]
[3238]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 17656--17656
[]\T1/pcr/m/n/9 ## 1. If the zero inflation rate becomes decoupled from the li
near predictor,[]
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[]\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun
ded in regions[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17669--17669
[]\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[]
[3239]
[3240]
[3241]) (./nlme-pkg.tex
[3242]
Chapter 25.
[3243]
Underfull \hbox (badness 1009) in paragraph at lines 78--87
[]\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served
- fit-ted) are used; else, if
[3244]
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[]\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served
- fit-ted) are used; else, if
[3245]
[3246]
[3247]
[3248]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 448--448
[] \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[]
[3249]
[3250]
[3251]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 589--589
[]\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 251-254 ---------------------------
---------------[]
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[]\T1/pcr/m/n/9 # Compare an "lme" object with a "gls" object (test would be n
on-sensical!)[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 608--608
[]\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 222-225 ---------------------------
---------------[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 615--615
[]\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 352-365 ---------------------------
---------------[]
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[3255]
[3256]
[3257]
[3258]
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[] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil
lary fissure"),[]
[3259]
[3260]
Underfull \hbox (badness 5446) in paragraph at lines 1140--1142
[]\T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel
.htm[]\T1/ptm/m/n/10 ', the first edi-tion of
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[3265]
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[3267]
Underfull \hbox (badness 10000) in paragraph at lines 1617--1620
[][][]\T1/pcr/m/n/10 lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fixed.
effects.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 ranef.lmList[][][][
]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.ranef.lmList[][][][]\T1/ptm/m/n/10
,
Underfull \hbox (badness 3780) in paragraph at lines 1634--1636
[]\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a
ted with each com-po-nent of the
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Underfull \hbox (badness 2042) in paragraph at lines 1975--1981
\T1/ptm/m/n/10 is in-ner to the []\T1/pcr/m/n/10 displayLevel []\T1/ptm/m/n/10
group-ing fac-tor. If equal to []\T1/pcr/m/n/10 TRUE[]\T1/ptm/m/n/10 ,
[3273]
[3274]
Underfull \hbox (badness 1132) in paragraph at lines 2127--2129
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
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[3276]
Underfull \hbox (badness 4168) in paragraph at lines 2238--2244
[][][]\T1/pcr/m/n/10 ACF.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corAR
MA[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/1
0 , [][][]\T1/pcr/m/n/10 Dim.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m
/n/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 ,
[3277]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2263--2263
[] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[]
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Underfull \hbox (badness 10000) in paragraph at lines 2816--2820
[][][]\T1/pcr/m/n/10 corFactor[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cor
Matrix.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 recalc.corStruct[
][][][]\T1/ptm/m/n/10 ,
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Underfull \hbox (badness 6493) in paragraph at lines 3548--3556
[][][]\T1/pcr/m/n/10 corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corGau
s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corLin[][][][]\T1/ptm/m/n/10 , [
][][]\T1/pcr/m/n/10 corRatio[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corSp
her[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][][]\T
1/ptm/m/n/10 ,
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Underfull \hbox (badness 10000) in paragraph at lines 5116--5120
[][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/p
cr/m/n/10 getCovariate.data.frame[][][][]\T1/ptm/m/n/10 ,
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Underfull \hbox (badness 10000) in paragraph at lines 5540--5543
[][][]\T1/pcr/m/n/10 getGroups.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/
m/n/10 getGroups.data.frame[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 getGro
ups.gls[][][][]\T1/ptm/m/n/10 ,
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Underfull \hbox (badness 2799) in paragraph at lines 6044--6050
\T1/ptm/m/n/10 covariance ma-trix, ei-ther []\T1/pcr/m/n/10 "random.effects" []
\T1/ptm/m/n/10 for the random-effects
[3337]
Underfull \hbox (badness 7133) in paragraph at lines 6105--6109
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in [
]\T1/pcr/m/n/10 model[]\T1/ptm/m/n/10 ,
[3338]
Underfull \hbox (badness 2057) in paragraph at lines 6194--6205
[][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gl
sControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 glsObject[][][][]\T1/ptm/
m/n/10 , [][][]\T1/pcr/m/n/10 glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m
/n/10 plot.gls[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.gls[][][][]
\T1/ptm/m/n/10 ,
[3339]
Underfull \hbox (badness 10000) in paragraph at lines 6258--6260
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
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Underfull \hbox (badness 7133) in paragraph at lines 6505--6509
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in [
]\T1/pcr/m/n/10 model[]\T1/ptm/m/n/10 ,
[3344]
Underfull \hbox (badness 10000) in paragraph at lines 6602--6608
[][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gn
lsControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gnlsObject[][][][]\T1/pt
m/m/n/10 , [][][]\T1/pcr/m/n/10 gnlsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc
r/m/n/10 predict.gnls[][][][]\T1/ptm/m/n/10 ,
Overfull \hbox (54.78088pt too wide) in paragraph at lines 6629--6629
[]\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min
Scale = 0.001,
[3345]
Underfull \hbox (badness 10000) in paragraph at lines 6667--6669
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
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[3349]
Underfull \hbox (badness 10000) in paragraph at lines 6936--6943
[][][]\T1/pcr/m/n/10 formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gappl
y[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gsummary[][][][]\T1/ptm/m/n/10 ,
[][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.nff
GroupedData[][][][]\T1/ptm/m/n/10 ,
[3350]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6954--6954
[] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6959--6959
[]\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted
from object[]
Underfull \hbox (badness 2875) in paragraph at lines 6981--6983
[]\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a []\T1/pcr/m/n/10 gr
oupedData []\T1/ptm/m/n/10 ob-ject or a
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[3353]
Underfull \hbox (badness 10000) in paragraph at lines 7196--7202
[][][]\T1/pcr/m/n/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr
/m/n/10 Initialize.glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initi
alize.lmeStruct[][][][]\T1/ptm/m/n/10 ,
[3354]
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[3356]
Underfull \hbox (badness 1997) in paragraph at lines 7341--7349
[]\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial
-iza-tion and op-ti-
Underfull \hbox (badness 2205) in paragraph at lines 7341--7349
\T1/ptm/m/n/10 miza-tion al-go-rithms used in []\T1/pcr/m/n/10 lme[]\T1/ptm/m/n
/10 . De-faults to []\T1/pcr/m/n/10 list(niterEM=20,
Underfull \hbox (badness 3118) in paragraph at lines 7364--7367
[][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initializ
e.reStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.corStruct[][
][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.varFunc[][][][]\T1/ptm/m/
n/10 ,
[3357]
[3358]
[3359]
Underfull \hbox (badness 3354) in paragraph at lines 7574--7576
[]\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when []\T1/pcr/m/n/
10 which []\T1/ptm/m/n/10 is not equal to
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[3367]
Underfull \hbox (badness 10000) in paragraph at lines 8101--8118
[][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lm
e.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lme.groupedData[][][][]\T
1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lmeControl[][][][]\T1/ptm/m/n/10 , [][][]\T
1/pcr/m/n/10 lmeObject[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8101--8118
[][][]\T1/pcr/m/n/10 lmeStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lmL
ist[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/1
0 , [][][]\T1/pcr/m/n/10 plot.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
predict.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 qqnorm.lme[][][][]\T1/
ptm/m/n/10 ,
[3368]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8144--8144
[] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data
= TRUE)[]
Underfull \hbox (badness 1642) in paragraph at lines 8153--8175
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
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[3371]
[3372]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8418--8418
[]\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni
terEM = 25,
Underfull \hbox (badness 1189) in paragraph at lines 8443--8445
[]\T1/ptm/m/n/10 maximum num-ber of eval-u-a-tions of the ob-jec-tive func-tion
per-mit-ted for
[3373]
Underfull \hbox (badness 10000) in paragraph at lines 8466--8468
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8509--8509
[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
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Underfull \hbox (badness 10000) in paragraph at lines 9266--9273
[][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 ,[][][]\T1/pcr/m/n/10 gls[][][][
]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logLik.corStruct[][][][]\T1/ptm/m/n/10 ,
[][][]\T1/pcr/m/n/10 logLik.glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 logLik.lmeStruct[][][][]\T1/ptm/m/n/10 ,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9277--9277
[]\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML")
[3386]
[3387]
[3388]
[3389]
[3390]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Matrix})
has been already used, duplicate ignored
<to be read again>
\relax
l.9628 ...rA{Matrix}{Assign Matrix Values}{Matrix}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Matrix.1}
) has been already used, duplicate ignored
<to be read again>
\relax
l.9628 ...rA{Matrix}{Assign Matrix Values}{Matrix}
[3391]
Underfull \hbox (badness 10000) in paragraph at lines 9648--9651
[]\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a
s
Underfull \hbox (badness 3108) in paragraph at lines 9692--9695
[]\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive
-definite
Underfull \hbox (badness 2521) in paragraph at lines 9692--9695
\T1/ptm/m/n/10 ma-trix rep-re-sented by []\T1/pcr/m/n/10 object[]\T1/ptm/m/n/10
. Must have the same di-men-sions as
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[3402]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10362--10362
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,
[3403]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10366--10366
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,[]
Underfull \hbox (badness 1596) in paragraph at lines 10395--10421
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3404]
[3405]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10549--10549
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,[]
[3406]
[3407]
[3408]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10700--10700
[] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
NULL, ...)[]
Underfull \hbox (badness 2213) in paragraph at lines 10711--10716
[]\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][][]\T1/pcr/m/n/10 nlmi
nb[][][] []\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 iter.max[]\T1/ptm/m/n/10 ) or the [
][][]\T1/pcr/m/n/10 nlm[][][]
Underfull \hbox (badness 6961) in paragraph at lines 10733--10737
[]\T1/ptm/m/n/10 a log-i-cal value passed as the []\T1/pcr/m/n/10 trace []\T1/p
tm/m/n/10 to [][][]\T1/pcr/m/n/10 nlminb[][][](.., control=
[3409]
Underfull \hbox (badness 10000) in paragraph at lines 10752--10754
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
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[3411]
[3412]
[3413]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 11048--11048
[]\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one*
message instead of one *each*[]
Overfull \hbox (90.78033pt too wide) in paragraph at lines 11049--11049
[]\T1/pcr/m/n/9 mat.class <- class(matrix(1)) # ("matrix", "array") for R >= 4
.0.0; ("matrix" in older R)[]
[3414]
[3415]
[3416]
[3417]
[3418]
[3419]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11439--11439
[]\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*))
[3420]
[3421]
[3422]
[3423]
[3424]
[3425]
Underfull \hbox (badness 6268) in paragraph at lines 11826--11836
[][][]\T1/pcr/m/n/10 pdBlocked[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdC
ompSymm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdDiag[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 pdFactor[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
pdIdent[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 pdMatrix[][][][]\T1/ptm/m/n/10 ,
[3426]
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Underfull \hbox (badness 10000) in paragraph at lines 12087--12093
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 coef.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdBlocked[][][][]\T1
/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/
pcr/m/n/10 pdConstruct[][][][]\T1/ptm/m/n/10 ,
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[3434]
Underfull \hbox (badness 6876) in paragraph at lines 12409--12411
[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 value []\T1/ptm/m/n/10 is an \T1/ptm/m/it/
10 ini-tial-ized []\T1/pcr/m/n/10 pdMat []\T1/ptm/m/n/10 ob-ject, []\T1/pcr/m/n
/10 object []\T1/ptm/m/n/10 will be con-structed from
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[3436]
Underfull \hbox (badness 2452) in paragraph at lines 12565--12572
[][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdC
ompSymm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdDiag[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 pdIdent[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
pdNatural[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdSymm[][][][]\T1/ptm/m/
n/10 , [][][]\T1/pcr/m/n/10 reStruct[][][][]\T1/ptm/m/n/10 ,
[3437]
Underfull \hbox (badness 10000) in paragraph at lines 12631--12637
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdFactor[][][][]\T1/p
tm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 pdMatrix.reStruct[][][][]\T1/ptm/m/n/10 ,
[3438]
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[3440]
[3441]
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[3443]
[3444]
[3445]
[3446]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 13220--13220
[]\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*))
[3447]
[3448]
[3449]
[3450]
[3451]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13585--13585
[]\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline =
0, id = 0.05)[]
[3452]
Underfull \hbox (badness 10000) in paragraph at lines 13612--13615
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nffGroupe
dData[]\T1/ptm/m/n/10 , rep-re-sent-ing a
[3453]
Underfull \hbox (badness 1838) in paragraph at lines 13655--13662
[]\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If []\T1/pcr/m/
n/10 TRUE []\T1/ptm/m/n/10 and ei-ther []\T1/pcr/m/n/10 inner
Underfull \hbox (badness 3713) in paragraph at lines 13655--13662
[]\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 innerGroups []\T1/ptm/m/n/10 are non-[]\T1
/pcr/m/n/10 NULL[]\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent []\T1/pcr/m/n/
10 inner
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[]\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
panel,[]
[3454]
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[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nfnGroupe
dData[]\T1/ptm/m/n/10 , rep-re-sent-ing a
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[]\T1/pcr/m/n/10 groupedData []\T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary
co-vari-ate and a sin-gle
[3455]
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[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nmGrouped
Data[]\T1/ptm/m/n/10 , rep-re-sent-ing a
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[3457]
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[][][]\T1/pcr/m/n/10 groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 c
ollapse.groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.nfnGroupe
dData[][][][]\T1/ptm/m/n/10 ,
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[3465]
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[]\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[]
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fects}) has been already used, duplicate ignored
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\relax
l.15098 ...Extract Random Effects}{random.effects}
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fects.1}) has been already used, duplicate ignored
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l.15098 ...Extract Random Effects}{random.effects}
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[3485]
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[]\T1/pcr/m/n/9 plot(Remifentanil, type = "l", lwd = 2) # shows the 65 patient
s\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 remi profiles
[3486]
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[]\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served
- fit-ted) are used; else, if
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[3488]
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[] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[]
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[3491]
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[3493]
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[][][]\T1/pcr/m/n/10 groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 l
me[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/10 , [
][][]\T1/pcr/m/n/10 solve.reStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
summary.reStruct[][][][]\T1/ptm/m/n/10 ,
[3494]
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[] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[]
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[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
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[3504]
[3505]
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\T1/pcr/m/n/10 of an Identity" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pdIdent[]\
T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "General Positive-Definite,
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\T1/pcr/m/n/10 Natural Parametrization" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 p
dNatural[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "General
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\T1/pcr/m/n/10 Positive-Definite" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pdSymm[
]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 data.class(object)
[3507]
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[]\T1/pcr/m/n/10 "Constant plus power of variance
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[]\T1/pcr/m/n/10 "Constant plus proportion of variance
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[][][]\T1/pcr/m/n/10 varComb[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varCo
nstPower[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varConstProp[][][][]\T1/p
tm/m/n/10 , [][][]\T1/pcr/m/n/10 varExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m
/n/10 varFixed[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varIdent[][][][]\T1
/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 # Generate some synthetic data using the two-component error m
odel and use
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[]\T1/pcr/m/n/9 # overparameterisation in the case of a constant term in the v
ariance function[]
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[][][]\T1/pcr/m/n/10 Variogram.corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n
/10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.co
rLin[][][][]\T1/ptm/m/n/10 ,
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[][][]\T1/pcr/m/n/10 Variogram.corRatio[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m
/n/10 Variogram.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogr
am.corSpher[][][][]\T1/ptm/m/n/10 ,
[3522]
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
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[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 "[][]corR
atio[][][]"[]\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
[3526]
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
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[][][]\T1/pcr/m/n/10 corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Va
riogram[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.default[][][][]\
T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.corExp[][][][]\T1/ptm/m/n/10 ,
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[][][]\T1/pcr/m/n/10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 Variogram.corLin[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.co
rRatio[][][][]\T1/ptm/m/n/10 ,
[3527]
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
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[3529]
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[]\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served
- fit-ted) are used; else, if
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[3531]
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[]\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served
- fit-ted) are used; else, if
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[3535]
[3536]
[3537]
[3538]
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[3540]) (./nnet-pkg.tex
Chapter 26.
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l.47 ...t Multinomial Log-linear Models}{multinom}
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1}) has been already used, duplicate ignored
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l.47 ...t Multinomial Log-linear Models}{multinom}
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[] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
FALSE,[]
[3542]
[3543]
[3544]
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[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3545]
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[]\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c(
0,0,1),50)),[]
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[]\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[]
[3546]
[3547]
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[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3548]) (./rpart-pkg.tex
Chapter 27.
[3549]
[3550]
[3551]
[3552]
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[]\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse =
TRUE, ...)[]
[3553]
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\T1/ptm/m/n/10 age: []\T1/pcr/m/n/10 pretty = 0 []\T1/ptm/m/n/10 im-plies []\T1
/pcr/m/n/10 minlength = 0L[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pretty = NULL []\
T1/ptm/m/n/10 im-plies
[3554]
[3555]
[3556]
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[]\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 FALSE[]\T1/ptm/m/n/10 , the leaf nodes wil
l be at the hor-i-zon-tal plot co-or-di-nates of
[3557]
[3558]
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[] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
""),[]
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[]\T1/ptm/m/n/10 Logical. If []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 (de-fault),
adds to the la-bel
Underfull \hbox (badness 1142) in paragraph at lines 771--775
\T1/pcr/m/n/10 #events level1/ #events level2/ \T1/ptm/m/n/10 etc. for method [
]\T1/pcr/m/n/10 class[]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 n
[3559]
[3560]
[3561]
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[]\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[]
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[]\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"),[]
[3562]
[3563]
[3564]
[3565]
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[]\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m
ethod,
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[] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[]
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[]\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the []\T1/pcr/m/n
/10 rpart []\T1/ptm/m/n/10 al-go-rithm. See
[3566]
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[]\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the
text is clipped[]
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[]\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c
p = 0.01,
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[] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate
= 2, xval = 10,[]
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[]\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val-
ues are `[]\T1/pcr/m/n/10 diploid[]\T1/ptm/m/n/10 ',
[3574]
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[] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
FALSE,[]
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[3577]) (./spatial-pkg.tex
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Chapter 28.
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[3597]) (./survival-pkg.tex
[3598]
Chapter 29.
[3599]
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[]\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data
= lung, nmin = 1[]
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[]\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2) # Nearly the same, until t
he last point[]
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[]\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a
nd Grambsch.[]
[3601]
[3602]
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[]\T1/ptm/m/n/10 an op-tional list or vec-tor of group-ing el-e-ments, each as
long as
[3603]
[3604]
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\relax
l.384 ... Myelogenous Leukemia survival data}{aml}
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l.384 ... Myelogenous Leukemia survival data}{aml}
[3605]
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[]\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da
ta = ovarian)
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[]\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[]
[3606]
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[] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
lung)[]
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[]\T1/ptm/m/n/10 If H(t; z) is the pre-dicted cu-mu-la-tive haz-ard for an ob-s
er-va-tion with co-vari-ate vec-tor z,
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[3609]
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[]\T1/pcr/m/n/9 py <- pseudo(survfit(Surv(time, status) ~1, lung), time=730) #
2 year survival
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[]\T1/pcr/m/n/10 brier(fit, times, newdata, ties = TRUE, detail = FALSE, timef
ix = TRUE,
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[3612]
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[] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[]
[3613]
[3614]
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[] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[]
[3615]
[3616]
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[]\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi
al and negative-binomial data.
[3617]
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[]\T1/pcr/m/n/9 ppois(4, 10.24153) #chance of seeing 4 or fewer events wit
h large rate[]
[3618]
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[]\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert)
[3619]
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[]\T1/pcr/m/n/9 marginal.model <- coxph(Surv(time, status) ~ rx, data= rats, c
luster=litter,
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<to be read again>
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l.1407 ...erapy for Stage B/C colon cancer}{colon}
[3620]
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[] \T1/pcr/m/n/10 influence=0, ranks = FALSE, reverse=FALSE, timefix=TRUE, ke
epstrata=10, ...)[]
[3622]
[3623]
[3624]
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[]\T1/pcr/m/n/9 options(na.action = na.exclude) # predict all 1384 obs, incl
uding missing[]
[3625]
[3626]
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[]\T1/pcr/m/n/10 cox.zph(fit, transform="km", terms=TRUE, singledf=FALSE, glob
al=TRUE)
[3627]
[3628]
[3629]
[3630]
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[]\T1/ptm/m/n/10 One user mis-take that has re-cently arisen is to slav-ishly f
ol-low the ad-vice of
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\T1/ptm/m/n/10 some cod-ing guides and prepend []\T1/pcr/m/n/10 survival:: []\T
1/ptm/m/n/10 onto ev-er-thing, in-clud-ing the spe-
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\T1/ptm/m/n/10 cial terms, e.g., []\T1/pcr/m/n/10 survival::coxph(survival:Surv
(time, status) ~ age +
[3631]
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[][][]\T1/pcr/m/n/10 coxph.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
coxphms.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 coxph.control[][][]
[]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cluster[][][][]\T1/ptm/m/n/10 , [][][]\
T1/pcr/m/n/10 strata[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Surv[][][][]\
T1/ptm/m/n/10 ,
[3632]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2312--2312
[]\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix
=TRUE)[]
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[3634]
[3635]
[3636]
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[3638]
[3639]
[3640]
[3641]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2942--2942
[] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" "
exponential"[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2983--2983
[]\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass,
etype,
[3642]
[3643]
[3644]
[3645]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3227--3227
[]\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[]
[3646]
[3647]
[3648]
[3649]
Underfull \hbox (badness 1019) in paragraph at lines 3489--3491
[]\T1/ptm/m/n/10 outcome: []\T1/pcr/m/n/10 censor[]\T1/ptm/m/n/10 , []\T1/pcr/m
/n/10 thymic lymphoma[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 reticulum cell sarcoma
other
[3650]
[3651]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 3634--3634
[]\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney)
[3652]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3669--3669
[] \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre
ssion", "death")))[]
Underfull \hbox (badness 1389) in paragraph at lines 3683--3685
[]\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan
-Meier plot gen-er-ated with
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3694--3694
[] \T1/pcr/m/n/10 conf.type = c("log", "log-log", "plain", "logit", "ar
csin"),[]
[3653]
[3654]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3835--3835
[] \T1/pcr/m/n/9 rmap=list(sex=sex, age=age*365.35, year=as.Da
te(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/01/01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[]
[3655]
[3656]
Overfull \hbox (467.89665pt too wide) in alignment at lines 3976--3976
[] []
[3657]
[3658]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4098--4098
[]\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[]
[3659]
[3660]
[3661]
[3662]
[3663]
[3664]
[3665]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4549--4549
[] \T1/pcr/m/n/9 entry.dt = as.Date(paste("2011", 1:10, "5"
, sep=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 -\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[]
[3666]
[3667]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4699--4699
[]\T1/pcr/m/n/9 tdata <- data.frame(x= lung$age, y = 10*log(lung$age-35) + rno
rm(228, 0, 2))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4704--4704
[]\T1/pcr/m/n/9 knots <- unlist(attributes(fit1$model[[2]])[c(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 Boundary.knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , \TS1/pcr/m/n/9 '\T1
/pcr/m/n/9 knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )])[]
[3668]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4708--4708
[]\T1/pcr/m/n/9 unname(coef(fit1)[-1] - coef(fit1)[1]) # differences: yhat[2:
4] - yhat[1][]
[3669]
[3670]
[3671] [3672]
[3673]
[3674]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5131--5131
[] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca
le=1,[]
[3675]
[3676]
[3677]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5369--5369
[]\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign),
collapse,[]
[3678]
[3679]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5522--5522
[]\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5530--5530
[] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means
, na.rm=TRUE)[]
[3680]
[3681]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5616--5616
[]\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival
is at +infinity[]
[3682]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5694--5694
[] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars"), expand=FALSE
, ...)[]
[3683]
Underfull \hbox (badness 1852) in paragraph at lines 5766--5768
[]\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.survfit"[]\T1/pt
m/m/n/10 , which is the re-sult of the
[3684]
[3685]
[3686]
[3687]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6020--6020
[]\T1/pcr/m/n/9 rhat <- predict(rfit, newdata=expand.grid(ph.ecog=0:3, sex=1:2
), se.fit=TRUE)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6032--6032
[]\T1/pcr/m/n/9 # the estimate for ph.ecog=3 is very unstable (n=1), pseudoval
ues smooth it.[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6034--6034
[]\T1/pcr/m/n/9 # In all the above we should be using the robust variance, e.g
., svyglm, but[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6058--6058
[]\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me
thod,
Overfull \hbox (36.78088pt too wide) in paragraph at lines 6059--6059
[] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co
mbine, ...)[]
[3688]
[3689]
[3690]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 6222--6222
[] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[]
[3691]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6324--6324
[]\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age
+ sex, mgus,[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6345--6345
[]\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50
,60,70,100)) +[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6347--6347
[]\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[]
[3692]
[3693]
[3694]
[3695]
[3696]
[3697]
[3698]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6801--6801
[]\T1/pcr/m/n/9 gfit <- survfit(Surv(day1, day2, status) ~ batch, braking, id=
locomotive)[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 6803--6803
[] \T1/pcr/m/n/9 xlab="Locomotive Age in Months", ylab="Mean cumulative nu
mber replacements")[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6806--6806
[]\T1/pcr/m/n/9 # natural target, an estimate of the number of replacements b
y a given time[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6808--6808
[]\T1/pcr/m/n/9 # When two valve seats failed at the same inspection, we need
to jitter one[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6810--6810
[]\T1/pcr/m/n/9 ties <- which(with(valveSeat, diff(id)==0 & diff(time)==0)) #
first of a tie[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6814--6814
[]\T1/pcr/m/n/9 vdata$time1 <- ifelse(!duplicated(vdata$id), 0, c(0, temp[-len
gth(temp)]))[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 6841--6841
[] \T1/pcr/m/n/10 collapse=FALSE, weighted= (type %in% c("dfbeta", "dfbe
tas")), ...)[]
[3699]
[3700]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 6935--6935
[] \T1/pcr/m/n/10 type="pstate", collapse=FALSE, weighted= collapse, data.f
rame=FALSE,[]
[3701]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 7034--7034
[]\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[]
Underfull \hbox (badness 1043) in paragraph at lines 7046--7049
[]\T1/pcr/m/n/10 "dfbetas"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "working"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "ldcase"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lsresp
"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ldshape"[]\T1/ptm/m/n/10 , and
[3702]
[3703]
[3704]
[3705]
[3706]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7353--7353
[]\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), lung)[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 7354--7354
[]\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), lung)[]
[3707]
[3708]
[3709]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 7544--7544
[]\T1/pcr/m/n/10 rttright(formula, data, weights, subset, na.action, times, id
, timefix = TRUE,
[3710]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 7627--7627
[]\T1/pcr/m/n/9 cdf <- cdf[!duplicated(aml$time[index], fromLast=TRUE)] # rem
ove duplicate times[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7631--7631
[]\T1/pcr/m/n/9 wt2 <- rttright(Surv(dtime, death) ~ hormon, rotterdam, times=
365*c(3, 5))[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder})
has been already used, duplicate ignored
<to be read again>
\relax
l.7635 ...ata from a soldering experiment}{solder}
[3711]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7690--7690
[]\T1/pcr/m/n/9 dummy <- expand.grid(Opening= c("S", "M", "L"), Solder=c("Thin
", "Thick"))[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 7692--7692
[] \T1/pcr/m/n/9 dimnames=list(Opening= c("S", "M", "L"), Solder=c(
"Thin", "Thick")))[]
[3712]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 7752--7752
[]\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1,
col = 1,
[3713]
[3714]
[3715]
[3716]
[3717]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8118--8118
[]\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r
r =expected,[]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8119--8119
[]\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli
ne = FALSE,[]
[3718]
[3719]
[3720]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 8277--8277
[] \T1/pcr/m/n/10 extend=FALSE, rmean=getOption(\TS1/pcr/m/n/10 '\T1/pcr/m/n/
10 survfit.rmean\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ), data.frame=FALSE, dosum, ...
)[]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8280--8280
[] \T1/pcr/m/n/10 extend=FALSE, rmean=getOption(\TS1/pcr/m/n/10 '\T1/pcr/m/n/
10 survfit.rmean\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ), data.frame=FALSE, ...)[]
[3721]
[3722]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 8471--8471
[] \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/
10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p
cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/
n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10
, \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T
S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[]
[3723]
[3724]
[3725]
Underfull \hbox (badness 1253) in paragraph at lines 8750--8753
[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 median[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10
quantile []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 plot []\T1/ptm/m/n/10 meth-ods
first con-struct a sur-vival curve us-ing
[3726]
[3727]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8889--8889
[]\T1/pcr/m/n/10 survcheck(formula, data, subset, na.action, id, istate, istat
e0="(s0)",
[3728]
[3729]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9021--9021
[]\T1/pcr/m/n/10 survcondense(formula, data, subset, weights, na.action= na.pa
ss, id,
[3730]
[3731]
[3732]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9221--9221
[]\T1/pcr/m/n/9 check <- coxph(Surv(time, status) ~ factor(pat.karno) + strata
(inst), lung)[]
[3733]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 9227--9227
[] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1
, year=accept.dt),[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 9252--9252
[] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[]
Underfull \hbox (badness 1038) in paragraph at lines 9294--9300
[]\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre
-dicted sur-vival
[3734]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 9346--9346
[] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[]
[3735]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9432--9432
[]\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival
by 1/2 years[]
[3736]
[3737]
[3738]
Underfull \hbox (badness 10000) in paragraph at lines 9652--9657
[][][]\T1/pcr/m/n/10 survfit.formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 survfit.coxph[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 survfit.object[][
][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.survfit[][][][]\T1/ptm/m/n/10
,
[3739]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9672--9672
[] \T1/pcr/m/n/10 se.fit=TRUE, conf.int=.95, individual=FALSE, stype=2,
ctype,[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 9673--9673
[] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit",
"arcsin"),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 9678--9678
[] \T1/pcr/m/n/10 se.fit=FALSE, conf.int=.95, individual=FALSE, stype=2
, ctype,[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 9679--9679
[] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit",
"arcsin"),[]
[3740]
[3741]
[3742]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9901--9901
[] \T1/pcr/m/n/10 stype=1, ctype=1, id, cluster, robust, istate, timefi
x=TRUE,[]
[3743]
Underfull \hbox (badness 4441) in paragraph at lines 10042--10052
[]\T1/ptm/m/n/10 by de-fault, the surv-fit rou-tines only re-turn in-for-ma-tio
n at the
[3744]
Underfull \hbox (badness 2653) in paragraph at lines 10054--10059
\T1/pcr/m/n/10 ctype=1[]\T1/ptm/m/n/10 , "fleming-harrington" which is equiv-a-
lent to []\T1/pcr/m/n/10 stype=2,
[3745]
[3746]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10242--10242
[]\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored
(status=3),[]
[3747]
[3748]
[3749]
[3750]
[3751]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 10674--10674
[]\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
survtype,
[3752]
Underfull \hbox (badness 1354) in paragraph at lines 10715--10719
[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
e time range
[3753]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 10761--10761
[]\T1/pcr/m/n/10 survConcordance(formula, data, weights, subset, na.action) #
use concordance
[3754]
[3755]
Underfull \hbox (badness 2035) in paragraph at lines 10925--10932
\T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][][]\T1/pcr/m/n/10 su
rvreg.distributions[][][][]\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 10925--10932
\T1/ptm/m/n/10 These in-clude []\T1/pcr/m/n/10 "weibull"[]\T1/ptm/m/n/10 , []\T
1/pcr/m/n/10 "exponential"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "gaussian"[]\T1/p
tm/m/n/10 ,
Underfull \hbox (badness 1297) in paragraph at lines 10925--10932
[]\T1/pcr/m/n/10 "logistic"[]\T1/ptm/m/n/10 ,[]\T1/pcr/m/n/10 "lognormal" []\T1
/ptm/m/n/10 and []\T1/pcr/m/n/10 "loglogistic"[]\T1/ptm/m/n/10 . Oth-er-wise, i
t is
[3756]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11015--11015
[]\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[]
[3757]
[3758]
[3759]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 11172--11172
[] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[]
[3760]
[3761]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11304--11304
[] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x
^2*temp -1))[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 11307--11307
[] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[]
[3762]
[3763]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11483--11483
[]\T1/pcr/m/n/9 pfit2 <- pyears(Surv(years, death) ~ fgrp + agegrp, scale =100
0, data=test)[]
[3764]
[3765]
[3766]
[3767]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11712--11712
[]\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic
al trial plus[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11713--11713
[]\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data
set has data[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11719--11719
[] \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day
, alk.phos))[]
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[]\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil
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Chapter 1.
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[]\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber []\T1/pcr/m/n/
10 x []\T1/ptm/m/n/10 such that []\T1/pcr/m/n/10 1 + x != 1[]\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 It equals []\T1/pcr/m/n/10 double.base ^ ulp.digits []\T1/ptm/m/
n/10 if ei-ther []\T1/pcr/m/n/10 double.base []\T1/ptm/m/n/10 is
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\T1/ptm/m/n/10 2 or []\T1/pcr/m/n/10 double.rounding []\T1/ptm/m/n/10 is 0; oth
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[]\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber []\T1/pcr/m/n/10 x [
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\T1/ptm/m/n/10 equals []\T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits []\T
1/ptm/m/n/10 if []\T1/pcr/m/n/10 double.base
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[]\T1/ptm/m/n/10 is 2 or []\T1/pcr/m/n/10 double.rounding []\T1/ptm/m/n/10 is 0
; oth-er-wise, it is []\T1/pcr/m/n/10 (double.base
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\T1/pcr/m/n/10 ^ double.neg.ulp.digits) / 2[]\T1/ptm/m/n/10 . Nor-mally []\T1/p
cr/m/n/10 1.110223e-16[]\T1/ptm/m/n/10 . As
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[]\T1/ptm/m/n/10 the num-ber of \T1/ptm/m/it/10 bytes \T1/ptm/m/n/10 in the C [
]\T1/pcr/m/n/10 time_t []\T1/ptm/m/n/10 type: a 64-bit []\T1/pcr/m/n/10 time_t
[]\T1/ptm/m/n/10 (value
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[]\T1/pcr/m/n/10 8[]\T1/ptm/m/n/10 ) is much pre-ferred these days. Note that t
his is the type used by
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[]\T1/ptm/m/n/10 introduced in \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.0.0. When [][]
[]\T1/pcr/m/n/10 capabilities[][][]("long.double") []\T1/ptm/m/n/10 is
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[]\T1/pcr/m/n/10 *.exponent[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 *.min.exp[]\T1/p
tm/m/n/10 , and []\T1/pcr/m/n/10 *.max.exp[]\T1/ptm/m/n/10 , com-puted en-tirel
y anal-o-gously to their
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[]\T1/ptm/m/n/10 Note that it is le-gal for a plat-form to have a `[]\T1/pcr/m/
n/10 long double[]\T1/ptm/m/n/10 ' C type which is
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\T1/ptm/m/n/10 iden-ti-cal to the `[]\T1/pcr/m/n/10 double[]\T1/ptm/m/n/10 ' ty
pe --- this hap-pens on ARM CPUs. In that case
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[][][]\T1/pcr/m/n/10 capabilities[][][]("long.double") []\T1/ptm/m/n/10 will be
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[][][]\T1/pcr/m/n/10 R.version[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10
Sys.info[][][] []\T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-l
ar,
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[]
\T1/pcr/m/n/10 insertions[]\T1/ptm/m/n/10 ',
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[]\T1/pcr/m/n/9 agrep("laysy", c("1 lazy", "1", "1 LAZY"), max.distance = 2, v
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[] \T1/pcr/m/n/10 ..., check.attributes = TRUE, check.class = TRUE, g
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[]\T1/pcr/m/n/9 all.equal(tan(d45), one, tolerance = 0, scale = 1+(-2:2)/1e9)
# "absolute"[]
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[]\T1/pcr/m/n/9 mtext(paste("mean(all.equal(x1, x2*(1 + eps_k))) {100 x} Mean
rel.diff.=",[]
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[]\T1/pcr/m/n/9 all.equal(two^20, 2^20, check.attributes = FALSE)# "target is
bar, current is numeric"[]
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[]\T1/pcr/m/n/9 all.equal(two^20, 2^20, check.attributes = FALSE, check.class
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[]\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F
ALSE)
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[]\T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion, where \T1/phv/m/n/10 R \T1/p
tm/m/n/10 uses ``floored'' in-te-ger di-vi-sion, i.e., []\T1/pcr/m/n/10 q <- x
%/% y :=
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\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . oracle
. com / cd / E19957-[]01 / 806-[]3568 / ncg _
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[] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em
pty.names = TRUE,[]
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[]\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more
than 256 (or
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[]\T1/pcr/m/n/9 names(dL <- as.data.frame(L))
# "NA."[]
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[]\T1/pcr/m/n/9 names(dL1 <- as.data.frame(L, col.names = names(L)))
# "NA."[]
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[]\T1/pcr/m/n/9 names(dL1.<- as.data.frame(L, check.name
s=FALSE)) # "NA"[]
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[]\T1/pcr/m/n/9 names(dL2 <- as.data.frame(L, col.names = names(L), check.name
s=FALSE)) # NA[]
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[]\T1/pcr/m/n/9 names(dLn <- as.data.frame(L, new.names = TRUE, check.name
s=FALSE)) # NA[]
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[]\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[]
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[]\T1/ptm/m/n/10 If [][][]\T1/pcr/m/n/10 is.object[][][](x) []\T1/ptm/m/n/10 is
true and it has a [][][]\T1/pcr/m/n/10 class[][][] []\T1/ptm/m/n/10 for which
an
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[]\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla
ss "POSIXlt"[]
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[]\T1/pcr/m/n/9 if(file.exists(tab)) { # typically on Windows; on Linux when
\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 configure --with-internal-tzcode\TS1/cmtt/m/n/9
`[]
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[]\T1/ptm/m/n/10 There are no re-stric-tions on the name given as []\T1/pcr/m/n
/10 x[]\T1/ptm/m/n/10 : it can be a non-syntactic name (see
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[]\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse1(substitute(what), back
tick=FALSE),
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[]\T1/pcr/m/n/10 unCfillPOSIXlt(x) []\T1/ptm/m/n/10 is a fast [][]prim-i-tive[]
[][] ver-sion of []\T1/pcr/m/n/10 balancePOSIXlt(x,
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[]\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2,
lwd = 1, bty="n")[]
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[]\T1/pcr/m/n/9 plot(range(x0), c(1e-40, 1), log = "xy", xlab = "x", ylab = ""
, type = "n",[]
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[] \T1/pcr/m/n/9 main = "Bessel Functions J_nu(x) near 0\n log - log sc
ale") ; axis(2, at=1)[]
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[]\T1/pcr/m/n/9 plot(range(x0), 10^c(-100, 80), log = "xy", xlab = "x", ylab =
"", type = "n",[]
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[] \T1/pcr/m/n/9 main = "Bessel Functions K_nu(x) near 0\n log - log sc
ale") ; axis(2, at=1)[]
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[]\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5,
sep = ", ")),[]
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[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
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[]\T1/pcr/m/n/9 L <- as.list(E <- setNames( , c("if", "for", "while", "repeat"
, "function",[]
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[] \T1/pcr/m/n/9 "(", "{", "[", "<-", "<<-",
"->", "=")))[]
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[]\T1/pcr/m/n/9 for(i in seq_along(L)) L[[i]] <- call(E[[i]]) # instead of lap
ply(E, call) ..[]
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[]\T1/pcr/m/n/9 list_ <- function (...) \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 names<-
\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 (list(...), vapply(sys.call()[-1L], as.character
, ""))[]
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[]\T1/pcr/m/n/9 (Tab <- noquote(sapply(list_(is.call, typeof, class, mode), \(
F) sapply(L, F))))[]
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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an
ob-ject
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\T1/ptm/m/n/10 of class []\T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"[]\T1/ptm/
m/n/10 , []\T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" []\T1/ptm/m/n/10 o
r
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[] \T1/pcr/m/n/10 Xchk = any(nas %in% c("X11", "jpeg", "png", "tif
f")))[]
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[]\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par
-i-son[][][] and
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[]\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[]
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[]\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na
med ar-gu-
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[]\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu
e and valid
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[]\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[]
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[]\T1/pcr/m/n/9 as.character(list(A = "Abc", xy = c("x", "y"))) # "Abc" "c(\"
x\", \"y\")"[]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c
har-ac-ter by
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[]\T1/ptm/m/n/10 When a generic func-tion []\T1/pcr/m/n/10 fun []\T1/ptm/m/n/10
is ap-plied to an ob-ject with class at-tribute []\T1/pcr/m/n/10 c("first",
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[]\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i
n-tro-duc-tion see [][]$\T1/pcr/m/n/10 https : / /
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[]\T1/pcr/m/n/9 stopifnot(identical(as.complex(NA_real_), NA_real_ + 0i)) # ha
s always been true[]
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[]\T1/pcr/m/n/9 NAs <- vapply(list(NA, NA_integer_, NA_real_, NA_character_, N
A_complex_),[]
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[]\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile
r, math-library:[]
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[]\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[]
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[]\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class []\T1/pcr/m/n
/10 interrupt []\T1/ptm/m/n/10 that in-her-its di-rectly from class
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[]\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols.
They can be es-tab-lished us-ing
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[]\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i
s []\T1/pcr/m/n/10 interactive[]\T1/ptm/m/n/10 . This should
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[]\T1/pcr/m/n/10 zstdfile(description, open = "", encoding = getOption("encodi
ng"),[]
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[]\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[]
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[]\T1/ptm/m/n/10 character string, par-tially matched to []\T1/pcr/m/n/10 c("de
fault", "internal",
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[]\T1/pcr/m/n/10 file[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pipe[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 fifo[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 url[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 gzfile[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 bzfile[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 xzfile[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 zstdfile[]\T1/
ptm/m/n/10 , []\T1/pcr/m/n/10 unz[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 socketConnection[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 socketAcce
pt []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 serverSocket []\T1/ptm/m/n/10 re-turn
a con-nec-tion ob-ject
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[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
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[]\T1/pcr/m/n/10 file []\T1/ptm/m/n/10 can be used with []\T1/pcr/m/n/10 descri
ption = "clipboard" []\T1/ptm/m/n/10 in mode []\T1/pcr/m/n/10 "r" []\T1/ptm/m/n
/10 only. This
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[]\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[]
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[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
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[]\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect
s to https://[]
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[]\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[]
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[]\T1/pcr/m/n/10 data.frame []\T1/ptm/m/n/10 con-verts each of its ar-gu-ments
to a data frame by call-ing
Underfull \hbox (badness 1975) in paragraph at lines 8897--8907
[][][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)[]\T1/ptm/m/n/10 . As
that is a generic func-tion, meth-ods can be
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[] \T1/pcr/m/n/9 c = seq(as.Date("2004-01-01"), by = "week", l
ength.out = 3),[]
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\T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") []\T1/ptm/m
/n/10 may give []\T1/pcr/m/n/10 NA[]\T1/ptm/m/n/10 , and
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[]\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: --------
-------------[]
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[]\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO
!\n"); pi+2})[]
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[] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "(
", "function"),[]
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[] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh
owAttributes"),[]
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[]\T1/pcr/m/n/10 ..deparseOpts []\T1/ptm/m/n/10 is the [][][]\T1/pcr/m/n/10 cha
racter[][][] []\T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used b
y
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[]\T1/ptm/m/n/10 Surround un-eval-u-ated ex-pres-sions, but not [][][]\T1/pcr/m
/n/10 formula[][][][]\T1/ptm/m/n/10 s, with
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[]\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t
er-mi-nant if
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[] \T1/pcr/m/n/10 z <- as.POSIXct(c("2016-12-31 23:59:59", "2017-01-01 00:0
0:01"))[]
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[]\T1/pcr/m/n/10 provideDimnames(x) []\T1/ptm/m/n/10 pro-vides []\T1/pcr/m/n/10
dimnames []\T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has
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[]\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE
RS)))) # recycling[]
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[]\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
on both levels[]
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[]\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of []\
T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . Cur-rently this is only used by
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[]\T1/pcr/m/n/9 ## From R 4.1.0 to 4.1.2, ...names() sometimes did not match n
ames(list(...));[]
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[]\T1/pcr/m/n/9 chk.n2 <- function(...) stopifnot(identical(print(...names()),
names(list(...))))[]
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19
85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .
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\T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr
/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _
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\T1/pcr/m/n/10 754-[]2019$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / /
en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/
pcr/m/n/10 https :
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[] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA
ttributes"))[]
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[]\T1/pcr/m/n/9 ## Write an ASCII version of the \TS1/pcr/m/n/9 '\T1/pcr/m/n/9
base\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 function mean() to our temp file, ..[]
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[]\T1/pcr/m/n/9 drop(1:3 %*% 2:4) # scalar product - w/o drop(.), would retur
n 1x1 matrix[]
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[]\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9]))
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[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for
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[]\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) []\T1/ptm/m/n/10 is equiv-a-len
t to but faster than
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[]\T1/ptm/m/n/10 Do not use []\T1/pcr/m/n/10 dyn.unload []\T1/ptm/m/n/10 on a D
LL loaded by [][][]\T1/pcr/m/n/10 library.dynam[][][][]\T1/ptm/m/n/10 : use
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[]\T1/ptm/m/n/10 Changing the cur-rent en-cod-ing from a run-ning R ses-sion ma
y lead to con-fu-sion (see
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[]\T1/pcr/m/n/9 Encoding(x.) # "unknown" (UTF-8 loc.) | "latin1" (8859-1/CP-12
52 loc.) | ....[]
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[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of
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[]\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][][]\T1/pcr/m/n/1
0 dev2bitmap[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 bitmap[][][] []\T1/pt
m/m/n/10 and
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[]\T1/ptm/m/n/10 The path to HTML []\T1/pcr/m/n/10 tidy[]\T1/ptm/m/n/10 . Used
by []\T1/pcr/m/n/10 R CMD check []\T1/ptm/m/n/10 if
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[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
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[]\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing []\T1/pc
r/m/n/10 where []\T1/ptm/m/n/10 as
Underfull \hbox (badness 5970) in paragraph at lines 13268--13270
[]\T1/pcr/m/n/10 get0(): []\T1/ptm/m/n/10 The object---as from [][][]\T1/pcr/m/
n/10 get[][][](x, *)[]\T1/ptm/m/n/10 --- if []\T1/pcr/m/n/10 exists(x, *) []\T1
/ptm/m/n/10 is true, oth-er-wise
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[]\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide
a constructor[]
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[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
done: see
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[]\T1/ptm/m/n/10 Junction points and sym-bolic links are fol-lowed, so in-for-m
a-tion is given about the
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[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as []\T1/pcr
/m/n/10 PATH []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 R_LIBS []\T1/ptm/m/n/10 with
[]\T1/pcr/m/n/10 fsep =
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[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
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[][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil
e.access[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.path[][][][]\T1/ptm/
m/n/10 , [][][]\T1/pcr/m/n/10 file.show[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m
/n/10 list.files[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 unlink[][][][]\T1
/ptm/m/n/10 ,
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .
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[] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B
as it exists already[]
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[]\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
= "0777")[]
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[][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil
e.exists[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.path[][][][]\T1/ptm/
m/n/10 , [][][]\T1/pcr/m/n/10 list.files[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/
m/n/10 unlink[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 basename[][][][]\T1/
ptm/m/n/10 ,
Overfull \hbox (9.78043pt too wide) in paragraph at lines 15439--15439
[]\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive = TRUE)[]
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[]\T1/pcr/m/n/10 packageNotFoundError []\T1/ptm/m/n/10 cre-ates an er-ror con-d
i-tion ob-ject of class
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[]\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio
ns it is found:[]
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[]\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE,
Overfull \hbox (6.78088pt too wide) in paragraph at lines 15552--15552
[] \T1/pcr/m/n/10 left.open = FALSE, checkSorted = TRUE, checkNA =
TRUE)[]
[224]
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[]\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr
i-bu-tion func-tion, and in-deed,
Overfull \hbox (52.98038pt too wide) in paragraph at lines 15642--15642
[]\T1/pcr/m/n/9 stopifnot(identical(it, ## suppressing the checks is faster *B
UT* dangerous, unless[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 15643--15643
[] \T1/pcr/m/n/9 ## you *know* that X is sorted and
tt contains no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 15644--15644
[] \T1/pcr/m/n/9 findInterval(tt, X, checkSorted=FALSE, che
ckNA=FALSE)))[]
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[] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15758--15758
[] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[]
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[]\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have
type symbol (aka name).[]
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[]\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co
mbination with[]
[231]
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[]\T1/ptm/m/n/10 either a log-i-cal spec-i-fy-ing whether el-e-ments of a real
or com-plex vec-
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\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger
penalty (see
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[]\T1/pcr/m/n/10 big.mark[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 big.interval[]\T1/
ptm/m/n/10 , []\T1/pcr/m/n/10 small.mark[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sma
ll.interval[]\T1/ptm/m/n/10 ,
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Underfull \hbox (badness 6944) in paragraph at lines 16188--16191
[][][]\T1/pcr/m/n/10 formatC[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 paste
[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 as.character[][][][]\T1/ptm/m/n/1
0 , [][][]\T1/pcr/m/n/10 sprintf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 p
rint[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 prettyNum[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 toString[][][][]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[]
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[]\T1/pcr/m/n/10 prettyNum() []\T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (p
os-si-bly for-mat-ted) num-bers, also in
Overfull \hbox (48.78088pt too wide) in paragraph at lines 16376--16376
[] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark =
decimal.mark,[]
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[]\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric
(x)),[]
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[]\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][]
[]\T1/pcr/m/n/10 complex[][][] []\T1/ptm/m/n/10 only for
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[]\T1/pcr/m/n/10 "f" []\T1/ptm/m/n/10 gives num-bers in the usual []\T1/pcr/m/n
/10 xxx.xxx []\T1/ptm/m/n/10 for-mat; []\T1/pcr/m/n/10 "e" []\T1/ptm/m/n/10 and
[]\T1/pcr/m/n/10 "E" []\T1/ptm/m/n/10 give
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[]\T1/ptm/m/n/10 This works via []\T1/pcr/m/n/10 prettyNum()[]\T1/ptm/m/n/10 ,
which calls []\T1/pcr/m/n/10 .format.zeros(*,
Underfull \hbox (badness 10000) in paragraph at lines 16518--16523
[]\T1/ptm/m/n/10 For num-bers, []\T1/pcr/m/n/10 formatC() []\T1/ptm/m/n/10 call
s []\T1/pcr/m/n/10 prettyNum() []\T1/ptm/m/n/10 when needed which it-self calls
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[]\T1/ptm/m/n/10 If you set []\T1/pcr/m/n/10 format []\T1/ptm/m/n/10 it over-ri
des the set-ting of []\T1/pcr/m/n/10 mode[]\T1/ptm/m/n/10 , so []\T1/pcr/m/n/10
formatC(123.45, mode =
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Underfull \hbox (badness 10000) in paragraph at lines 16535--16543
[]\T1/pcr/m/n/10 prettyNum []\T1/ptm/m/n/10 is the util-ity func-tion for pret-
ti-fy-ing []\T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 x []\T1/ptm/m/n
/10 can be com-plex (or
[239]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 16642--16642
[]\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big
.mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[]
Underfull \vbox (badness 10000) has occurred while \output is active
[240]
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[]\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you
want see the effect[]
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[]\T1/pcr/m/n/10 Reduce(f, x, init, right = FALSE, accumulate = FALSE, simplif
y = TRUE)
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 17335--17335
[]\T1/pcr/m/n/9 ## very low-level: get()ing the "missing argument", e.g., insi
de browser()[]
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[] \T1/pcr/m/n/9 is.symbol(E$m) # => valid argument to get(), and *also* ge
ts \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 missing arg\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[]
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[]\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil
l a DLLInfoList[]
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Underfull \hbox (badness 2418) in paragraph at lines 17637--17641
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing [
]\T1/pcr/m/n/10 CRoutine[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 CallRoutine[]\T1/pt
m/m/n/10 ,
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 name []\T1/ptm/m/n/10 con-tains only one s
ym-bol name and []\T1/pcr/m/n/10 unlist []\T1/ptm/m/n/10 is []\T1/pcr/m/n/10 TR
UE[]\T1/ptm/m/n/10 , then the sin-gle
Underfull \hbox (badness 2326) in paragraph at lines 17679--17686
[][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][][]\T1/ptm/m/n/10 , [][][]\T1
/pcr/m/n/10 is.loaded[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .C[][][][]\T
1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .Fortran[][][][]\T1/ptm/m/n/10 , [][][]\T1/
pcr/m/n/10 .External[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .Call[][][][]
\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 ## Not run: ## for translation, those strings should appear in
R-pkg.pot as[]
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[]\T1/pcr/m/n/9 if(is.na(thisLang) || !nzchar(thisLang)) thisLang <- "en" # "f
actory" default[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 17863--17863
[]\T1/pcr/m/n/9 gettext(enT, domain="R-stats")# "leeres Modell angegeben" (if
translation works)[]
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[]\T1/pcr/m/n/9 ## Here, we reset to the *original* setting before the full ex
ample started:[]
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[]\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE,
Overfull \hbox (0.78088pt too wide) in paragraph at lines 18034--18034
[]\T1/pcr/m/n/10 grepv(pattern, x, ignore.case = FALSE, perl = FALSE, value =
TRUE,[]
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Underfull \hbox (badness 1867) in paragraph at lines 18062--18069
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
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Overfull \hbox (20.58041pt too wide) in paragraph at lines 18391--18391
[] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around
"checking hack"[]
Underfull \vbox (badness 10000) has occurred while \output is active
[265]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 18420--18420
[]\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[]
Underfull \vbox (badness 10000) has occurred while \output is active
[266]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 18476--18476
[] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[]
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Overfull \hbox (9.78043pt too wide) in paragraph at lines 18858--18858
[]\T1/pcr/m/n/9 (ii <- grouping(x <- c(1, 1, 3:1, 1:4, 3), y <- c(9, 9:1), z <
- c(2, 1:9)))
[271]
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[]\T1/pcr/m/n/9 z <- gzcon(url("https://www.stats.ox.ac.uk/pub/datasets/csb/ch
12.dat.gz"))[]
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Overfull \hbox (0.78088pt too wide) in paragraph at lines 19134--19134
[]\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE)
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Underfull \hbox (badness 1360) in paragraph at lines 19297--19301
[]\T1/ptm/m/n/10 The most portable name for the ISO 8859-15 en-cod-ing, com-mon
ly known as `Latin 9',
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\T1/ptm/m/n/10 is []\T1/pcr/m/n/10 "iso885915"[]\T1/ptm/m/n/10 : most plat-form
s sup-port both []\T1/pcr/m/n/10 "latin-9" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/1
0 "latin9" []\T1/ptm/m/n/10 but GNU
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Underfull \hbox (badness 1163) in paragraph at lines 19517--19519
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 https : / / unicode-[]org . github . io / icu /
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19525--19525
[]\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s
ettings, we can only reset to the default.[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 19555--19555
[]\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE,
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[] \T1/pcr/m/n/10 num.eq = FALSE, single.NA = FALSE, attrib.as.se
t = FALSE,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19650--19650
[] \T1/pcr/m/n/10 ignore.bytecode = FALSE, ignore.environment = F
ALSE,[]
[283]
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[]\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------
----------------[]
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[]\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is
ignored by default[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 19712--19712
[]\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share
an environment:[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19718--19718
[]\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi
ng "srcref" :[]
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[]\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u
se ifelse(),[]
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[]\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[]
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Underfull \hbox (badness 10000) in paragraph at lines 20058--20060
[]\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][][]\T
1/pcr/m/n/10 stop[][][] []\T1/ptm/m/n/10 and
[289]
Underfull \hbox (badness 2057) in paragraph at lines 20161--20187
[][][]\T1/pcr/m/n/10 as.character[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
as.complex[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 as.double[][][][]\T1/pt
m/m/n/10 , [][][]\T1/pcr/m/n/10 as.integer[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc
r/m/n/10 as.logical[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 as.raw[][][][]
\T1/ptm/m/n/10 ,
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Underfull \hbox (badness 10000) in paragraph at lines 20359--20367
\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . oracle
. com / cd / E19957-[]01 / 806-[]3568 / ncg _
[293]
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[295]
Underfull \hbox (badness 4699) in paragraph at lines 20559--20562
[]\T1/pcr/m/n/10 is.atomic []\T1/ptm/m/n/10 is true for the [][]atomic[][][] ty
pes ([]\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "integer"[]\
T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "numeric"[]\T1/ptm/m/n/10 ,
[296]
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[]\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[]
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Underfull \hbox (badness 4739) in paragraph at lines 20828--20830
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[300]
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[]\T1/pcr/m/n/9 isSymmetric(D3) # FALSE (as row and co
lumn names differ)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20884--20884
[]\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE (as names are
not checked)[]
[301]
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[]\T1/pcr/m/n/10 .kappa_tri(z, exact = FALSE, LINPACK = TRUE, norm = NULL, upl
o = "U", ...)[]
[302]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 21001--21001
[]\T1/pcr/m/n/10 rcond(x, norm = c("O","I","1"), triangular = FALSE, uplo = "U
", ...)[]
[303]
Underfull \hbox (badness 2961) in paragraph at lines 21085--21088
[]\T1/ptm/m/n/10 LAPACK and LIN-PACK are from [][]$\T1/pcr/m/n/10 https : / / n
etlib . org / lapack/$[][] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / /
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[]\T1/pcr/m/n/9 ## Moore-Penrose inverse { ~= MASS::ginv(); differing tol (val
ue & meaning)}:[]
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[]\T1/pcr/m/n/9 try( kappa(m76, exact=TRUE, norm="1") )# error in solve().. m
ust be square[]
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[]\T1/pcr/m/n/9 ## ==> use pseudo-inverse instead of solve() for rectangular {
and norm != "2"}:[]
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[] \T1/pcr/m/n/9 inv_z = solve(A, tol = 1e-19))) # 5.22057e16 on x86_
64 Linux with GCC[]
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[]\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p
hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to
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[]\T1/ptm/m/n/10 In late 2017 a []\T1/pcr/m/n/10 libcurl []\T1/ptm/m/n/10 in-st
al-la-tion was seen di-vided into two li-braries, []\T1/pcr/m/n/10 libcurl []\T
1/ptm/m/n/10 and
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[][][]$\T1/pcr/m/n/10 https : / / curl . se / docs / sslcerts . html$[][] \T1/p
tm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / curl . se / docs /
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[]\T1/ptm/m/n/10 At startup, the li-brary search path is ini-tial-ized from the
en-vi-ron-ment vari-ables []\T1/pcr/m/n/10 R_LIBS[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 LOCALAPPDATA []\T1/ptm/m/n/10 (usu-ally []\T1/pcr/m/n/10 C:\Us
ers\username\AppData\Local[]\T1/ptm/m/n/10 ) on Win-dows is a
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\T1/ptm/m/n/10 hid-den di-rec-tory and may not be viewed by some soft-ware. It
may be opened by
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[]\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use
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[][][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][][]\T1/ptm/m/n/10 : thi
s will sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 library []\T1/ptm/m/n/10 is called with no
[]\T1/pcr/m/n/10 package []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 help []\T1/ptm/m
/n/10 ar-gu-ment, it lists all avail-able pack-
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[][][]\T1/pcr/m/n/10 attach[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 detach
[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 search[][][][]\T1/ptm/m/n/10 , []
[][]\T1/pcr/m/n/10 objects[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 autoloa
d[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 requireNamespace[][][][]\T1/ptm/
m/n/10 ,
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[]\T1/ptm/m/n/10 Do not use [][][]\T1/pcr/m/n/10 dyn.unload[][][] []\T1/ptm/m/n
/10 on a DLL loaded by []\T1/pcr/m/n/10 library.dynam[]\T1/ptm/m/n/10 : use
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[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
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[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
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[][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil
e.access[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 files[][][] []\T1/ptm/
m/n/10 for many more file han-dling func-tions and
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[] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments
as for lists[]
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[] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
prob = 0.2))),[]
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[]\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the
same names ![]
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[]\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w
/ same name in .GlobalEnv[]
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[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways
be sup-
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[]\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/
ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of
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[]\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other
Unix-alikes[]
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[]\T1/pcr/m/n/9 c(m = months(then), wd = weekdays(then)) # in C_TIME locale \T
S1/pcr/m/n/9 '\T1/pcr/m/n/9 cT\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 ; typically German
[]
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[]\T1/pcr/m/n/9 c(m = months(then), wd = weekdays(then)) # "standard" (still p
latform specific ?)[]
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[]\T1/pcr/m/n/9 ## Not run: Sys.setlocale("LC_COLLATE", "C") # turn off loca
le-specific sorting,[]
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[]\T1/pcr/m/n/9 Sys.setenv("LANGUAGE" = "es") # set the language for error/war
ning messages[]
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[][][]\T1/pcr/m/n/10 raw[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logical[]
[][] []\T1/ptm/m/n/10 or `number-like' vec-tors (i.e., of types [][][]\T1/pcr/m
/n/10 double[][][] []\T1/ptm/m/n/10 (class
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[]\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary = r ), complex(real =
r , imaginary = NA ),[]
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[] \T1/pcr/m/n/9 complex(real = r , imaginary = NaN), complex(real = N
aN, imaginary = r ))[]
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[]\T1/pcr/m/n/9 zM ##--> many "NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s" (= 1) and th
e four non-NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s (3 different ones, at 7,9,10)[]
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[]\T1/pcr/m/n/9 match.arg(c("a", ""), c("", NA, "bb", "abc"), several.ok=TRUE
) # |--> "abc"[]
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[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion
(also known as a `clo-sure'):
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[]\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross \T1/ptm/m/n/10 prod-ucts, []
[][]\T1/pcr/m/n/10 crossprod[][][]() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 tcro
ssprod() []\T1/ptm/m/n/10 are typ-i-cally prefer-able.
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[]\T1/pcr/m/n/10 memCompress(from, type = c("gzip", "bzip2", "xz", "zstd", "no
ne"))
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\T1/ptm/m/n/10 al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 https : / / lea
rn . microsoft . com / en-[]gb / windows /
Underfull \hbox (badness 10000) in paragraph at lines 25332--25340
\T1/pcr/m/n/10 desktop / Memory / physical-[]address-[]extension$[][] \T1/ptm/m
/n/10 and [][]$\T1/pcr/m/n/10 https : / / learn .
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[] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
all,[]
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[]\T1/pcr/m/n/10 anyNA(recursive = FALSE) []\T1/ptm/m/n/10 works the same way a
s []\T1/pcr/m/n/10 is.na[]\T1/ptm/m/n/10 ; []\T1/pcr/m/n/10 anyNA(recursive =
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[]\T1/pcr/m/n/10 as.name []\T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-
nally to a char-ac-ter vec-tor (so meth-ods for
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[]\T1/ptm/m/n/10 For an [][][]\T1/pcr/m/n/10 environment[][][] env[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 names(env) []\T1/ptm/m/n/10 gives the names of the cor-r
e-spond-ing list,
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\T1/ptm/m/n/10 i.e., []\T1/pcr/m/n/10 names(as.list(env, all.names = TRUE)) []\
T1/ptm/m/n/10 which are also given by [][][]\T1/pcr/m/n/10 ls[][][](env,
Underfull \hbox (badness 3148) in paragraph at lines 26148--26154
\T1/pcr/m/n/10 all.names = TRUE, sorted = FALSE)[]\T1/ptm/m/n/10 . If the en-vi
-ron-ment is used as a hash ta-ble,
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[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of []\T1/pcr/m/n/1
0 c("bytes", "chars",
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[]\T1/ptm/m/n/10 optional [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 e
ven-tu-ally to be passed to []\T1/pcr/m/n/10 print()[]\T1/ptm/m/n/10 , used by
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\T1/ptm/m/n/10 tion []\T1/pcr/m/n/10 GetFinalPathNameByHandle []\T1/ptm/m/n/10
and in case of an er-ror (such as in-suf-fi-cient per-
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[]\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s
tartup mes-sages given by
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[]\T1/pcr/m/n/10 .onAttach[]\T1/ptm/m/n/10 . These mes-sages (and any es-sen-ti
al ones from []\T1/pcr/m/n/10 .onLoad[]\T1/ptm/m/n/10 ) should use
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[]\T1/ptm/m/n/10 Uses of []\T1/pcr/m/n/10 library []\T1/ptm/m/n/10 with ar-gu-m
ent []\T1/pcr/m/n/10 help []\T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion ab
out the pack-
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\T1/ptm/m/n/10 age should use []\T1/pcr/m/n/10 format []\T1/ptm/m/n/10 on the c
om-puted pack-age in-for-ma-tion ob-ject and pass this to
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[]\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ
e.only)
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[] \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk
gs"))[]
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[]\T1/pcr/m/n/10 loadNamespace []\T1/ptm/m/n/10 does not at-tach the name space
it loads to the search path.
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[]\T1/pcr/m/n/10 attachNamespace []\T1/ptm/m/n/10 can be used to at-tach a fram
e con-tain-ing the ex-ported val-ues of a
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[]\T1/pcr/m/n/10 isNamespaceLoaded(pkg) []\T1/ptm/m/n/10 is equiv-a-lent to but
more ef-fi-cient than []\T1/pcr/m/n/10 pkg %in%
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[] \T1/pcr/m/n/9 ## The string "foo" and the symbol \TS1/pcr/m/n/9 '\T1/pcr/m/
n/9 foo\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 can be used interchangeably here:[]
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[]\T1/ptm/m/n/10 The de-fault method for []\T1/pcr/m/n/10 is.numeric []\T1/ptm/
m/n/10 re-turns []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 if its ar-gu-ment is of
[][]mode[][][]
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\T1/ptm/m/n/10 ject as ob-tained by [][][]\T1/pcr/m/n/10 R.version[][][][]\T1/p
tm/m/n/10 . For []\T1/pcr/m/n/10 as.numeric_version []\T1/ptm/m/n/10 and
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[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
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[]\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/
10 R \T1/ptm/m/n/10 starts up. Ini-
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[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
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[]\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][][]\T1/pcr/
m/n/10 setRepositories[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 28609--28615
\T1/ptm/m/n/10 e.g. the de-fault `[]\T1/pcr/m/n/10 "https://bioconductor.org"[]
\T1/ptm/m/n/10 ' or the Eu-ro-pean mir-ror
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\T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de
"[]\T1/ptm/m/n/10 '. Can be set by
Underfull \hbox (badness 1389) in paragraph at lines 28648--28650
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
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[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by
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[]\T1/ptm/m/n/10 Used by [][][]\T1/pcr/m/n/10 install.packages[][][] []\T1/ptm/
m/n/10 (and in-di-rectly
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[]\T1/ptm/m/n/10 default email-ing method used by [][][]\T1/pcr/m/n/10 create.p
ost[][][] []\T1/ptm/m/n/10 and hence [][][]\T1/pcr/m/n/10 bug.report[][][] []\T
1/ptm/m/n/10 and
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[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see
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[]\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec,
300X faster[]
Underfull \vbox (badness 10000) has occurred while \output is active
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[]\T1/ptm/m/n/10 where el-e-ment []\T1/pcr/m/n/10 A[c(arrayindex.x, arrayindex.
y)] = FUN(X[arrayindex.x],
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[]\T1/pcr/m/n/10 str2expression(s) []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 str2la
ng(s) []\T1/ptm/m/n/10 re-turn spe-cial ver-sions of []\T1/pcr/m/n/10 parse(tex
t=s,
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[]\T1/pcr/m/n/9 tryCatch(parse(text = txt, srcfile = sf), error = function(e)
"Syntax error.")[]
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\T1/ptm/m/n/10 zero-length [][][]\T1/pcr/m/n/10 character[][][](0)[]\T1/ptm/m/n
/10 . Note that when []\T1/pcr/m/n/10 collapse []\T1/ptm/m/n/10 is a string,
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[][][]\T1/pcr/m/n/10 toString[][][] []\T1/ptm/m/n/10 typ-i-cally calls []\T1/pc
r/m/n/10 paste(*, collapse=", ")[]\T1/ptm/m/n/10 . String ma-nip-u-la-tion with
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[]\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as
the longest input.[]
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[]\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha
t you wanted[]
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[]\T1/pcr/m/n/9 ## zero length arguments recycled as \TS1/cmtt/m/n/9 `\T1/pcr/
m/n/9 ""\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 -- NB: \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 {
}\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 <==> character(0) here[]
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[]\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 recycle0 = TRUE\TS1/pcr/m/n/9
' \T1/pcr/m/n/9 allows standard vectorized behaviour, i.e., zero-length[]
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[]\T1/pcr/m/n/9 ## recycling resulting in zero-length result
character(0):[]
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[]\T1/pcr/m/n/9 paste("The value is", val[valid], "-- not so good!") # -> "..
value is -- not .."[]
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[]\T1/pcr/m/n/9 paste("The value is", val[valid], "-- good: empty!", recycle0=
TRUE) # -> character(0)[]
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[]\T1/pcr/m/n/9 paste("foo", {}, "bar", collapse = "|") # |--
> "foo bar"[]
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[]\T1/pcr/m/n/9 ## If all arguments are empty (and collapse a string), "" r
esults always[]
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[]\T1/pcr/m/n/9 mtcars |> subset(cyl == 4) |> nrow() # same as nrow(subset(mt
cars, cyl == 4))[]
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[]\T1/pcr/m/n/9 stop() |> (function(...) {})() # stop() is not used on RHS so
is not evaluated[]
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[]\T1/ptm/m/n/10 All other []\T1/pcr/m/n/10 type[]\T1/ptm/m/n/10 s give a warn-
ing or an er-ror; us-ing, e.g., []\T1/pcr/m/n/10 type =
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Underfull \hbox (badness 2277) in paragraph at lines 30191--30196
\T1/ptm/m/n/10 i.e., strictly in-clude the bounds of []\T1/pcr/m/n/10 x[]\T1/pt
m/m/n/10 . New from \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0, al-low-ing
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[]\T1/ptm/m/n/10 This func-tion is al-most never used: []\TS1/cmtt/m/n/10 `\T1/
pcr/m/n/10 name\TS1/cmtt/m/n/10 ` []\T1/ptm/m/n/10 or, more care-fully, [][][]\
T1/pcr/m/n/10 get[][][](name, envir =
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[]\T1/pcr/m/n/9 try(structure(mysqrt, comment = "primitive function")) # depre
cation warning; soon an error[]
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[]\T1/ptm/m/n/10 character string (or []\T1/pcr/m/n/10 NULL[]\T1/ptm/m/n/10 ) i
n-di-cat-ing [][][]\T1/pcr/m/n/10 NA[][][] []\T1/ptm/m/n/10 val-ues in printed
out-put, see
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[]\T1/ptm/m/n/10 Option []\T1/pcr/m/n/10 width []\T1/ptm/m/n/10 con-trols the p
rint-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion
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[]\T1/pcr/m/n/9 (x <- 2^seq(-8, 30, by=1/4)) # auto-prints; by default all in
"exponential" format[]
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Underfull \hbox (badness 2961) in paragraph at lines 31146--31149
[]\T1/ptm/m/n/10 LAPACK and LIN-PACK are from [][]$\T1/pcr/m/n/10 https : / / n
etlib . org / lapack/$[][] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / /
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[] \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 =
rep(c(0,0,1),2))[]
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[]\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3
\u147b\u203c")[]
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[]\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\
U147b\U203c"[]
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[]\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm
l#Literal-constants[]
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[]\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[]
Underfull \vbox (badness 10000) has occurred while \output is active
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[]\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use []\T1/pcr/m/n/10 R.v
ersion$os []\T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use
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[]\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[]
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[]\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind =
NULL)[]
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Underfull \hbox (badness 3713) in paragraph at lines 31921--31932
[]\T1/pcr/m/n/10 normal.kind []\T1/ptm/m/n/10 can be []\T1/pcr/m/n/10 "Kinderma
n-Ramage"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Buggy Kinderman-Ramage" []\T1/ptm
/m/n/10 (not
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\T1/ptm/m/n/10 Now see [][]$\T1/pcr/m/n/10 https : / / www . math . sci . hiros
hima-[]u . ac . jp / ~m-[]mat / MT / VERSIONS /
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[]\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca
n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the
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[] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m
ax", "min"))[]
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[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no []\T1/pcr/m/n/10 N
A[]\T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
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[]\T1/pcr/m/n/9 rapply(X, function(x) x, how = "replace") -> X.; stopifnot(ide
ntical(X, X.))[]
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[]\T1/pcr/m/n/9 rapply(X, deparse, control = "all") # passing extras. argument
of deparse()[]
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[]\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "list")[]
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[]\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[]
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[]\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", h
ow = "unlist")[]
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[]\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[]
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[]\T1/pcr/m/n/9 ## Bit representation [ sign | exponent | mantissa ] of doubl
e prec numbers :[]
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[]\T1/pcr/m/n/9 bitC <- function(x) noquote(vapply(as.double(x), function(x) {
# split one double[]
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[]\T1/pcr/m/n/9 d2bI <- function(x) vapply(as.double(x), function(x) intToBits
(numToInts(x)), raw(64L))[]
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[]\T1/pcr/m/n/9 d2b <- function(x) vapply(as.double(x), function(x)
numToBits(x) , raw(64L))[]
Underfull \vbox (badness 10000) has occurred while \output is active
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[]\T1/ptm/m/n/10 The sec-tion `Pro-cess-ing doc-u-men-ta-tion files' in the `Wr
it-ing R Ex-ten-sions' man-ual:
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[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
to
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\T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the
mode:
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\T1/ptm/m/n/10 one of []\T1/pcr/m/n/10 "numeric"[]\T1/ptm/m/n/10 , []\T1/pcr/m/
n/10 "double"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "integer"[]\T1/ptm/m/n/10 , []
\T1/pcr/m/n/10 "int"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/
10 ,
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[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 infoRDS[]\T1/ptm/m/n/10 , an \T1/phv/m/n/
10 R \T1/ptm/m/n/10 list with el-e-ments []\T1/pcr/m/n/10 version []\T1/ptm/m/n
/10 (ver-sion num-ber, cur-rently 2 or 3),
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[]\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[]
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[]\T1/pcr/m/n/10 regexpr []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 gregexpr []\T1/p
tm/m/n/10 sup-port `named cap-ture'. If groups are named, e.g.,
Underfull \hbox (badness 1968) in paragraph at lines 34049--34051
[]\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P
OSIX stan-dard, and the
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Underfull \hbox (badness 10000) in paragraph at lines 34060--34062
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 https : / /
pubs . opengroup . org / onlinepubs /
Underfull \hbox (badness 1975) in paragraph at lines 34063--34067
[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 pcre2pattern []\T1/ptm/m/n/10 or []\T1/pc
r/m/n/10 pcrepattern man []\T1/ptm/m/n/10 page (found as part of [][]$\T1/pcr/m
/n/10 https : / / www .
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 34435--34435
[]\T1/pcr/m/n/9 rep(1:4, each = 2, times = 3) # length 24, 3 complete
replications[]
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[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
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[]\T1/pcr/m/n/10 signif []\T1/ptm/m/n/10 rounds the val-ues in its first ar-gu-
ment to the spec-i-fied num-ber of \T1/ptm/m/it/10 sig-nif-i-cant
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\T1/ptm/m/n/10 dig-its. Hence, for []\T1/pcr/m/n/10 numeric x[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 signif(x, dig) []\T1/ptm/m/n/10 is the same as []\T1/pcr/m/n/
10 round(x, dig -
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[] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"))[]
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[] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[]
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[] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[]
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[] \T1/pcr/m/n/10 useHash = (n > 1e+07 && !replace && is.null(prob)
&& size <= n/2))[]
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[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
FALSE)[]
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 strip.white []\T1/ptm/m/n/10 is of length
1, it ap-plies to all fields; oth-er-wise, if
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[]\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n")
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[]\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence []\T1/pcr/
m/n/10 1, 2, ..., length(along.with)[]\T1/ptm/m/n/10 .
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[]\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence []\T1/pcr/m/n/10 1, 2
, ..., length(from) []\T1/ptm/m/n/10 (as if ar-gu-ment
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[]\T1/ptm/m/n/10 A vec-tor of class []\T1/pcr/m/n/10 "Date"[]\T1/ptm/m/n/10 . T
ype []\T1/pcr/m/n/10 "[][]integer[][][]" []\T1/ptm/m/n/10 is of-ten pre-served
on pur-pose, sav-ing
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[]\T1/pcr/m/n/9 ## find all 7th of the month _strictly_ inside two dates, the
last being a 7th.[]
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[]\T1/pcr/m/n/10 getAllConnections []\T1/ptm/m/n/10 re-turns a se-quence of in-
te-ger con-nec-tion de-scrip-tors for use
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\T1/ptm/m/n/10 with []\T1/pcr/m/n/10 getConnection[]\T1/ptm/m/n/10 , cor-re-spo
nd-ing to the row names of the ta-ble re-turned by
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[]\T1/ptm/m/n/10 In Win-dows, com-mand line in-ter-pre-ta-tion is done by the a
p-pli-ca-tion as well as the
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\T1/ptm/m/n/10 shell. It may de-pend on the com-piler used: Mi-crosoft's rules
for the C run-time
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\T1/ptm/m/n/10 are given at [][]$\T1/pcr/m/n/10 https : / / learn . microsoft .
com / en-[]us / cpp / c-[]language /
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\T1/pcr/m/n/10 parsing-[]c-[]command-[]line-[]arguments ? view = msvc-[]160$[][
]\T1/ptm/m/n/10 . It may de-pend on the
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[] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index
.return = FALSE)[]
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[]\T1/pcr/m/n/9 sort_by.data.frame(mtcars, ~ list(am, -mpg)) |> subset(select
= c(am, mpg))[]
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[] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length
= Inf,[]
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[] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes"
, "keepNA"),[]
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[][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 vec-tor, passed as []\T1/
pcr/m/n/10 control []\T1/ptm/m/n/10 to [][][]\T1/pcr/m/n/10 deparse[][][]()[]\T
1/ptm/m/n/10 , see also
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[][][]\T1/pcr/m/n/10 .deparseOpts[][][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \
T1/ptm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to
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[]\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments
should print:)[]
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[]\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m
/n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[]
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[]\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
being added[]
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[][][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919
799 / functions /
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[]\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known")
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[]\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
FALSE)[]
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[]\T1/ptm/m/n/10 Stack over-flow er-rors can be caught and han-dled by ex-it-in
g han-dlers es-tab-lished with
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[]\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three
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[]\T1/ptm/m/n/10 A func-tion []\T1/pcr/m/n/10 .First []\T1/ptm/m/n/10 (and [][]
[]\T1/pcr/m/n/10 .Last[][][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-at
e `\T1/pcr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have been
saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want a dif-fer-ent
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\T1/ptm/m/n/10 set of pack-ages than the de-fault ones when you start, in-sert
a call to [][][]\T1/pcr/m/n/10 options[][][] []\T1/ptm/m/n/10 in the
Underfull \hbox (badness 1231) in paragraph at lines 39331--39341
\T1/pcr/m/n/10 = character()) []\T1/ptm/m/n/10 will at-tach no ex-tra pack-ages
on startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (or
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\T1/ptm/m/n/10 set []\T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL []\T1/ptm/m/n/10 as
an en-vi-ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/10 ).
Us-ing
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[]\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file
s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 '
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\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for
first in architecture-specific di-rec-to-ries,
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\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be
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Underfull \hbox (badness 1460) in paragraph at lines 39402--39409
[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is
also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/pt
m/m/n/10 ' which is read
Underfull \hbox (badness 1038) in paragraph at lines 39402--39409
\T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron-
ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the
Underfull \hbox (badness 2573) in paragraph at lines 39402--39409
\T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i
n site or user en-vi-ron-ment
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[]\T1/pcr/m/n/9 # Variable expansion in double quotes, string literals with ba
ckslashes in[]
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Underfull \hbox (badness 5985) in paragraph at lines 39549--39552
[]\T1/ptm/m/n/10 The de-fault han-dler stores the er-ror mes-sage in a buffer;
it can be re-trieved by
Underfull \hbox (badness 1460) in paragraph at lines 39549--39552
[]\T1/pcr/m/n/10 geterrmessage()[]\T1/ptm/m/n/10 . It also stores a trace of th
e call stack that can be re-trieved by
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[]\T1/ptm/m/n/10 alternative to []\T1/pcr/m/n/10 exprs []\T1/ptm/m/n/10 or []\T
1/pcr/m/n/10 ...[]\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an
[571]
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[] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e
xprs = exprs)))
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[]\T1/pcr/m/n/9 stopifnot(all.equal(pi, 3.141593), 2 < 2, (1:10 < 12), "a" <
"b") |> try()[]
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[]\T1/pcr/m/n/9 stopifnot(all.equal(rep(list(pi),4), list(3.1, 3.14, 3.141, 3.
1415))) |> try()[]
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[]\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 {Yes, learn how to use do.c
all(substitute, ...) in a powerful manner !!}[]
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[]\T1/pcr/m/n/9 bdy <- do.call(substitute, list(bdy, list(stopifnot =
quote(warnifnot))))[]
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[]\T1/pcr/m/n/9 bdy[[N-1]] <- do.call(substitute, list(bdy[[N-1]], list(stop =
quote(warning))))[]
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[]\T1/ptm/m/n/10 integer de-ter-min-ing the []\T1/pcr/m/n/10 format()[]\T1/ptm/
m/n/10 ing of sec-onds when needed. Note
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[]\T1/pcr/m/n/9 ## time with fractional seconds (setting \TS1/cmtt/m/n/9 `\T1/
pcr/m/n/9 tz = ..\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 for reproducible output)[]
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[]\T1/pcr/m/n/9 z3 # prints without fractional seconds by default, digits.sec
= NULL ("= 0")[]
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[]\T1/pcr/m/n/9 format(s1 <- seq.Date(as.Date(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 19
78-01-01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ), by = \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 day
\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , len = 7), "%a")[]
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[]\T1/pcr/m/n/9 format(s2 <- seq.Date(as.Date(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 20
00-01-01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ), by = \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 mon
th\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , len = 12), "%b")[]
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[] \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[]
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[] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[]
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[]\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[]
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Overfull \hbox (52.98038pt too wide) in paragraph at lines 41140--41140
[]\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e
verything gets added.[]
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[]\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also
missing, ....[]
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[]\T1/pcr/m/n/10 format(x, digits = max(3L, getOption("digits") - 3L), zdigits
= 4L, ...)[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 41184--41184
[]\T1/pcr/m/n/10 print(x, digits = max(3L, getOption("digits") - 3L), zdigits
= 4L, ...)[]
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[]\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision
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[] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[]
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Overfull \hbox (20.58041pt too wide) in paragraph at lines 41784--41784
[]\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux,
macOS, FreeBSD:[]
Underfull \hbox (badness 2293) in paragraph at lines 41814--41820
[]\T1/ptm/m/n/10 This ex-pands tilde (see [][]tilde ex-pan-sion[][][]) and wild
-cards in file paths. For pre-cise de-
Underfull \hbox (badness 1237) in paragraph at lines 41814--41820
\T1/ptm/m/n/10 tails of wild-cards ex-pan-sion, see your sys-tem's doc-u-men-ta
-tion on the []\T1/pcr/m/n/10 glob []\T1/ptm/m/n/10 sys-tem call.
[603]
Underfull \hbox (badness 4792) in paragraph at lines 41832--41837
[]\T1/ptm/m/n/10 If a file-name starts with []\T1/pcr/m/n/10 . []\T1/ptm/m/n/10
this may need to be matched ex-plic-itly: for ex-am-ple
Underfull \hbox (badness 1107) in paragraph at lines 41832--41837
[]\T1/pcr/m/n/10 Sys.glob("*.RData") []\T1/ptm/m/n/10 may or may not match `\T1
/pcr/m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match
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Underfull \hbox (badness 10000) in paragraph at lines 42124--42128
[]\T1/pcr/m/n/10 sys.status() []\T1/ptm/m/n/10 re-turns a list with com-po-nent
s []\T1/pcr/m/n/10 sys.calls[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sys.parents []\
T1/ptm/m/n/10 and
Underfull \hbox (badness 1584) in paragraph at lines 42139--42142
[]\T1/pcr/m/n/10 sys.call []\T1/ptm/m/n/10 re-turns a call, []\T1/pcr/m/n/10 sy
s.function []\T1/ptm/m/n/10 a func-tion def-i-ni-tion, and []\T1/pcr/m/n/10 sys
.frame []\T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths
), keepNA=TRUE))[]
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Overfull \hbox (19.22812pt too wide) in paragraph at lines 42357--42357
[]\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/cmtt
/m/n/9 `\T1/pcr/m/n/9 A+C\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 could also be used
[611]
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Underfull \hbox (badness 1082) in paragraph at lines 42502--42505
[]\T1/ptm/m/n/10 logical. If []\T1/pcr/m/n/10 TRUE[]\T1/ptm/m/n/10 , func-tions
keep their source in-clud-ing com-ments, see
Underfull \hbox (badness 10000) in paragraph at lines 42529--42531
[][][]\T1/pcr/m/n/10 source[][][][]\T1/ptm/m/n/10 , and [][][]\T1/pcr/m/n/10 lo
adNamespace[][][] []\T1/ptm/m/n/10 which is called from [][][]\T1/pcr/m/n/10 li
brary[][][](.) []\T1/ptm/m/n/10 and uses
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Underfull \hbox (badness 1038) in paragraph at lines 42696--42699
[]\T1/ptm/m/n/10 a log-i-cal (not []\T1/pcr/m/n/10 NA[]\T1/ptm/m/n/10 ) in-di-c
at-ing whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or
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Underfull \hbox (badness 1442) in paragraph at lines 43080--43084
\T1/ptm/m/n/10 con-sider it to be piped or redi-rected: []\T1/pcr/m/n/10 stdout
= TRUE []\T1/ptm/m/n/10 uses a pipe whereas []\T1/pcr/m/n/10 stdout =
[623]
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[]\T1/ptm/m/n/10 Use [][][]\T1/pcr/m/n/10 ftable[][][] []\T1/ptm/m/n/10 for pri
nt-ing (and more) of mul-ti-di-men-sional ta-bles. [][][]\T1/pcr/m/n/10 margin.
table[][][][]\T1/ptm/m/n/10 ,
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Underfull \hbox (badness 7888) in paragraph at lines 43453--43457
[]\T1/ptm/m/n/10 On 64-bit plat-forms []\T1/pcr/m/n/10 bin []\T1/ptm/m/n/10 can
have $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., []\T1/pcr/
m/n/10 length(bin) >
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Overfull \hbox (63.78036pt too wide) in paragraph at lines 43715--43715
[] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1"
, "2"), c("A", "B")))),[]
Overfull \hbox (30.0281pt too wide) in paragraph at lines 43717--43717
[] \T1/pcr/m/n/9 array(list(\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 2\TS1/cm
tt/m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), names = nq),[]
Overfull \hbox (55.67578pt too wide) in paragraph at lines 43719--43719
[] \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 4\TS1/cmtt/m/n/9 ` \T1/pcr/m
/n/9 = NULL, \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 5\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 =
NULL), dim=4, dimnames=list(as.character(2:5)))))[]
Underfull \hbox (badness 10000) in paragraph at lines 43732--43734
[]\T1/pcr/m/n/10 removeTaskCallback []\T1/ptm/m/n/10 un-registers a func-tion t
hat was reg-is-tered ear-lier via
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Underfull \hbox (badness 3872) in paragraph at lines 43931--43934
[]\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call
-backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer .
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Underfull \hbox (badness 1655) in paragraph at lines 44420--44427
\T1/ptm/m/n/10 may also be known as `[]\T1/pcr/m/n/10 GB[]\T1/ptm/m/n/10 ', `[]
\T1/pcr/m/n/10 GB-Eire[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 Europe/Belfast[]\T1
/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 Europe/Guernsey[]\T1/ptm/m/n/10 ',
Underfull \hbox (badness 2253) in paragraph at lines 44428--44433
[]\T1/pcr/m/n/10 OlsonNames []\T1/ptm/m/n/10 re-turns a char-ac-ter vec-tor, se
e the ex-am-ples for typ-i-cal cases. It may
Underfull \hbox (badness 1655) in paragraph at lines 44428--44433
\T1/ptm/m/n/10 have an at-tribute []\T1/pcr/m/n/10 "Version"[]\T1/ptm/m/n/10 ,
some-thing like `[]\T1/pcr/m/n/10 "2023a"[]\T1/ptm/m/n/10 '. (It does on sys-te
ms us-ing
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Underfull \hbox (badness 4467) in paragraph at lines 44482--44491
[]\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 OlsonNames []\T1/ptm/m/n/10 re-
turns the time-zone names known to the cur-rently se-
Underfull \hbox (badness 3954) in paragraph at lines 44482--44491
\T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t
he file sys-tem varies,
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Underfull \hbox (badness 1337) in paragraph at lines 44579--44587
\T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de
r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 /
usr/local/etc\T1/ptm/m/n/10 ' or
Underfull \hbox (badness 10000) in paragraph at lines 44588--44591
[]\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym
-link tar-get name of
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Underfull \hbox (badness 3460) in paragraph at lines 44647--44650
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / data . iana . org /
Underfull \hbox (badness 4429) in paragraph at lines 44651--44653
[][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h
tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol-
Overfull \hbox (31.3804pt too wide) in paragraph at lines 44660--44660
[]\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET",
"Eire", ..., but[]
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Overfull \hbox (15.18042pt too wide) in paragraph at lines 45001--45001
[]\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15
g)\n", ncp))),[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 45003--45003
[]\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp
root finding:[]
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Overfull \hbox (84.78088pt too wide) in paragraph at lines 45100--45100
[] \T1/pcr/m/n/10 getOption("deparse
.max.lines", -1L)))[]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 45102--45102
[] \T1/pcr/m/n/10 getOption("deparse
.max.lines", -1L)))[]
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Underfull \hbox (badness 6542) in paragraph at lines 45376--45378
[]\T1/pcr/m/n/10 cospi(x)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sinpi(x)[]\T1/ptm/
m/n/10 , and []\T1/pcr/m/n/10 tanpi(x)[]\T1/ptm/m/n/10 , com-pute []\T1/pcr/m/n
/10 cos(pi*x)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sin(pi*x)[]\T1/ptm/m/n/10 , an
d
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[]\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[
\t\r\n]")
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Underfull \hbox (badness 1708) in paragraph at lines 45563--45571
[]\T1/pcr/m/n/10 try []\T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any
er-rors that oc-cur dur-ing the eval-u-a-tion. If
Underfull \hbox (badness 3713) in paragraph at lines 45563--45571
\T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][
][]\T1/pcr/m/n/10 stderr[][][] []\T1/ptm/m/n/10 con-nec-tion un-less
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Underfull \hbox (badness 4859) in paragraph at lines 45603--45608
[][][]\T1/pcr/m/n/10 options[][][] []\T1/ptm/m/n/10 for set-ting er-ror han-dle
rs and sup-press-ing the print-ing of er-ror mes-sages;
[659]
Underfull \hbox (badness 3895) in paragraph at lines 45665--45678
[]\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the
struc-ture []\T1/pcr/m/n/10 TypeTable []\T1/ptm/m/n/10 in
Underfull \hbox (badness 1303) in paragraph at lines 45665--45678
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue
s are the vec-tor types []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/
m/n/10 "integer"[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2452) in paragraph at lines 45665--45678
[]\T1/pcr/m/n/10 "promise"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "object"[]\T1/ptm
/m/n/10 , []\T1/pcr/m/n/10 "language"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "char"
[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "..."[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "a
ny"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "expression"[]\T1/ptm/m/n/10 ,
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Overfull \hbox (9.78043pt too wide) in paragraph at lines 46018--46018
[]\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[]
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[]\T1/ptm/m/n/10 When a func-tion call-ing []\T1/pcr/m/n/10 UseMethod("fun") []
\T1/ptm/m/n/10 is ap-plied to an ob-ject with class vec-tor
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 46536--46536
[]\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local
es and fonts[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 46545--46545
[]\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little-
endian platforms[]
[673]
Underfull \hbox (badness 1721) in paragraph at lines 46607--46624
[][][]\T1/pcr/m/n/10 file.rename[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 f
ile.symlink[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 dir.create[][][][]\
T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 dir.exists[][][][]\T1/ptm/m/n/10 , [][][]\
T1/pcr/m/n/10 normalizePath[][][][]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 try( substr(x, 1,1) ) # gives \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 in
valid multibyte string\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 error in a UTF-8 locale[]
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[]\T1/ptm/m/n/10 The atomic modes are []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/1
0 , []\T1/pcr/m/n/10 "integer"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "numeric" []\
T1/ptm/m/n/10 (syn-onym []\T1/pcr/m/n/10 "double"[]\T1/ptm/m/n/10 ),
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 mode = "any"[]\T1/ptm/m/n/10 , []\T1/pcr/m
/n/10 is.vector []\T1/ptm/m/n/10 may re-turn []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/
n/10 for the atomic modes, [][][]\T1/pcr/m/n/10 list[][][] []\T1/ptm/m/n/10 and
[676]
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[678]
Underfull \hbox (badness 1014) in paragraph at lines 47004--47007
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the warn-ing should be out-put im-me
-di-ately, even if
[679]
[680]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 47113--47113
[] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes
sages:\n"),[]
[681]
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[]\T1/pcr/m/n/9 ## at the end prints all three warnings, from the \TS1/pcr/m/n
/9 '\T1/pcr/m/n/9 option(warn = 0)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 above[]
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[]\T1/pcr/m/n/9 x <- 1:36; for(n in 1:13) for(m in 1:12) A <- matrix(x, n,m) #
There were 105 warnings ...[]
[682]
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[]\T1/pcr/m/n/10 weekdays []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 months []\T1/pt
m/m/n/10 re-turn a char-ac-ter vec-tor of names in the lo-cale in use, i.e.,
[683]
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[]\T1/pcr/m/n/9 ## Show how easily you get month, day, year, day (of {month, w
eek, yr}), ... :[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 47305--47305
[]\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Even simpler: Date -> Matrix
- dropping time info {sec,min,hour, isdst}[]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 47308--47308
[]\T1/pcr/m/n/9 d2mat(seq(as.Date("2000-02-02"), by=1, length.out=30)) # has R
1.0.0\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s release date[]
[684]
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 arr.ind == TRUE []\T1/ptm/m/n/10 and []\T1
/pcr/m/n/10 x []\T1/ptm/m/n/10 is an [][][]\T1/pcr/m/n/10 array[][][] []\T1/ptm
/m/n/10 (has a [][][]\T1/pcr/m/n/10 dim[][][] []\T1/ptm/m/n/10 at-tribute), the
re-sult is
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[]\T1/pcr/m/n/10 arrayInd(which(x), dim(x), dimnames(x))[]\T1/ptm/m/n/10 , name
ly a ma-trix whose rows each
[685]
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[]\T1/ptm/m/n/10 For a [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 vec-
tor []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 with both []\T1/pcr/m/n/10 FALSE []\T1/
ptm/m/n/10 and []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 val-ues, []\T1/pcr/m/n/10
which.min(x) []\T1/ptm/m/n/10 and
[686]
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[]\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is
at least one:[]
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[693]
Underfull \hbox (badness 2846) in paragraph at lines 47999--48003
[]\T1/pcr/m/n/10 .packages() []\T1/ptm/m/n/10 re-turns the names of the cur-ren
tly at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[694]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 48039--48039
[]\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[]
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[]\T1/pcr/m/n/10 .standard_regexps []\T1/ptm/m/n/10 re-turns a list of `stan-da
rd' reg-exps, in-clud-ing el-e-ments named
[695]) (./compiler-pkg.tex
[696]
Chapter 2.
[697]
Underfull \hbox (badness 2884) in paragraph at lines 107--121
[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 options []\T1/ptm/m/n/10 ar-gu-ment can b
e used to con-trol com-piler op-er-a-tion. There are cur-
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\T1/ptm/m/n/10 rently four op-tions: []\T1/pcr/m/n/10 optimize[]\T1/ptm/m/n/10
, []\T1/pcr/m/n/10 suppressAll[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 suppressUndef
ined[]\T1/ptm/m/n/10 , and
[698]
[699]
[700]) (./datasets-pkg.tex
Chapter 3.
[701]
[702]
[703]
[704]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 297--297
[] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[]
[705]
[706]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 375--375
[]\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi
ven = FALSE)[]
[707]
[708]
[709]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 613--613
[] \T1/pcr/m/n/9 start = c(lrc = log(.35)), algorithm = "plinear", t
race = TRUE)[]
[710]
[711]
Underfull \hbox (badness 4779) in paragraph at lines 700--703
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[712]
[713]
Underfull \hbox (badness 4779) in paragraph at lines 832--835
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[714]
[715]
Underfull \hbox (badness 1097) in paragraph at lines 1034--1038
[]\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th
e iden-ti-fi-ca-tion of crim-i-nals.
[716]
[717]
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[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[718]
[719]
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[721]
[722]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1463--1463
[]\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
time (sec)")[]
[723]
[724]
Underfull \hbox (badness 10000) in paragraph at lines 1548--1551
[]\T1/ptm/m/n/10 Finally, []\T1/pcr/m/n/10 freeny []\T1/ptm/m/n/10 is a data fr
ame with vari-ables []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lag.q
uarterly.revenue[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2903) in paragraph at lines 1548--1551
[]\T1/pcr/m/n/10 price.index[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 income.level[]\
T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 market.potential []\T1/ptm/m/n/10 ob-taine
d from the above
[725]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1641--1641
[] \T1/pcr/m/n/9 xlab = "Hip Angle", ylab = "Knee Angle", main = "\TS1/pcr
/m/n/9 '\T1/pcr/m/n/9 gait\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 data : Boy 1")[]
Overfull \hbox (112.38031pt too wide) in paragraph at lines 1643--1643
[]\T1/pcr/m/n/9 matlines(gait[, -1, 1], gait[, -1, 2], type = "l", lty = 1, co
l = adjustcolor("thistle", 1/3))[]
[726]
[727]
[728]
Underfull \hbox (badness 4779) in paragraph at lines 1809--1812
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[729]
[730]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1907--1907
[]\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil
y = binomial())[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1915--1915
[] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
data = infert)[]
[731]
[732]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 2032--2032
[]\T1/pcr/m/n/9 ## Iris versicolor "differs twice as much from I. setosa as fr
om I. virginica"[]
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[]\T1/pcr/m/n/9 ## equivalence of legacy array (iris3) and data.frame (iris) r
epresentation[]
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[] \T1/pcr/m/n/9 sub(" W.",".Width", dn
i3[[2]])))),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2042--2042
[] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d
ni3[[3]]))))[]
[733]
[734]
[735]
Underfull \hbox (badness 4779) in paragraph at lines 2245--2248
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[736]
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[738]
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[740]
[741]
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[743]
[744]
Underfull \hbox (badness 4779) in paragraph at lines 2810--2813
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[745]
[746]
[747]
[748]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3084--3084
[]\T1/pcr/m/n/9 plot(bill_dep ~ bill_len, data = penguins, pch = sym[sex], col
= pal[species])[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 3092--3092
[]\T1/pcr/m/n/9 m <- glm(sex ~ bill_len + bill_dep + body_mass, data = adelie,
family = binomial)[]
[749]
[750]
[751]
[752]
[753]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3420--3420
[]\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main =
1.2, pch = ".")[]
[754]
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[]\T1/pcr/m/n/9 myrandu <- matrix(NA_real_, 400, 3, dimnames = list(NULL, c("x
","y","z")))[]
[755]
[756]
[757]
[758]
[759]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 3773--3773
[]\T1/pcr/m/n/9 ## Alaska and Hawaii are placed just off the West Coast (for c
ompact map drawing):[]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 3775--3775
[]\T1/pcr/m/n/9 ## state.center2 := version of state.center with "correct" coo
rdinates for AK & HI:[]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 3776--3776
[]\T1/pcr/m/n/9 ## From https://pubs.usgs.gov/gip/Elevations-Distances/elvadis
t.html#Geographic%20Centers[]
[760]
Underfull \hbox (badness 1259) in paragraph at lines 3833--3836
\T1/ptm/m/n/10 Av. Cir-cu-laire, 3, B-1180 BRUS-SELS Cur-rently at [][]$\T1/pcr
/m/n/10 https : / / www . sidc . be / SILSO /
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[]\T1/pcr/m/n/9 ## How to recreate the "old" sunspot.month (R <= 3.0.3) =: sun
spot.month.0[]
[761]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3936--3936
[]\T1/pcr/m/n/9 (t2 <- c(min( end(sm)[1],end(sy)[1]), 12)) # Dec 1983 (will n
ot be updated!)[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3940--3940
[] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[]
[762] [763]
[764]
Underfull \hbox (badness 4779) in paragraph at lines 4088--4091
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[765]
[766]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4297--4297
[] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
supplement")[]
[767]
Underfull \hbox (badness 10000) in paragraph at lines 4333--4335
[]\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/pcr/m/n/10 h
ttps : / / web . archive . org / web /
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\T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma
n / sitephotos /
[768]
[769]
[770]
[771]
[772]
[773] [774]
[775]
[776]
[777]
[778]
[779]
[780]
[781]) (./grDevices-pkg.tex
[782]
Chapter 4.
[783]
[784]
[785]
[786]
Underfull \hbox (badness 4752) in paragraph at lines 299--304
[]\T1/ptm/m/n/10 Apart from that, []\T1/pcr/m/n/10 axisTicks() []\T1/ptm/m/n/10
just calls the C func-tion []\T1/pcr/m/n/10 CreateAtVector() []\T1/ptm/m/n/10
in
Underfull \hbox (badness 2865) in paragraph at lines 299--304
\T1/ptm/m/n/10 `\T1/ptm/m/sl/10 R\T1/pcr/m/n/10 /src/main/plot.c\T1/ptm/m/n/10
' which is also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack
-age func-tion
[787]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 351--351
[]\T1/pcr/m/n/9 aX(2, print(ya <- axisTicks(pu[3:4], log = TRUE))) # 10 20 50
100 (y axis)[]
[788]
[789]
[790]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 537--537
[]\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[]
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Underfull \hbox (badness 2245) in paragraph at lines 919--924
[]\T1/ptm/m/n/10 Hexadecimal string col-ors can be in the long hex-adec-i-mal f
orm (e.g., []\T1/pcr/m/n/10 "#rrggbb" []\T1/ptm/m/n/10 or
[797]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 983--983
[]\T1/pcr/m/n/9 names(clmult) <- sapply(clmult, function(x) paste(crgb[,x[1]],
collapse = ","))[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 990--990
[] \T1/pcr/m/n/9 lattice::cloud(blue ~ red + green, data = as.data.frame(tc
), col = cNms)[]
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[]\T1/pcr/m/n/9 cNms[isC] # "white" "black" "blue" "cyan" "green" "magenta" "r
ed" "yellow"[]
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[] \T1/pcr/m/n/9 plot3d (tc, col = cNms, size = 11) # --> rotate w/ mouse; e
nlarged corners:[]
Underfull \vbox (badness 10000) has occurred while \output is active
[798]
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Underfull \hbox (badness 5175) in paragraph at lines 1239--1241
[]\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm
. The source code is in
[802]
[803]
[804]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1410--1410
[]\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab",
scale.in = 255))[]
[805]
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[807]
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[]\T1/ptm/m/n/10 character: Does the de-vice sup-port pat-tern fills? One or mo
re of
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[]\T1/pcr/m/n/10 c("LinearGradient", "RadialGradient", "TilingPattern")
[808]
[809]
[810]
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[812]
Underfull \hbox (badness 1565) in paragraph at lines 1962--1967
[]\T1/ptm/m/n/10 The de-fault for []\T1/pcr/m/n/10 dev.print []\T1/ptm/m/n/10 i
s to pro-duce and print a postscript copy. This will not
Underfull \hbox (badness 1354) in paragraph at lines 1962--1967
\T1/ptm/m/n/10 sys-tem: see [][][]\T1/pcr/m/n/10 postscript[][][] []\T1/ptm/m/n
/10 for how to set this up. Win-dows users may pre-fer to use
[813]
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[]\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res
= 72,[]
[814]
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[]\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of []\T1/pcr
/m/n/10 ghostscript[]\T1/ptm/m/n/10 , but are likely to in-
Underfull \hbox (badness 2057) in paragraph at lines 2086--2096
[]\T1/pcr/m/n/10 "tiffg4"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiffgray"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "tifflzw"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiffp
ack"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiff12nc"[]\T1/ptm/m/n/10 , []\T1/pcr/
m/n/10 "tiff24nc"[]\T1/ptm/m/n/10 ,
[815]
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[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the
set-ting of
[816]
[817]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2335--2335
[]\T1/pcr/m/n/10 embedGlyphs(file, glyphInfo, outfile = file, options = charac
ter())[]
[818]
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[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
doc-u-men-ta-tion) are
Underfull \hbox (badness 4927) in paragraph at lines 2390--2393
[]\T1/pcr/m/n/10 embedGlyphs() []\T1/ptm/m/n/10 is rec-om-mended for []\T1/pcr/
m/n/10 pdf() []\T1/ptm/m/n/10 files that con-tain type-set glyphs (see
[819]
[820]
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[]\T1/ptm/m/n/10 are given, then it uses those in a call to []\T1/pcr/m/n/10 se
tGraphicsEventHandlers []\T1/ptm/m/n/10 to re-place
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\T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co
m-pat-i-bil-ity with pre-2.12.0
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\T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e
vent han-dlers is to set them us-ing
Underfull \hbox (badness 1221) in paragraph at lines 2509--2519
[]\T1/pcr/m/n/10 setGraphicsEventHandlers []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10
setGraphicsEventEnv []\T1/ptm/m/n/10 on one or more graph-ics
[821]
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[]\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[]
[822]
[823]
[824]
[825]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 2869--2869
[]\T1/pcr/m/n/10 gray.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re
v = FALSE)
Overfull \hbox (30.78088pt too wide) in paragraph at lines 2870--2870
[]\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re
v = FALSE)[]
[826]
[827]
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Underfull \hbox (badness 10000) in paragraph at lines 3143--3144
[830]
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[833]
[834]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3472--3472
[]\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized
= FALSE)[]
[835]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3556--3556
[]\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv",
scale.in = 255))[]
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[]\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale.
out = NULL))[]
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[]\T1/pcr/m/n/10 nclass.FD []\T1/ptm/m/n/10 uses the Freedman-Diaconis choice b
ased on the inter-quartile range
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[]\T1/pcr/m/n/10 palette.colors(n = NULL, palette = "Okabe-Ito", alpha, recycl
e = FALSE,[]
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[]\T1/pcr/m/n/9 (palette(gray(seq(0,.9,length.out = 25)))) # gray scales; prin
t old palette[]
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[]\T1/pcr/m/n/9 ## Demonstrate the colors 1:8 in different palettes using a cu
stom matplot()[]
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[] \T1/pcr/m/n/9 matplot(x, type = "l", lwd = 4, lty = 1, col = 1:n, ylab =
"", main=main)[]
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[]\T1/pcr/m/n/9 palROB <- colorRampPalette(c("red", "darkorange2", "blue"), sp
ace = "Lab")[]
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[]\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE,
fixup = TRUE)
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[]\T1/ptm/m/n/10 the type of palettes to list: []\T1/pcr/m/n/10 "qualitative"[]
\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sequential"[]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 For ex-am-ple, []\T1/pcr/m/n/10 "Dark 3" []\T1/ptm/m/n/10 work
s well for shad-ing points or lines in up to five groups,
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\T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space
& oldid = 883465135$[][]\T1/ptm/m/n/10 .
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[]\T1/ptm/m/n/10 as `\T1/pcr/m/n/10 "CP1250.enc"\T1/ptm/m/n/10 ' (Cen-tral Eu-r
o-pean), []\T1/pcr/m/n/10 "CP1251.enc"
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\T1/ptm/m/n/10 PostScript fonts fam-i-lies of those names which are in-cluded (
or cloned) in all com-mon
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\T1/ptm/m/n/10 cod-ings (ex-cept []\T1/pcr/m/n/10 "TeXtext"[]\T1/ptm/m/n/10 ) a
gree over that range. Some en-cod-ings are su-per-sets of
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\T1/ptm/m/n/10 ISO-Latin1. How-ever, if ac-cented and spe-cial char-ac-ters do
not come out as you ex-
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[]\T1/ptm/m/n/10 arguments []\T1/pcr/m/n/10 width[]\T1/ptm/m/n/10 , []\T1/pcr/m
/n/10 height[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 onefile[]\T1/ptm/m/n/10 , []\T1
/pcr/m/n/10 family[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 title[]\T1/ptm/m/n/10 , [
]\T1/pcr/m/n/10 fonts[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 version[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 paper[]\T1/ptm/m/n/
10 , []\T1/pcr/m/n/10 encoding[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 bg[]\T1/ptm/m
/n/10 , []\T1/pcr/m/n/10 fg[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pointsize[]\T1/p
tm/m/n/10 , []\T1/pcr/m/n/10 pagecentre[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 colormodel[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 useDingbats[]\T1
/ptm/m/n/10 , []\T1/pcr/m/n/10 useKerning[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 fi
llOddEven[]\T1/ptm/m/n/10 ,
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pdfTeX warning (ext4): destination with the same identifier (name{Rfn.symbol})
has been already used, duplicate ignored
<to be read again>
\relax
l.4896 \aliasA{symbol}{plotmath}{symbol}
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[]\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, [][]$\T1/pcr/m/n/10 https : / / ww
w . iso . org / standard / 34342 . html$[][]\T1/ptm/m/n/10 . See also
[863]
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[]\T1/pcr/m/n/9 ## Not run: dev.print(png, filename = "myplot.png", width = 10
24, height = 768)[]
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[]\T1/ptm/m/n/10 For use with []\T1/pcr/m/n/10 onefile = FALSE[]\T1/ptm/m/n/10
, give a C in-te-ger for-mat such as
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[]\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t
ion by Brian D'Urso
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[][][]\T1/pcr/m/n/10 postscriptFonts[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 Devices[][][][]\T1/ptm/m/n/10 , and [][][]\T1/pcr/m/n/10 check.options[][][]
[]\T1/ptm/m/n/10 which is called from both
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[]\T1/pcr/m/n/10 "AvantGarde"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Bookman"[]\T1
/ptm/m/n/10 , []\T1/pcr/m/n/10 "Courier"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "He
lvetica"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Helvetica-Narrow"[]\T1/ptm/m/n/10
,
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[]\T1/pcr/m/n/10 "NewCenturySchoolbook"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Pal
atino" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "Times"[]\T1/ptm/m/n/10 ; []\T1/pc
r/m/n/10 "URWGothic"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 "URWBookman"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "NimbusMon"[]\
T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "NimbusSan" []\T1/ptm/m/n/10 (syn-onym []\T1/p
cr/m/n/10 "URWHelvetica"[]\T1/ptm/m/n/10 ),
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[]\T1/ptm/m/n/10 There are also map-pings for []\T1/pcr/m/n/10 "ComputerModern"
[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ComputerModernItalic" []\T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/10 "Japan1"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Japan1HeiMin"[]\T
1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Japan1GothicBBB"[]\T1/ptm/m/n/10 , and []\T1/p
cr/m/n/10 "Japan1Ryumin" []\T1/ptm/m/n/10 for
[870]
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[]\T1/pcr/m/n/10 BousungEG-Light-GB []\T1/ptm/m/n/10 can be found at [][]$\T1/p
cr/m/n/10 https : / / ftp . gnu . org / pub / non-[]gnu /
[871]
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[]\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[]
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[]\T1/ptm/m/n/10 Calling []\T1/pcr/m/n/10 quartz() []\T1/ptm/m/n/10 sets [][][]
\T1/pcr/m/n/10 .Device[][][] []\T1/ptm/m/n/10 to []\T1/pcr/m/n/10 "quartz" []\T
1/ptm/m/n/10 for on-screen de-vices and to
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[] \T1/pcr/m/n/9 quartzFonts("mono") # the list(mono = ..) sublist o
f quartzFonts()[]
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\T1/ptm/m/n/10 play List", [][]$\T1/pcr/m/n/10 https : / / stattech . wordpress
. fos . auckland . ac . nz / 2015 / 12 / 21 /
[880]
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[]\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15,
sep = "."))[]
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[]\T1/pcr/m/n/10 rgb2hsv []\T1/ptm/m/n/10 trans-forms col-ors from RGB space (r
ed/green/blue) into HSV space
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[]\T1/pcr/m/n/9 p <- persp(x, y, fxy <- outer(x,y), phi = 20, theta = 15, r =
3, ltheta = -75,[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6893--6893
[]\T1/pcr/m/n/9 ## now some "horizontal rays" (going from center to very left
or very right):[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 6895--6895
[] \T1/pcr/m/n/9 lines(trans3d(x=seq(x1, x2, by=0.5), y= -0.7, z = z, pmat
= p, continuous = CNT),[]
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[]\T1/pcr/m/n/9 doHor(-10, 0, z = -0.5, col = 2) # x in [-10, 0] -- to the v
ery left : fine[]
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[]\T1/pcr/m/n/9 doHor(-.5, 2, z = -0.52,col = 4) # x in [-0.5, 2] only {to th
e right} --> all fine[]
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[]\T1/pcr/m/n/9 ## but now, x in [-0.5, 20] -- "too far" ==> "wrap around" pro
blem (without \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 continuous=TRUE\TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 ):[]
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[]\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp
inch,
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[]\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize
= 12,[]
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[]\T1/ptm/m/n/10 arguments []\T1/pcr/m/n/10 width[]\T1/ptm/m/n/10 , []\T1/pcr/m
/n/10 height[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pointsize[]\T1/ptm/m/n/10 , []\
T1/pcr/m/n/10 record[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 rescale[]\T1/ptm/m/n/10
,
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[]\T1/pcr/m/n/10 xpinch[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 ypinch[]\T1/ptm/m/n/
10 , []\T1/pcr/m/n/10 bg[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 canvas[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 gamma[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 xpos[]\T1/ptm/m
/n/10 , []\T1/pcr/m/n/10 ypos[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 buffered[]\T1/
ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 restoreConsole[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 clickToConfi
rm[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 title[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10
fillOddEven []\T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/9 windows() # make sure we have the right device type (availabl
e on Windows only)[]
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[]\T1/ptm/m/n/10 The \T1/phv/m/n/10 R \T1/ptm/m/n/10 func-tion is a wrap-per fo
r two de-vices, one based on Xlib ([][]$\T1/pcr/m/n/10 https : / /
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\T1/pcr/m/n/10 en . wikipedia . org / wiki / Xlib$[][]\T1/ptm/m/n/10 ) and one
us-ing cairo-graph-ics ([][]$\T1/pcr/m/n/10 https : / / www .
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[] \T1/pcr/m/n/10 fonts, family, xpos, ypos, title, type, antialias, symbol
family)[]
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[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
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[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" []\T1/ptm/m/n/10 for CJ
K lan-guages and
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[]\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of []
\T1/pcr/m/n/10 quote(pi) []\T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/10 expression(10^degree)[]\T1/ptm/m/n/10 ) have been seen on Linu
x sys-tems which have the Wine
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[]\T1/pcr/m/n/10 type = "Xlib" []\T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-d
o-Color', `GrayScale', []\T1/pcr/m/n/10 StaticGray []\T1/ptm/m/n/10 and
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[] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
= 6, xpos = 0,[]
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[]\T1/pcr/m/n/9 op <- options(warn = 2)# ==> warnings would be errors, we supp
ress the one "we know":[]
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[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., []\T1/pcr/m/n/10
number[i] []\T1/ptm/m/n/10 is the mul-ti-plic-ity of
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[]\T1/pcr/m/n/9 xy <- data.frame(x = round(sort(stats::rnorm(100))), y = stats
::rnorm(100))[]
[901]
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[903]) (./graphics-pkg.tex
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Chapter 5.
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[]\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag
es, use []\T1/pcr/m/n/10 library(help =
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[] \T1/pcr/m/n/10 gap.axis <- if(perpendicular(side, las)) 0.25 else 1[]
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[]\T1/ptm/m/n/10 When []\T1/pcr/m/n/10 at = NULL[]\T1/ptm/m/n/10 , pretty tick
mark lo-ca-tions are com-puted in-ter-nally (the same way
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[]\T1/pcr/m/n/9 ## now shrink the window (in x- and y-direction) and observe t
he axis labels drawn[]
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[]\T1/pcr/m/n/9 axis.Date(3, at = as.integer(as.Date("2023-04-01")), col.axis
= "darkgreen")[]
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[]\T1/pcr/m/n/9 axis.POSIXct(3, at = as.POSIXct("2022-10-01 00:01:30"), col.ax
is = "orange")[]
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[]\T1/pcr/m/n/9 axis.POSIXct(3, at = as.numeric(as.POSIXct("2022-10-01 00:00:3
0")) + 0.25,[]
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[] \T1/pcr/m/n/9 col.axis = "forestgreen", col = "darkgreen", m
gp = c(3,2,0))[]
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[]\T1/pcr/m/n/9 plot(data.frame(HST, y = 1), xaxt = "n", xlab = "Hawaii Standa
rd Time (HST)")[]
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[]\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][][]\T1/pcr
/m/n/10 par[][][]("xaxp") []\T1/ptm/m/n/10 or
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[][][]\T1/pcr/m/n/10 par[][][]("yaxp") []\T1/ptm/m/n/10 de-pend-ing on the []\T
1/pcr/m/n/10 side []\T1/ptm/m/n/10 ar-gu-ment ([]\T1/pcr/m/n/10 par("xaxp") []\
T1/ptm/m/n/10 if
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[] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[]
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[] \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend =
NULL, ...)[]
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[][][]\T1/pcr/m/n/10 plot[][][](..., type = "h")[]\T1/ptm/m/n/10 , [][][]\T1/pc
r/m/n/10 dotchart[][][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 hist[][][] []\T1
/ptm/m/n/10 for bars of a \T1/ptm/m/it/10 con-tin-u-ous \T1/ptm/m/n/10 vari-abl
e.
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[] \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = "
# {passengers}", legend.text = TRUE)[]
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[]\T1/pcr/m/n/9 (xt <- xtabs(Freq ~ Survived + Class + Sex, d.Titanic, subset
= Age=="Adult"))[]
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[]\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur
vived, *)", color=TRUE)[]
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[]\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches ..
outside hinges"):[]
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\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 horizontal []\T1/ptm/m/n/10 is false, and
[]\T1/pcr/m/n/10 xlim []\T1/ptm/m/n/10 hor-i-zon-tally. []\T1/pcr/m/n/10 xaxt[]
\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 yaxt[]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 whisker line type (de-fault: []\T1/pcr/m/n/10 "dashed"[]\T1/pt
m/m/n/10 ),
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[]\T1/pcr/m/n/9 boxplot(z, col.axis = "skyblue3", main = "boxplot(*, col.axi
s=..,main=..)")[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1595--1595
[]\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main = "plot(*, col.axi
s=..,main=..)")[]
[929]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1601--1601
[]\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill
= "grey40",[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1602--1602
[] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 1635--1635
[] \T1/pcr/m/n/10 yaxlabels = NULL, xlim = NULL, ylim = c(0, 1), weights = NU
LL, ...)[]
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[934]
Underfull \hbox (badness 10000) in paragraph at lines 1908--1914
[][][]\T1/pcr/m/n/10 contourLines[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
filled.contour[][][] []\T1/ptm/m/n/10 for color-filled con-tours, [][][]\T1/pcr
/m/n/10 contourplot[][][] []\T1/ptm/m/n/10 (and
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1928--1928
[]\T1/pcr/m/n/9 contour(x, x, z, ylim = c(-6, 6), nlevels = 20, lty = 2, metho
d = "simple",[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1940--1940
[]\T1/pcr/m/n/9 contour(z, levels=levs[-c(1,length(levs))], col = 1:5, lwd = 1
:3 *1.5, lty = 1:3)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1956--1956
[]\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1965--1965
[]\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[]
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[936]
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[]\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns,
[937]
[938]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 2179--2179
[]\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.values = given
.depth, rows = 1)[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2184--2184
[]\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c(
TRUE, FALSE))[]
[939]
[940]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 2358--2358
[]\T1/pcr/m/n/10 dotchart(x, labels = NULL, groups = NULL, gdata = NULL, offse
t = 1/8,
Overfull \hbox (54.78088pt too wide) in paragraph at lines 2359--2359
[] \T1/pcr/m/n/10 ann = par("ann"), xaxt = par("xaxt"), frame.plot = T
RUE, log = "",[]
[941]
Underfull \hbox (badness 1430) in paragraph at lines 2389--2391
[]\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use []\T1/pcr/m/n/10
"n" []\T1/ptm/m/n/10 to sup-press and see also
[942]
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[] \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO
rRd", rev = TRUE),[]
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[] \T1/pcr/m/n/10 plot.title, plot.axes, key.title, key.axes, ke
y.border = NULL,[]
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\T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n
ot ap-ply to
[943]
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[][][]\T1/pcr/m/n/10 contour[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 image
[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 hcl.colors[][][][]\T1/ptm/m/n/10
, [][][]\T1/pcr/m/n/10 gray.colors[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
palette[][][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 contourplot[][][] []\T1/p
tm/m/n/10 and
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[]\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c
(mx, my, 7))[]
[948]
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[]\T1/pcr/m/n/9 plot(8:270, log="xy") ; grid() # at (1, 10, 100); if preferrin
g "all" grid lines:[]
[949]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2882--2882
[] \T1/pcr/m/n/10 density = NULL, angle = 45, col = "lightgray", border =
NULL,[]
[950]
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\T1/pcr/m/n/10 1)[]\T1/ptm/m/n/10 , they are the rel-a-tive fre-quen-cies []\T1
/pcr/m/n/10 counts/n []\T1/ptm/m/n/10 and in gen-eral sat-isfy
[951]
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[]\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe
r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3066--3066
[]\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a
suggestion only"[]
[952]
Underfull \hbox (badness 10000) in paragraph at lines 3128--3131
[][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][][]\T1
/pcr/m/n/10 hist.default[][][] []\T1/ptm/m/n/10 such as
[953]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 3179--3179
[]\T1/pcr/m/n/9 ## The default fuzz in hist.default() "kills" this, with a "w
rong" message:[]
[954]
[955]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3343--3343
[]\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL
SE, pch = 19, ...)[]
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[] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel)
, n = 1, plot = plot, ...)[]
[956]
[957]
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 useRaster []\T1/ptm/m/n/10 is not spec-i-f
ied, raster im-ages are used when the
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[][][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") []\T1/ptm/m/n/10 is true,
the grid is reg-u-lar and ei-ther
Underfull \hbox (badness 10000) in paragraph at lines 3490--3495
[][][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage []\T1/pt
m/m/n/10 is []\T1/pcr/m/n/10 "yes" []\T1/ptm/m/n/10 or it is
[958]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 3525--3525
[]\T1/pcr/m/n/9 # Visualize as matrix. Need to transpose matrix and then flip
it horizontally:[]
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[]\T1/pcr/m/n/9 imageM <- function(m, grid = max(dim(m)) <= 25, asp = (nrow(m)
-1)/(ncol(m)-1), ...) {[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 3530--3530
[] \T1/pcr/m/n/9 axis(side, at=at, labels=as.character(j+1L), col="gray
", col.axis=1, ...)[]
[959]
[960]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3687--3687
[]\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space =
0, horiz = TRUE)[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 3706--3706
[] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col =
par("fg"),[]
[961]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3710--3710
[] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
FALSE,[]
[962]
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Overfull \hbox (36.7804pt too wide) in paragraph at lines 3895--3895
[] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c
ex = 0.8, adj = 0)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3896--3896
[] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3900--3900
[] \T1/pcr/m/n/9 cex = 1+(-1:2)/8, trace = TRUE)# trace: show computed l
engths & coords[]
[964]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 3910--3910
[] \T1/pcr/m/n/9 title("legend(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 top\TS1/pcr/m/n/
9 '\T1/pcr/m/n/9 , lty = c(2, -1, 1), pch = c(NA, 3, 4), merge = TRUE)",[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3941--3941
[] \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj
= c(0, 0.3))[]
Underfull \vbox (badness 10000) has occurred while \output is active
[965]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3967--3967
[]\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Filled\TS1/pcr/m/n/9 ' \T1/pc
r/m/n/9 boxes -- see also example(barplot) which may call legend(*, fill=)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3969--3969
[]\T1/pcr/m/n/9 legend("topright", rownames(VADeaths), fill = gray.colors(nrow
(VADeaths)))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3980--3980
[]\T1/pcr/m/n/9 legend("bottomright", paste("sin(", 1:7, "pi * x)"), col = 1:7
, lty = 1:7,[]
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[]\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c
ol = "blue")[]
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[]\T1/pcr/m/n/9 legend("topleft", "(x,y)", pch=1, title= "topleft, inset =
.05", inset = .05)[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 4005--4005
[]\T1/pcr/m/n/9 legend("topright", "(x,y)", pch=1, title= "topright, inset
= .02",inset = .02)[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 4013--4013
[] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[]
Underfull \vbox (badness 10000) has occurred while \output is active
[966]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4023--4023
[]\T1/pcr/m/n/9 legend("bottomleft", c("This legend", "has", "optimally sized"
, "columns."),[]
Underfull \hbox (badness 10000) in paragraph at lines 4085--4089
[][][]\T1/pcr/m/n/10 lines.formula[][][] []\T1/ptm/m/n/10 for the for-mula meth
od; [][][]\T1/pcr/m/n/10 points[][][][]\T1/ptm/m/n/10 , par-tic-u-larly for []\
T1/pcr/m/n/10 type %in%
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[] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb
ose"))[]
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[]\T1/pcr/m/n/9 nd <- length(dv <- seq(as.Date("1959-02-21"), by = "weeks", le
ngth.out = 100))[]
Underfull \vbox (badness 10000) has occurred while \output is active
[971]
[972]
Underfull \hbox (badness 3930) in paragraph at lines 4432--4434
[]\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a
mul-ti-ple of
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Underfull \hbox (badness 1286) in paragraph at lines 4748--4751
[]\T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify []\T1/pcr/m/n
/10 oma []\T1/ptm/m/n/10 when chang-ing
Underfull \hbox (badness 3229) in paragraph at lines 4756--4761
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are
to be used, see
[978]
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[]\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel
= panel.cor,[]
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[] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma
=c(2,2,3,2))[]
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[980]
Underfull \hbox (badness 1264) in paragraph at lines 5118--5131
\T1/ptm/m/n/10 func-tions such as [][][]\T1/pcr/m/n/10 plot.default[][][][]\T1/
ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.window[][][][]\T1/ptm/m/n/10 , [][][]\T1
/pcr/m/n/10 points[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lines[][][][]\T
1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 abline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc
r/m/n/10 axis[][][][]\T1/ptm/m/n/10 ,
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[984 </build/r/src/R-4.5.1/library/graphics/help/figures/mai.pdf>]
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Underfull \vbox (badness 10000) has occurred while \output is active
[985]
[986 </build/r/src/R-4.5.1/library/graphics/help/figures/oma.pdf>]
[987]
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[]\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9,
physicians = 9,[]
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[] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[]
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[991]
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[]\T1/pcr/m/n/9 points(trans3d(xy[,1], xy[,2], z = 6, pmat = res), co
l = 2, pch = 16)[]
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[]\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p
yramid" = 5),[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 6061--6061
[] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow
3"), border = FALSE)[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot}) ha
s been already used, duplicate ignored
<to be read again>
\relax
l.6120 \aliasA{plot}{plot.default}{plot}
[995]
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[997]
[998]
[999]
[1000]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6463--6463
[]\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext
remely silly[]
[1001]
[1002]
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[] \T1/pcr/m/n/10 main = paste("Histogram of", paste(x$xname, co
llapse = "\n")),[]
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[1004]
[1005]
[1006]
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[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[1007]
[1008]
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[]\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th
is works as a mul-ti-ple of
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[][]
[1009 </build/r/src/R-4.5.1/library/graphics/help/figures/pch.pdf>]
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[]\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b
lue", cex = .6,[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 7124--7124
[]\T1/pcr/m/n/9 ## Illustration of pch = 0:25 (as in the figure shown above in
PDF/HTML help)[]
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[]\T1/pcr/m/n/9 ## Not run: png("pch.png", height = 0.7, width = 7, res = 100,
units = "in")[]
[1010]
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[] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab =
"", main = main)[]
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[1011]
[1012]
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[]\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev
in Buhr
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[] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b
order = "red")[]
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[]\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats::
rnorm(n)))))[]
[1013]
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[]\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther []\T
1/pcr/m/n/10 "winding" []\T1/ptm/m/n/10 or
[1014]
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[1016]
[1017]
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[]\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7
, end = 0.1))[]
[1018]
[1019]
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[1021]
[1022]
[1023]
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[]\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
ace = "Lab")[]
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[]\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit
h obs.number):[]
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[]\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE),[]
[1024]
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[] \T1/pcr/m/n/10 xlim = NULL, ylim = c(0, 1), axes = TRUE, weights =
NULL, ...)[]
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[] \T1/pcr/m/n/10 subset = NULL, weights = NULL, drop.unused.levels =
FALSE)[]
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[1027]
[1028]
[1029]
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[]\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us = FALSE,[]
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[]\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us = FALSE,[]
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[] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
, key.loc = 0:1,[]
[1030]
[1031]
[1032]
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[]\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont =
NULL, ...)
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[]\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont =
NULL, ...)[]
[1033]
[1034]
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[]\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL,
...,[]
[1035]
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[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 number[i] == 1[]\T1/ptm/m/n/10 , a (sligh
tly en-larged) usual plot-ting sym-bol ([]\T1/pcr/m/n/10 pch[]\T1/ptm/m/n/10 )
is drawn. For
[1036]
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[]\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035
, seg.lwd = .8)[]
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[]\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100,
lambda = 2),[]
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[]\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
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[] \T1/pcr/m/n/9 "Le fran�ais, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est facile:
R�gles, Libert�, Egalit�, Fraternit�...")[]
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[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color []\T1/pcr/m
/n/10 par(c("font.sub",
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[]\T1/ptm/m/n/10 The po-si-tions of []\T1/pcr/m/n/10 xlab[]\T1/ptm/m/n/10 , []\
T1/pcr/m/n/10 ylab []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 sub []\T1/ptm/m/n/10 a
re []\T1/pcr/m/n/10 line []\T1/ptm/m/n/10 (de-fault for []\T1/pcr/m/n/10 xlab [
]\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 ylab []\T1/ptm/m/n/10 be-ing
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pdfTeX warning (ext4): destination with the same identifier (name{Rfn.units}) h
as been already used, duplicate ignored
<to be read again>
\relax
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pdfTeX warning (ext4): destination with the same identifier (name{Rfn.units.1})
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[]\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th
e poly-gon. See
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[]\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code =
2, length = 0.1)[]
[1046]) (./grid-pkg.tex
Chapter 6.
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[]\T1/ptm/m/n/10 Modification of the view-port (should all be valid ar-gu-ments
to the
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[] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un
it(1, "inches")))[]
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[] \T1/pcr/m/n/9 vpList(vpStack(viewport(x=0.1, y=0.1, width=0.5
, height=0.5,[]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="B"),[]
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[] \T1/pcr/m/n/9 viewport(x=0.1, y=0.1, width=0.5
, height=0.5,[]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="C"),[]
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[] \T1/pcr/m/n/9 viewport(x=0.1, y=0.1, width=0.5
, height=0.5,[]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="D")),[]
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject
de-scrib-ing a cir-cle), but only
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[] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[]
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[]\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla
ck"), name="r1")[]
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[]\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey"
), name="r2")[]
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[]\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi
te"), name="r3")[]
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[]\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio
ns []\T1/pcr/m/n/10 preDrawDetails[]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 Both func-tions call []\T1/pcr/m/n/10 editDetails []\T1/ptm/m/
n/10 to al-low a grob to per-form cus-tom ac-tions and
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de
-scrib-ing a frame), but only
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[]\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global =
FALSE)[]
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[]\T1/ptm/m/n/10 The jus-ti-fi-ca-tion of the glyphs rel-a-tive to the ([]\T1/p
cr/m/n/10 x[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 ) lo-ca-tion.
Can be
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[]\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs =
FALSE,[]
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[] \T1/pcr/m/n/9 children=gList(grob(name="child", vp
="vp1::vp2")),[]
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[] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp =
NULL)[]
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[]\T1/ptm/m/n/10 A func-tion that re-turns an affine trans-for-ma-tion ma-trix;
see
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[]\T1/ptm/m/n/10 Another pos-si-ble use of []\T1/pcr/m/n/10 grid.group() []\T1/
ptm/m/n/10 is to spec-ify both []\T1/pcr/m/n/10 src []\T1/ptm/m/n/10 and []\T1/
pcr/m/n/10 dst []\T1/ptm/m/n/10 and com-bine
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[]\T1/ptm/m/n/10 is only drawn where it is NOT over-lapped by []\T1/pcr/m/n/10
src[]\T1/ptm/m/n/10 . The fol-low-ing (ex-tended) Porter-
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[]\T1/pcr/m/n/10 "multiply"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "screen"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "overlay"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "darke
n"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lighten"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n
/10 "color.dodge"[]\T1/ptm/m/n/10 ,
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[] \T1/pcr/m/n/9 mask <- as.mask(rectGrob(gp=gpar(col=NA, fill="grey50")), ty
pe="luminance")[]
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[] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[]
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[] \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[]
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[]\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, width=0.25, height=0.25, just=
c("left", "bottom")))[]
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[]\T1/ptm/m/n/10 There are two hooks called []\T1/pcr/m/n/10 "before.grid.newpa
ge" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "grid.newpage" []\T1/ptm/m/n/10 (see
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[] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
NULL,[]
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[] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
NULL,[]
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[] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant
i-clockwise")[]
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[] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other
anti-clockwise")[]
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[]\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s
ame path, thus[]
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec
t de-scrib-ing seg-ments), but only
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[] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un
it(1, "inches")))[]
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[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
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[]\T1/pcr/m/n/9 grid.text(quote(frac(e^{-x^2/2}, sqrt(2*pi))), x=x, y=y, rot=s
tats::runif(20, -45,45),[]
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[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 gridCoords []\T1/ptm/m/n/10 a nu-meric ve
c-tor. For []\T1/pcr/m/n/10 gridGrobCoords []\T1/ptm/m/n/10 a list
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\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 "GridCoords" []\T1/ptm/m/n/10 ob-jects. For
[]\T1/pcr/m/n/10 gridGTreeCoords []\T1/ptm/m/n/10 a list of ei-ther
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[]\T1/ptm/m/n/10 Either a []\T1/pcr/m/n/10 "GridGrobCoords" []\T1/ptm/m/n/10 ob
-ject (a list of lists with com-po-nents []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 an
d []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 ) or a
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[]\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 grid.legend()[]\T1/ptm/m/n/10 : all the a
r-gu-ments above are passed to
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[]\T1/pcr/m/n/9 unitType(min(unit(1, "in"), unit(1, "npc") + unit(1, "mm")), r
ecurse=TRUE)[]
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[]\T1/pcr/m/n/10 viewportTransform(group, shear=groupShear(), flip=groupFlip()
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[]\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for
use in []\T1/pcr/m/n/10 downViewport []\T1/ptm/m/n/10 or
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[][][]\T1/pcr/m/n/10 viewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 push
Viewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 popViewport[][][][]\T1/pt
m/m/n/10 , [][][]\T1/pcr/m/n/10 downViewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/
pcr/m/n/10 seekViewport[][][][]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp
ar(col="red"))))[]
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Chapter 7.
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[]\T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how
co-erce meth-ods work. Use
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[][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] []\T1/ptm/m/n/10 for other in-
for-ma-tion about group generic func-tions; [][]Meth-
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[]\T1/pcr/m/n/9 ## vector. The next method will always be the default, usuall
y a primitive.[]
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[]\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w
ith no arguments[]
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[]\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho
ut arguments[]
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[]\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th
e default method[]
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[]\T1/pcr/m/n/9 ## call f() with 1 argument: the default "B0" is not passed b
y callNextMethod[]
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[]\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the
"B0" method[]
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[]\T1/pcr/m/n/9 ## Although the argument here is numeric, it\TS1/pcr/m/n/9 '\T
1/pcr/m/n/9 s still the "B0" method that\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s called[
]
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[]\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N
umber" method[]
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[]\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE))
) # the default[]
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[]\T1/ptm/m/n/10 The ar-gu-ment to []\T1/pcr/m/n/10 insertSource []\T1/ptm/m/n/
10 can be an ob-ject of class
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[]\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age
, use []\T1/pcr/m/n/10 where =
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[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an [][][]\T1/pcr/m/n/10 environment
[][][][]\T1/ptm/m/n/10 ) used for meth-ods dis-patch, call
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[]\T1/pcr/m/n/10 getMethods(f, where, table = FALSE) # deprecated -> use getMe
thodsForDispatch()[]
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[]\T1/ptm/m/n/10 As you might ex-pect [][][]\T1/pcr/m/n/10 setGeneric[][][] []\
T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 setGroupGeneric[][][] []\T1/ptm/m/n/10 c
re-ate ob-jects of class
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[]\T1/ptm/m/n/10 Object of class []\T1/pcr/m/n/10 "optionalMethod" []\T1/ptm/m/
n/10 (a union of classes []\T1/pcr/m/n/10 "function" []\T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[]
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[]\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[]
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[]\T1/ptm/m/n/10 Function []\T1/pcr/m/n/10 implicitGeneric() []\T1/ptm/m/n/10 r
e-turns the im-plicit generic ver-sion,
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[]\T1/pcr/m/n/10 setGenericImplicit() []\T1/ptm/m/n/10 turns a generic im-plici
t, []\T1/pcr/m/n/10 prohibitGeneric() []\T1/ptm/m/n/10 pre-vents
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[]\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][][]\T1/pcr/m/n/10
getClass[][][] []\T1/ptm/m/n/10 and the de-scrip-tion of class
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[]
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[] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longit
ude =
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[]\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) {
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[]\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character")
,
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[]\T1/ptm/m/n/10 A call to [][][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) []
\T1/ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to
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[]\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char
acter(),
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[] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac
cess,[]
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[]\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here)
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[]\T1/ptm/m/n/10 For ad-di-tional in-for-ma-tion see doc-u-men-ta-tion for the
im-por-tant steps: ([][][]\T1/pcr/m/n/10 setMethod[][][]()[]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha
t eval-u-ates a call to
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[]\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
inheritance[]
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[]\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli
er fails here)[]
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[]\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho
d for classB[]
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[]\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...)
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[]\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p
assed to
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[]\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o
ds for this class are found (us-ing
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[]\T1/ptm/m/n/10 The de-fault method for []\T1/pcr/m/n/10 $initialize() []\T1/p
tm/m/n/10 is equiv-a-lent to in-vok-ing the method
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[]\T1/ptm/m/n/10 Typically, a spe-cial-ized []\T1/pcr/m/n/10 $initialize() []\T
1/ptm/m/n/10 method car-ries out its own com-pu-ta-tions,
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\T1/ptm/m/n/10 then in-vokes []\T1/pcr/m/n/10 $initFields() []\T1/ptm/m/n/10 to
per-form stan-dard ini-tial-iza-tion, as shown in the
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[]\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func-
tion re-turned by
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[]\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen
se as any S4 class (see
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[][][]\T1/pcr/m/n/10 setValidity[][][][]\T1/ptm/m/n/10 ). Such meth-ods are of-
ten a good idea; they will be called by call-ing
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pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has
been already used, duplicate ignored
<to be read again>
\relax
l.6911 \aliasA{S4}{S3Part}{S4}
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[]\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement
version of as().[]
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[]\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data =
datasets::iris)[]
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[]\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con
tains = "mlm")[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Complex})
has been already used, duplicate ignored
<to be read again>
\relax
l.7167 \aliasA{Complex}{S4groupGeneric}{Complex}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Logic}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.7169 \aliasA{Logic}{S4groupGeneric}{Logic}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) ha
s been already used, duplicate ignored
<to be read again>
\relax
l.7170 \aliasA{Math}{S4groupGeneric}{Math}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.matrixOps
}) has been already used, duplicate ignored
<to be read again>
\relax
l.7172 ...sA{matrixOps}{S4groupGeneric}{matrixOps}
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been already used, duplicate ignored
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l.7173 \aliasA{Ops}{S4groupGeneric}{Ops}
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\relax
l.7174 \aliasA{Summary}{S4groupGeneric}{Summary}
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[]\T1/ptm/m/n/10 There are also S3 groups []\T1/pcr/m/n/10 Math[]\T1/ptm/m/n/10
, []\T1/pcr/m/n/10 Ops[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Summary[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 Complex []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 matrixOps[
]\T1/ptm/m/n/10 , see
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[]\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic
can be ob-tained by call-ing
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[]\T1/pcr/m/n/10 "abs"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sign"[]\T1/ptm/m/n/1
0 , []\T1/pcr/m/n/10 "sqrt"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ceiling"[]\T1/p
tm/m/n/10 , []\T1/pcr/m/n/10 "floor"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "trunc"
[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cummax"[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2012) in paragraph at lines 7249--7261
[]\T1/pcr/m/n/10 "acosh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "asin"[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 "asinh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "atan"[]\T1/p
tm/m/n/10 , []\T1/pcr/m/n/10 "atanh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "exp"[]
\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "expm1"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "c
os"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 "cosh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cospi"[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 "sin"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sinh"[]\T1/ptm
/m/n/10 , []\T1/pcr/m/n/10 "sinpi"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tan"[]\T
1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tanh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tanp
i"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 selectMethod("Re", signature = "testComplex") # shows Generic:
.. "Re" & .."Complex"[]
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[]\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t
ion ob-ject (see
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[]\T1/ptm/m/n/10 The typ-i-cal user level func-tion is []\T1/pcr/m/n/10 selectS
uperClasses() []\T1/ptm/m/n/10 which calls
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[]\T1/pcr/m/n/9 selectSuperClasses("C", dropVirtual=TRUE, directOnly=FALSE)# d
itto w/o "Root"[]
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[]\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(),
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[] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[]
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[]\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[]
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[] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
"setCount")[]
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[]\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo
rmal arguments[]
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[]\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre
es of freedom[]
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[]\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][]
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[]\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][]
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[]\T1/ptm/m/n/10 Chambers, John M. (2009) \T1/ptm/m/it/10 Class In-her-i-tance
in R [][]$\T1/pcr/m/n/10 https : / / johnmchambers . su .
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[]\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., []\T1/pcr/m/n/10 "functi
on" []\T1/ptm/m/n/10 for class
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[]\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl
ass, from the data part; e.g.,
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[]\T1/pcr/m/n/10 "functionWithTrace" []\T1/ptm/m/n/10 ex-tends []\T1/pcr/m/n/10
"function"[]\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends
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Chapter 8.
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[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `[]\T1/p
cr/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"[]\T1/ptm/m/n/10 ' [][]
RNG[][][]: see
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[]\T1/ptm/m/n/10 a vec-tor for []\T1/pcr/m/n/10 clusterApply []\T1/ptm/m/n/10 a
nd []\T1/pcr/m/n/10 clusterApplyLB[]\T1/ptm/m/n/10 , a ma-trix for
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[]\T1/ptm/m/n/10 Two ex-cep-tions: []\T1/pcr/m/n/10 parLapply []\T1/ptm/m/n/10
has ar-gu-ment []\T1/pcr/m/n/10 X []\T1/ptm/m/n/10 not []\T1/pcr/m/n/10 x []\T1
/ptm/m/n/10 for con-sis-tency with [][][]\T1/pcr/m/n/10 lapply[][][][]\T1/ptm/m
/n/10 , and
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[]\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD,
So-laris and Win-dows.
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[]\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for []\T1/pcr/m/
n/10 Rscript []\T1/ptm/m/n/10 such as
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[]\T1/pcr/m/n/10 mcfork []\T1/ptm/m/n/10 re-turns an ob-ject of the class []\T1
/pcr/m/n/10 "childProcess" []\T1/ptm/m/n/10 to the mas-ter and of class
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[]\T1/pcr/m/n/10 "masterProcess" []\T1/ptm/m/n/10 to the child: both the classe
s in-herit from class []\T1/pcr/m/n/10 "process"[]\T1/ptm/m/n/10 . If
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[] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini
ty.list = NULL)[]
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[]\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit
y.list = affL)[]
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[]\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch
eduled to suitable CPUs[]
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[]\T1/pcr/m/n/10 mcparallel []\T1/ptm/m/n/10 re-turns an ob-ject of the class [
]\T1/pcr/m/n/10 "parallelJob" []\T1/ptm/m/n/10 which in-her-its from
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[]\T1/ptm/m/n/10 The be-haviour with []\T1/pcr/m/n/10 mc.set.seed = TRUE []\T1/
ptm/m/n/10 is dif-fer-ent only if
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[]\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin
ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[]
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[] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[]
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[]\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format =
"%Y-%m-%d")))[]
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[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by []\T1/pcr/m/n/10
.Random.seed []\T1/ptm/m/n/10 when the
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[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 nextRNGStream []\T1/ptm/m/n/10 and []\T1/
pcr/m/n/10 nextRNGSubStream[]\T1/ptm/m/n/10 , a value which can be as-signed to
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Chapter 9.
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[]\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
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[]\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl
ine = TRUE))[]
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[]\T1/ptm/m/n/10 An in-te-ger be-tween 0 and []\T1/pcr/m/n/10 splineOrder(objec
t) - 1 []\T1/ptm/m/n/10 spec-i-fy-ing the
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[]\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37,
sparse = TRUE)))[]
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[1348]) (./stats-pkg.tex
Chapter 10.
[1349]
Underfull \hbox (badness 1077) in paragraph at lines 71--74
[]\T1/pcr/m/n/10 .MFclass() []\T1/ptm/m/n/10 re-turns a char-ac-ter string, one
of []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ordered"[]\T
1/ptm/m/n/10 , []\T1/pcr/m/n/10 "factor"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 (xl <- .getXlevels(terms(mf), mf)) # a list with one entry " $
Species" with 3 levels:[]
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[] \T1/pcr/m/n/9 identical(.getXlevels(terms(mc), mc), xl[0]) # a empty named
list, as no factors[]
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[]\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[]
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[]\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet =
FALSE)
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[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from []\T1/pcr/m/n/10 l
m []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 aov[]\T1/ptm/m/n/10 , or a for-mula for
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[] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm
= TRUE)[]
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[] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm
= TRUE)[]
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[] \T1/pcr/m/n/9 approx(xn, yn, xout=xout, method=M, rule=R, n
a.rm=na.)$y),[]
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[]\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$y) # warning, can be avoided by
specifying \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ties=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[
]
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[]\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE)
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[]\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[]
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[]\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Bartlett test of homo
geneity of
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[]\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p =
FALSE)[]
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[]\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p =
FALSE)[]
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Package amsmath Warning: Foreign command \atopwithdelims;
(amsmath) \frac or \genfrac should be used instead
(amsmath) on input line 3684.
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[]\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[]
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[]\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0)
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[]\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p
= FALSE)[]
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[]\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p
= FALSE)[]
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[]\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful
, but is ok![]
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[] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
df, ncp = L)),[]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10
(\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/
it/10 g[] \OT1/cmr/m/n/10 =
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[]\T1/pcr/m/n/10 confint(object, parm, level = 0.95, trace = FALSE, test=c("LR
T", "Rao"), ...)[]
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[]\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1))
, ci = c(-1,-1))[]
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[]\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci
= c(-0.9,0.1))[]
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[]\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works
with these :[]
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[]\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter"))
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[]\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i
ng co-vari-ances
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\T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi
-a-tion of)
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\T1/ptm/m/n/10 one of the strings []\T1/pcr/m/n/10 "everything"[]\T1/ptm/m/n/10
, []\T1/pcr/m/n/10 "all.obs"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "complete.obs"
[]\T1/ptm/m/n/10 ,
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[] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
...)[]
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[]\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
TRUE,
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[]\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
NULL)
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[]\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en
v = parent.frame())[]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor in-dex-ing []\T1/pcr/m/n/10 labels(termobj)
[]\T1/ptm/m/n/10 (that is, the
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
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[]\T1/ptm/m/n/10 Objects of class []\T1/pcr/m/n/10 "hclust" []\T1/ptm/m/n/10 ca
n be con-verted to class []\T1/pcr/m/n/10 "dendrogram" []\T1/ptm/m/n/10 us-ing
method
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[]\T1/pcr/m/n/10 rev.dendrogram []\T1/ptm/m/n/10 sim-ply re-turns the den-dro-g
ram []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 with re-versed nodes, see also
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\T1/ptm/m/n/10 has []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 y [
]\T1/ptm/m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be-
fore \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.1.2,
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[][][]\T1/pcr/m/n/10 dendrapply[][][] []\T1/ptm/m/n/10 for ap-ply-ing a func-ti
on to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][][]\T1/pcr/m/n/10 order.dend
rogram[][][] []\T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/9 str(dend1, max.level = 2, last.str = "\TS1/pcr/m/n/9 '\T1/pcr
/m/n/9 ") # only the first two sub-levels[]
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[]\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE,
type = "tr")[]
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[]\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p
cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[]
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[]\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[]
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[]\T1/pcr/m/n/9 abline(h = 1/1022, v = range(x), lty=2); axis(2, at=1/1022, "1
/(2n-2)", las=1)[]
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[] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[]
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[]\T1/pcr/m/n/10 "maximum"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "manhattan"[]\T1/
ptm/m/n/10 , []\T1/pcr/m/n/10 "canberra"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "bi
nary" []\T1/ptm/m/n/10 or
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[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from []\T1/
pcr/m/n/10 dist()[]\T1/ptm/m/n/10 , the
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[]\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht
tps : / / CRAN . R-[]project . org / view =
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[]\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences []
\T1/pcr/m/n/10 x[t][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 x[t-1][]\T1/ptm/m/n/10 ,
...,
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[]\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 na.action[][][] []\T1/ptm/m/n/10 to b
e used if []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 is used as a for-mula, in which c
ase
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[]\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q
uasipoisson())[]
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[1482]
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[]\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link
= "log")) # fails[]
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[]\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[]
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[] \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4
0k", "> 40k"),[]
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[] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod
erateS", "VeryS")))[]
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[]\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Fligner-Killeen test
of homogeneity of
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[][][]\T1/pcr/m/n/10 ftable.formula[][][] []\T1/ptm/m/n/10 for the for-mula in-
ter-face (which al-lows a []\T1/pcr/m/n/10 data = . []\T1/ptm/m/n/10 ar-gu-ment
);
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[]\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org
/ wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or
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[] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL
, ...)[]
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[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
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[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
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[]\T1/ptm/m/n/10 A spec-i-fi-ca-tion of the form []\T1/pcr/m/n/10 first:second
[]\T1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak-
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[]\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][][]\T1/pcr/m/n/10 coeffic
ients[][][][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 effects[]\T1/ptm/m/n/10 , []\T1/
pcr/m/n/10 fitted.values []\T1/ptm/m/n/10 and
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[]\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p
tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1
0 dev \OMS/cmsy/m/n/10 ^^@
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[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
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Underfull \hbox (badness 10000) in paragraph at lines 11235--11241
[][][]\T1/pcr/m/n/10 glm[][][] []\T1/ptm/m/n/10 for com-put-ing []\T1/pcr/m/n/1
0 glm.obj[]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 anova.glm[][][][]\T1/ptm/m/n/1
0 ; the cor-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions,
Underfull \hbox (badness 1418) in paragraph at lines 11273--11278
[]\T1/pcr/m/n/10 "average" []\T1/ptm/m/n/10 (= UP-GMA), []\T1/pcr/m/n/10 "mcqui
tty" []\T1/ptm/m/n/10 (= WPGMA), []\T1/pcr/m/n/10 "median" []\T1/ptm/m/n/10 (=
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\T1/ptm/m/n/10 There are [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/n/10 , [][
][]\T1/pcr/m/n/10 plot[][][] []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 identify []\
T1/ptm/m/n/10 (see [][][]\T1/pcr/m/n/10 identify.hclust[][][][]\T1/ptm/m/n/10 )
meth-ods and the
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[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these
de-fault to
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[]\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[]
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[] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma =
0.1),[]
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[]\T1/ptm/m/n/10 Character string to se-lect an []\T1/pcr/m/n/10 "additive" []\
T1/ptm/m/n/10 (the de-fault) or
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[]\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has
been already used, duplicate ignored
<to be read again>
\relax
l.12089 \aliasA{hat}{influence.measures}{hat}
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[]\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12164--12164
[]\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
...)[]
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[]\T1/ptm/m/n/10 The op-tional []\T1/pcr/m/n/10 infl[]\T1/ptm/m/n/10 , []\T1/pc
r/m/n/10 res []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 sd []\T1/ptm/m/n/10 ar-gu-me
nts are there to en-cour-age the use of these di-
Underfull \hbox (badness 1052) in paragraph at lines 12234--12236
[]\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 hat() []\T1/ptm/m/n/10 ex-ists
mainly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
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[]\T1/pcr/m/n/9 integrate(dnorm, 0, 20000) ## "fails" on many systems -- "wron
gly" giving \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 0\TS1/pcr/m/n/9 '[]
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[] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend =
TRUE,[]
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[] \T1/pcr/m/n/10 trace.label = deparse1(substitute(trace.fact
or)),[]
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[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][][]\T1/pcr/m/n/10 solve.de
fault[][][] []\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 SSinit =
Underfull \hbox (badness 4739) in paragraph at lines 12844--12846
[]\T1/ptm/m/n/10 the es-ti-mate at time $\OML/cmm/m/it/10 t \OMS/cmsy/m/n/10 ^^
@ \OT1/cmr/m/n/10 1$ \T1/ptm/m/n/10 of the state un-cer-tainty ma-trix $\OML/cm
m/m/it/10 Q$ \T1/ptm/m/n/10 (not up-dated by
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[]\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class []\T1/pcr/
m/n/10 "kmeans"[]\T1/ptm/m/n/10 , typ-i-cally the re-sult []\T1/pcr/m/n/10 ob [
]\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 ob <-
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[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
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\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 "Hartigan-Wong"[]\T1/ptm/m/n/10 ): if pos-i-ti
ve (or true), trac-ing in-for-ma-tion on the
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[]\T1/ptm/m/n/10 Gunar Schr�er and Di-et-rich Tren-kler (1995). Ex-act and Ran-
dom-iza-tion Dis-tri-bu-tions of
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[1553]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13846--13846
[]\T1/pcr/m/n/9 lag.plot(sqrt(sunspots), set.lags = c(1:4, 9:12), pch = ".", c
ol = "gold")[]
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[]\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep
t", "slope"))[]
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[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
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[]\T1/ptm/m/n/10 More []\T1/pcr/m/n/10 lm() []\T1/ptm/m/n/10 ex-am-ples are ava
il-able e.g., in [][][]\T1/pcr/m/n/10 anscombe[][][][]\T1/ptm/m/n/10 , [][][]\T
1/pcr/m/n/10 attitude[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 freeny[][][]
[]\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 els, [][][]\T1/pcr/m/n/10 influence[][][] []\T1/ptm/m/n/10 (etc
on that page) for re-gres-sion di-ag-nos-tics, [][][]\T1/pcr/m/n/10 weighted.re
siduals[][][][]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
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[]\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p =
FALSE)[]
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[]\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
FALSE)[]
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[]\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p =
FALSE)[]
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[]\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p =
FALSE)[]
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[]\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x)))
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[]\T1/ptm/m/n/10 character; one of []\T1/pcr/m/n/10 "logit"[]\T1/ptm/m/n/10 , [
]\T1/pcr/m/n/10 "probit"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cauchit"[]\T1/ptm/
m/n/10 , []\T1/pcr/m/n/10 "cloglog"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i
n R <= 3.5.0[]
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[] \T1/pcr/m/n/10 T = Thin.row(Proj(M) - Proj(X)), M = diag(nrow =
p), X = ~0,[]
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[]\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph)
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Underfull \hbox (badness 1490) in paragraph at lines 16594--16599
\T1/ptm/m/n/10 those spec-i-fied in []\T1/pcr/m/n/10 ... []\T1/ptm/m/n/10 which
are re-cy-cled to the num-ber of data frame rows. Un-like
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[]\T1/pcr/m/n/9 model.frame(dist ~ speed, data = cars, subset = speed < 10, z
= log(dist))[]
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[]\T1/ptm/m/n/10 a data frame cre-ated with [][][]\T1/pcr/m/n/10 model.frame[][
][][]\T1/ptm/m/n/10 . If an-other sort of ob-ject,
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[]\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts.arg = list(a = "contr.sum"
, b = contr.poly))[]
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[]\T1/pcr/m/n/9 m.orth <- model.matrix(~a+b, dd, contrasts.arg = list(a = "con
tr.helmert"))[]
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Overfull \hbox (9.78043pt too wide) in paragraph at lines 17307--17307
[]\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3)) # does not affect objects
with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[]
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[]\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x,
s, prob = 0.4)),[]
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[]\T1/pcr/m/n/9 ## adjusting the convergence test by adding \TS1/pcr/m/n/9 '\T
1/pcr/m/n/9 scaleOffset\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 to its denominator RSS:[]
Underfull \vbox (badness 10000) has occurred while \output is active
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Overfull \hbox (74.58035pt too wide) in paragraph at lines 18279--18279
[]\T1/pcr/m/n/9 ## Here, requiring close convergence, must use more accurate n
umerical differentiation,[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 18280--18280
[]\T1/pcr/m/n/9 ## as this typically gives Error: "step factor .. reduced belo
w \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 minFactor\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 .."[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 18284--18284
[]\T1/pcr/m/n/9 ## central differencing works here typically (PR#18165: not co
nverging on *some*):[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18285--18285
[]\T1/pcr/m/n/9 ctr2 <- nls.control(nDcentral=TRUE, tol = 8e-8, # <- even smal
ler than above[]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 18288--18288
[] \T1/pcr/m/n/9 (grepl("^aarch64.*linux", R.version$platform) && grepl
("^NixOS", osVersion)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18320--18320
[] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[]
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[]\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[]
[1624]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18543--18543
[]\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18590--18590
[]\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[]
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[] \T1/pcr/m/n/10 eps = .Machine$double.eps ^ (1/if(central) 3 els
e 2), central = FALSE)[]
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[]\T1/ptm/m/n/10 Method []\T1/pcr/m/n/10 "Brent" []\T1/ptm/m/n/10 is for one-di
mensional prob-lems only, us-ing [][][]\T1/pcr/m/n/10 optimize[][][](<ff>,
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Underfull \hbox (badness 1248) in paragraph at lines 19128--19131
[]\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma
-tion to the gra-di-ent, on
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[]\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i
t is un-able to re-duce
Underfull \hbox (badness 1478) in paragraph at lines 19149--19153
\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 control$trace []\T1/ptm/m/n/10 is pos-i-tive
. De-faults to ev-ery 10 it-er-a-tions for []\T1/pcr/m/n/10 "BFGS" []\T1/ptm/m/
n/10 and
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Underfull \hbox (badness 2042) in paragraph at lines 19207--19209
[]\T1/ptm/m/n/10 indicates an er-ror from the []\T1/pcr/m/n/10 "L-BFGS-B" []\T1
/ptm/m/n/10 method; see com-po-nent
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Overfull \hbox (15.18042pt too wide) in paragraph at lines 19313--19313
[] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[]
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[] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem",
axes = FALSE)[]
Overfull \hbox (123.1803pt too wide) in paragraph at lines 19374--19374
[]\T1/pcr/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b
ut NM may be ok and "unavoidable",[]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 19377--19377
[]\T1/pcr/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[]
[1637]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 19397--19397
[]\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max
(interval),
Overfull \hbox (36.78088pt too wide) in paragraph at lines 19400--19400
[]\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max
(interval),[]
Underfull \hbox (badness 2564) in paragraph at lines 19435--19446
[]\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 f []\T1/ptm/m/n/10 is never eva
l-u-ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m
/n/10 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/
10 tol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1082) in paragraph at lines 19435--19446
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately
[]\T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) []\T1/ptm/m/n/10 and $\OML
/cmm/m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa
[1638]
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[]\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x -
1)), 10), 10)[]
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[]\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp =
1, lty = 1:6,[]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
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Overfull \hbox (0.78088pt too wide) in paragraph at lines 20157--20157
[] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd =
1.5),[]
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[] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist
vs Leverage* " * h[ii] / (1 - h[ii]))),[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 20246--20246
[] \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else
points,[]
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[] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[]
[1651]
Underfull \hbox (badness 10000) in paragraph at lines 20308--20314
\T1/pcr/m/n/10 "bottomleft", legend = "Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s di
stance", lty = cook.lty,
Underfull \hbox (badness 10000) in paragraph at lines 20308--20314
\T1/pcr/m/n/10 col = cook.col, text.col = cook.col, bty = "n", x.intersp
Underfull \hbox (badness 10000) in paragraph at lines 20316--20322
[]\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment []\T
1/pcr/m/n/10 iter []\T1/ptm/m/n/10 in
Underfull \hbox (badness 10000) in paragraph at lines 20327--20330
[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 1 or 2, to be used in []\T1/pcr/m
/n/10 ylim <-
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[]\T1/pcr/m/n/9 nlmod <- nls(y ~ Const + A * exp(B * x), start=list(Const=100
, A=10, B=1))[]
[1656]
[1657]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 20725--20725
[] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
...)[]
[1658]
Underfull \hbox (badness 1194) in paragraph at lines 20735--20738
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
of the con-fi-dence
[1659]
Underfull \hbox (badness 1107) in paragraph at lines 20793--20795
[]\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate []
\T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . De-faults to
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20848--20848
[]\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[]
[1660]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 20855--20855
[]\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty =
1, y.intersp = 1)[]
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[]\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[]
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[1663]
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[] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no
cancellation[]
[1664]
Underfull \hbox (badness 7740) in paragraph at lines 21140--21142
[]\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Exact Poisson test" [
]\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 "Comparison of
[1665]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 21188--21188
[]\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple =
FALSE)
Underfull \hbox (badness 10000) in paragraph at lines 21244--21246
[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 poly(*, simple=TRUE)[]\T1/ptm/m/n/10 , []
\T1/pcr/m/n/10 polym(*, coefs=<non-NULL>)[]\T1/ptm/m/n/10 , and
[1666]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 21281--21281
[] \T1/pcr/m/n/9 zm <- zapsmall(polym ( 1:4, c(1, 4:6), degree = 3)) # or
just poly():[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 21286--21286
[]\T1/pcr/m/n/9 ## poly(<matrix>, df) --- used to fail till July 14 (vive la F
rance!), 2017:[]
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[] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tolerance = 1e-15)) # e
xactly equal typically[]
[1680]
Underfull \hbox (badness 6859) in paragraph at lines 22207--22214
[][][]\T1/pcr/m/n/10 predict.glm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 p
redict.lm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.loess[][][][]\T1
/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.nls[][][][]\T1/ptm/m/n/10 , [][][]\T
1/pcr/m/n/10 predict.poly[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 22218--22224
[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][][]\T1/pcr/m/n/10 predict.ar[
][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.Arima[][][][]\T1/ptm/m/n/1
0 , [][][]\T1/pcr/m/n/10 predict.arima0[][][][]\T1/ptm/m/n/10 ,
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Overfull \hbox (54.78088pt too wide) in paragraph at lines 22506--22506
[] \T1/pcr/m/n/10 rankdeficient = c("warnif", "simple", "non-estim", "N
A", "NAwarn"),[]
Underfull \hbox (badness 10000) in paragraph at lines 22532--22535
[]\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string
spec-i-fy-ing what should hap-pen in the
Underfull \hbox (badness 10000) in paragraph at lines 22532--22535
\T1/ptm/m/n/10 case of a rank de-fi-cient model, i.e., when []\T1/pcr/m/n/10 ob
ject$rank <
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Underfull \hbox (badness 5832) in paragraph at lines 22537--22542
\T1/ptm/m/n/10 cases, i.e., vec-tors not in the same pre-dic-tor sub-space as t
he
Underfull \hbox (badness 8151) in paragraph at lines 22537--22542
\T1/ptm/m/n/10 orig-i-nal data (with tol-er-ance []\T1/pcr/m/n/10 tol[]\T1/ptm/
m/n/10 ). In that case, the non-
Underfull \hbox (badness 1184) in paragraph at lines 22537--22542
\T1/ptm/m/n/10 estimable in-dices are also re-turned as at-tribute []\T1/pcr/m/
n/10 "non-estim" []\T1/ptm/m/n/10 (see
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Overfull \hbox (48.78088pt too wide) in paragraph at lines 23005--23005
[] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign
= TRUE, ...)[]
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Overfull \hbox (0.78088pt too wide) in paragraph at lines 23289--23289
[] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x
)) &&[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 23290--23290
[] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr("
, "p-v"),[]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
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[]\T1/pcr/m/n/9 with(d, qqplot(Female, Male, pch = 19, xlim = c(-31, 31), ylim
= c(-31, 31),[]
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Underfull \hbox (badness 10000) in paragraph at lines 24338--24340
[]\T1/ptm/m/n/10 Wicklin, R. (2017) Sam-ple quan-tiles: A com-par-i-son of 9 de
f-i-ni-tions;
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\T1/ptm/m/n/10 SAS Blog. [][]$\T1/pcr/m/n/10 https : / / blogs . sas . com / co
ntent / iml / 2017 / 05 / 24 /
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[]\T1/ptm/m/n/10 Wikipedia: [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . or
g / wiki / Quantile # Estimating _
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[] \T1/pcr/m/n/10 method = c("non.compact", "row.compact", "col.compact"
, "compact"),[]
[1716]
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[]\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for []\T
1/pcr/m/n/10 write() []\T1/ptm/m/n/10 and
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[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
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[]\T1/ptm/m/n/10 This, as [][][]\T1/pcr/m/n/10 reorder[][][]()[]\T1/ptm/m/n/10
, is a spe-cial case of sim-ply call-ing [][][]\T1/pcr/m/n/10 factor[][][](x, l
evels =
[1720]
Underfull \hbox (badness 7099) in paragraph at lines 24744--24746
[]\T1/ptm/m/n/10 This, as [][][]\T1/pcr/m/n/10 relevel[][][]()[]\T1/ptm/m/n/10
, is a spe-cial case of sim-ply call-ing [][][]\T1/pcr/m/n/10 factor[][][](x, l
evels =
Overfull \hbox (31.3804pt too wide) in paragraph at lines 24779--24779
[]\T1/pcr/m/n/9 bymedianR <- with(InsectSprays, reorder(spray, count, median,
decreasing=TRUE))[]
[1721]
[1722]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 24855--24855
[]\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd,
10:1, mean)")[]
[1723]
[1724]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 24972--24972
[]\T1/pcr/m/n/10 # varying = ___, # list / matrix / vector (use with
care)[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 24973--24973
[]\T1/pcr/m/n/10 # v.names = ___, # vector of variable names in long
format[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 24974--24974
[]\T1/pcr/m/n/10 # timevar, times, # name / values of constructed time
variable[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 24975--24975
[]\T1/pcr/m/n/10 # idvar, ids) # name / values of constructed id v
ariable[]
[1725]
[1726]
Underfull \hbox (badness 10000) in paragraph at lines 25132--25137
[][][]\T1/pcr/m/n/10 stack[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 aperm[]
[][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 relist[][][] []\T1/ptm/m/n/10 for r
e-shap-ing the re-sult of [][][]\T1/pcr/m/n/10 unlist[][][][]\T1/ptm/m/n/10 . [
][][]\T1/pcr/m/n/10 xtabs[][][] []\T1/ptm/m/n/10 and
Underfull \hbox (badness 2495) in paragraph at lines 25132--25137
[][][]\T1/pcr/m/n/10 as.data.frame.table[][][] []\T1/ptm/m/n/10 for cre-at-ing
con-tin-gency ta-bles and con-vert-ing them back to
Overfull \hbox (15.18042pt too wide) in paragraph at lines 25145--25145
[]\T1/pcr/m/n/9 ## long to wide (direction = "wide") requires idvar and timeva
r at a minimum[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25146--25146
[]\T1/pcr/m/n/9 reshape(Indometh, direction = "wide", idvar = "Subject", timev
ar = "time")[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 25165--25165
[]\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[]
[1727]
[1728]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 25270--25270
[] \T1/pcr/m/n/10 na.action = c("+Big_alternate", "-Big_alternate", "na.
omit", "fail"),[]
Underfull \hbox (badness 1033) in paragraph at lines 25313--25319
\T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10
where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/
m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where
[1729]
Underfull \hbox (badness 10000) in paragraph at lines 25334--25337
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult []\T1/pcr/m/n/10 y = r
unmed(x, k) []\T1/ptm/m/n/10 sim-ply has []\T1/pcr/m/n/10 y[j] =
[1730]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 25412--25412
[]\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 25438--25438
[]\T1/pcr/m/n/9 ## An example with initial NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s -
used to fail badly (notably for "Turlach"):[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 25450--25450
[]\T1/pcr/m/n/9 matplot(y = cbind(x15, rT15), type = "b", ylim = c(1,9), pch=1
:5, xlab = NA,[]
[1731]
[1732]
[1733]
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[1735]
[1736]
Underfull \vbox (badness 10000) has occurred while \output is active
[1737]
[1738]
Underfull \hbox (badness 6268) in paragraph at lines 25909--25914
[][][]\T1/pcr/m/n/10 SSasympOrig[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 S
Sbiexp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSfol[][][][]\T1/ptm/m/n/10
, [][][]\T1/pcr/m/n/10 SSfpl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSgo
mpertz[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSlogis[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 SSmicmen[][][][]\T1/ptm/m/n/10 ,
[1739]
[1740]
[1741]
Underfull \hbox (badness 1867) in paragraph at lines 26119--26121
[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods.
Passed to
Underfull \hbox (badness 10000) in paragraph at lines 26135--26139
[]\T1/ptm/m/n/10 where []\T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallba
ck = use.fallback) []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 PP
Underfull \hbox (badness 10000) in paragraph at lines 26135--26139
\T1/pcr/m/n/10 <- sum(!is.na([][]coef[][][](object))) []\T1/ptm/m/n/10 -- where
in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was
[1742]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 26177--26177
[]\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr
om summary(lm1)[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 26184--26184
[]\T1/pcr/m/n/9 stopifnot(all.equal(sigma(fm.DN1), summary(fm.DN1)$sigma, tole
rance=1e-15))[]
[1743]
[1744]
[1745]
Underfull \hbox (badness 2495) in paragraph at lines 26366--26375
[]\T1/ptm/m/n/10 For an in-verse gaus-sian GLM the model as-sumed is $\OML/cmm/
m/it/10 IG\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^V[]; ^^Uw[]\OT1/cmr/m/n/10 )$ \T1
/ptm/m/n/10 (see [][]$\T1/pcr/m/n/10 https : / / en .
[1746]
[1747]
Underfull \hbox (badness 2197) in paragraph at lines 26512--26515
[]\T1/pcr/m/n/10 psmirnov []\T1/ptm/m/n/10 gives the dis-tri-bu-tion func-tion,
[]\T1/pcr/m/n/10 qsmirnov []\T1/ptm/m/n/10 gives the quan-tile func-tion, and
Overfull \hbox (24.78088pt too wide) in paragraph at lines 26532--26532
[] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
= FALSE)[]
Underfull \hbox (badness 1412) in paragraph at lines 26539--26541
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1748]
[1749]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 26624--26624
[]\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 26649--26649
[]\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda
= NULL, cv = FALSE,
Overfull \hbox (66.78088pt too wide) in paragraph at lines 26652--26652
[] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee
p.stuff = FALSE)[]
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[1751]
[1752]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 26877--26877
[] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / t
ol) ))[]
Underfull \hbox (badness 2547) in paragraph at lines 26881--26887
[]\T1/ptm/m/n/10 The de-fault []\T1/pcr/m/n/10 all.knots = FALSE []\T1/ptm/m/n/
10 and []\T1/pcr/m/n/10 nknots = .nknots.smspl[]\T1/ptm/m/n/10 , en-tails us-in
g only
[1753]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26928--26928
[]\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi
ng splines")[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 26949--26949
[]\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # =
= unique(cars$speed)[]
[1754]
[1755]
[1756]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 27141--27141
[]\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail,
[1757]
[1758]
[1759]
[1760]
Underfull \hbox (badness 10000) in paragraph at lines 27406--27411
\T1/ptm/m/n/10 This makes the spec-tral den-sity a den-sity over the range []\T
1/pcr/m/n/10 (-frequency(x)/2,
[1761]
[1762]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 27520--27520
[] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[]
[1763]
[1764]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 27702--27702
[]\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi
* x) + rnorm(30)/10, 3)[]
[1765]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 27708--27708
[]\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean))
for when x has ties")[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 27717--27717
[]\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c
ol = 3, n = 1001)[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 27718--27718
[]\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c
ol = 4, n = 1001)[]
[1766]
Underfull \hbox (badness 2922) in paragraph at lines 27787--27792
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (9.78043pt too wide) in paragraph at lines 27824--27824
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim
= c(-.3, 5),[]
[1767]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 27827--27827
[] \T1/pcr/m/n/9 {f[phi](x) == phi[1] + (phi[2]-phi[1])*~e^
{-e^{phi[3]}*~x}}))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 27836--27836
[] \T1/pcr/m/n/9 c(0 , 1 ), 1, length = 0.08, angle = 25); text(0.
5, 1, quote(1))[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27837--27837
[] \T1/pcr/m/n/9 y0 <- 1 + 4*exp(-3/4) ; t.5 <- log(2) / exp(-3/4) ; AR2 <- 3
# (Asym + R0)/2[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 27841--27841
[] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi
[1]+phi[2],2), phi[1]),[]
[1768]
Underfull \hbox (badness 3240) in paragraph at lines 27895--27898
[][][]\T1/pcr/m/n/10 nls[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 selfStart
[][][][]\T1/ptm/m/n/10 ; []\T1/pcr/m/n/10 example(SSasympOff) []\T1/ptm/m/n/10
gives graph show-ing the []\T1/pcr/m/n/10 SSasympOff
Overfull \hbox (36.7804pt too wide) in paragraph at lines 27916--27916
[] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOff(xx, Asym = 5, lrc = log(
0.4), c0 = 3/4)) )[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27919--27919
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim
= c(-1, 8),[]
[1769]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28002--28002
[] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOrig(xx, Asym = 5, lrc = log
(log(2)))) )[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28006--28006
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim =
c(-1/4, 5),[]
[1770]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 28016--28016
[] \T1/pcr/m/n/9 axis(2, at = 5*c(1/2,1), labels= expression(frac(phi[1],2),
phi[1]), pos=0, las=1)[]
Overfull \hbox (106.98032pt too wide) in paragraph at lines 28021--28021
[] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
== frac(log(2), e^{phi[2]})}),[]
Underfull \hbox (badness 2922) in paragraph at lines 28057--28063
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1771]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28079--28079
[]\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28095--28095
[] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 =
1.5 * exp(-x)"),[]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 28109--28109
[]\T1/pcr/m/n/9 ## Fails by default (scaleOffset=0) on most platforms {also af
ter increasing maxiter !}[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28111--28111
[] \T1/pcr/m/n/9 nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d
atN, trace=TRUE)[]
Overfull \hbox (128.58029pt too wide) in paragraph at lines 28117--28117
[] \T1/pcr/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol=
1e-11, nDcentral=TRUE), trace=TRUE)[]
[1772]
[1773]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 28228--28228
[]\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input))
[1774]
Underfull \hbox (badness 2922) in paragraph at lines 28290--28295
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1775]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 28328--28328
[] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm
id", phi[4] == "scal")))[]
Underfull \hbox (badness 2922) in paragraph at lines 28377--28382
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1776]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28408--28408
[]\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = "
red", lwd=2)[]
Underfull \hbox (badness 2922) in paragraph at lines 28442--28447
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1777]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28467--28467
[]\T1/pcr/m/n/9 ## Initial values are in fact the converged one here, "Number
of iter...: 0" :[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 28471--28471
[]\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR
UE), trace = TRUE)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28491--28491
[] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3]
== "scal")))[]
[1778]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 28501--28501
[] \T1/pcr/m/n/9 segments(c(2,2.6,2.6), c(0, 2.5,3.5), # NB. SSlogis(x =
xmid = 2) = 2.5[]
Underfull \hbox (badness 2922) in paragraph at lines 28536--28541
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28558--28558
[]\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
digits = 3)[]
[1779]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 28576--28576
[] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS
micmen model")[]
[1780]
Underfull \hbox (badness 6493) in paragraph at lines 28628--28633
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 x[]\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28656--28656
[]\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28658--28658
[]\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 28662--28662
[]\T1/pcr/m/n/9 plot(weight ~ Time, Chick.6, xlim = c(0, 21), main = "SSweibul
l() fit to Chick.6")[]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 28665--28665
[]\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f
m1)[["Drop"]]), lty = 3)[]
[1781]
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[1783]
[1784]
[1785]
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[1787]
[1788]
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[1791]
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[1794]
Underfull \hbox (badness 3396) in paragraph at lines 29546--29548
[]\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.glm"[]\T1/ptm/m/
n/10 , usu-ally, a re-sult of a call to
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[1796]
[1797]
Underfull \hbox (badness 2237) in paragraph at lines 29725--29727
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1
/pcr/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if
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[1799]
Underfull \hbox (badness 2591) in paragraph at lines 29889--29891
[]\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.nls"[]\T1/ptm/m/
n/10 , usu-ally the re-sult of a call to
[1800]
Underfull \hbox (badness 2237) in paragraph at lines 29935--29938
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1
/pcr/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if
[1801]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 30008--30008
[]\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t
race = FALSE)
[1802]
[1803]
Underfull \hbox (badness 3407) in paragraph at lines 30117--30121
[]\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m
ented\T1/ptm/m/n/10 , see []\T1/pcr/m/n/10 corr []\T1/ptm/m/n/10 be-low)
[1804]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 30187--30187
[]\T1/pcr/m/n/9 symnum(ii, cutpoints = 2*(0:4), symbols = c(".", "-", "+", "$
"), show.max = TRUE)[]
[1805]
Underfull \hbox (badness 1337) in paragraph at lines 30250--30254
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
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[1807]
[1808]
[1809]
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[]\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200,
main = t.tit,[]
[1810]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 30567--30567
[] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com
mon",[]
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[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
resid-u-als, when
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[]\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[]
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[]\T1/ptm/m/n/10 There are meth-ods for classes []\T1/pcr/m/n/10 "aovlist"[]\T1
/ptm/m/n/10 , []\T1/pcr/m/n/10 "terms"[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 "
formula" []\T1/ptm/m/n/10 (see
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[]\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out =
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[]\T1/pcr/m/n/10 toeplitz2(x, nrow = length(x) +1 - ncol, ncol = length(x) +1
- nrow)[]
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[]\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 toeplitz(x, *)[]\T1/ptm/m/n/10 : the firs
t col-umn of the Toeplitz ma-trix; for
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[]\T1/pcr/m/n/9 # Matrix of character (could also have logical, raw, complex .
.) {also warning}:[]
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[] \T1/pcr/m/n/9 colnames(W) <- paste0(",", if(n <= 9) 1:n else c(1:9, lette
rs[seq_len(n-9)]))[]
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[]\T1/pcr/m/n/9 y.hat <- W. %*% y # y.hat := smoothed(y) ("mass preserving" ->
longer than y)[]
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[]\T1/pcr/m/n/9 plot(x,y, type="b", xlim=c(1,m)); curve(f(x), 1,n, col="gray",
lty=2, add=TRUE)[]
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[] \T1/pcr/m/n/10 class = if(nseries > 1) c("mts", "ts", "matrix", "array")
else "ts",[]
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[]\T1/pcr/m/n/10 is.mts(x) []\T1/ptm/m/n/10 tests if an ob-ject []\T1/pcr/m/n/1
0 x []\T1/ptm/m/n/10 is a mul-ti-vari-ate time se-ries, i.e., ful-fills []\T1/p
cr/m/n/10 is.ts(x)[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 utils:: methods(class = "ts") # all functions with methods ava
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[]\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
FALSE)
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[]\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
FALSE)[]
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[] \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con
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[] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace
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[]\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature
s: --------------[]
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[]\T1/pcr/m/n/9 ## where as \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 simply first enlarges the search interval:[]
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[]\T1/pcr/m/n/9 wilcox.test( 4:2, 3:1, paired=TRUE) # Warning: canno
t compute exact p-value with ties[]
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[]\T1/pcr/m/n/9 wilcox.test((4:2)/10, (3:1)/10, paired=TRUE, digits.rank = 9)
# same ties as (4:2, 3:1)[]
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[] \T1/pcr/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps
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[]\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE,
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[] \T1/pcr/m/n/10 exclude = if(!addNA) c(NA, NaN), drop.unused.levels = F
ALSE)[]
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Chapter 11.
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[] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[]
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[]\T1/pcr/m/n/9 ## Boundary case: This works, but fails if limits are set clos
er to 0 and 1[]
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Chapter 12.
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[]\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all.names = TRUE) # .Tcl.args put a ca
llback ref in here[]
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[]\T1/pcr/m/n/10 tcl []\T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-i
ng any Tk or Tcl com-mand by sim-ply run-ning
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[]\T1/pcr/m/n/9 eval.txt <- function() eval(str2lang(tclvalue(tkget(txt.w, "0.
0", "end"))))[]
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[][][]\T1/pcr/m/n/10 select.list[][][] []\T1/ptm/m/n/10 (a text ver-sion ex-cep
t on Win-dows and the ma-cOS GUI), [][][]\T1/pcr/m/n/10 menu[][][] []\T1/ptm/m/
n/10 (whose
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Chapter 13.
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[]\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
new methods.[]
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[]\T1/pcr/m/n/10 assertWarning() []\T1/ptm/m/n/10 as-serts that a warn-ing will
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[]\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
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\T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][][]\T1/pcr/m/n
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\T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named []\T1/pcr/m/n
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,
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[]\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gin
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\T1/ptm/m/n/10 If given, vi-gnette source files are by de-fault looked for in s
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diff \T1/ptm/m/n/10 or \T1/pcr/m/n/10 \dontshow\T1/ptm/m/n/10 , and \T1/pcr/m/n
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r
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[]\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", "
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[]\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co
mpress == "none")[]
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[] \T1/pcr/m/n/10 outputs = FALSE, sources = FALS
E, ...)[]
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[]\T1/pcr/m/n/10 check_packages_in_dir_details(dir, logs = NULL, drop_ok = TRU
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[]\T1/pcr/m/n/10 codocClasses []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 codocData [
]\T1/ptm/m/n/10 re-turn ob-jects of class []\T1/pcr/m/n/10 "codocClasses" []\T1
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' meta-data for the cu
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[]\T1/ptm/m/n/10 Functions []\T1/pcr/m/n/10 CRAN_current_db()[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 CRAN_aliases_db()[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 CRAN_rdx
refs_db()[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 CRAN_authors_db() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 CRAN_a
rchive_db() []\T1/ptm/m/n/10 (also used by []\T1/pcr/m/n/10 R CMD check[]\T1/pt
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T1/pcr/m/n/10 R_CRAN_WEB[]\T1/ptm/m/n/10 . The mir-ror to be used is re-ported
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[] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En
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s", "system.Rd"))[]
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[]\T1/ptm/m/n/10 By de-fault, the tags \T1/pcr/m/n/10 \S3method\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 \S4method\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \command\T1/ptm/m/n/10
, \T1/pcr/m/n/10 \docType\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \email\T1/ptm/m/n/10
,
[1949]
[1950]
[1951]
[1952]
[1953]
Underfull \hbox (badness 4108) in paragraph at lines 4462--4469
[]\T1/ptm/m/n/10 This func-tion starts the in-ter-nal HTTP server, which runs o
n the loop-back in-ter-face
[1954]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4563--4563
[] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett
es"),[]
[1955]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 4566--4566
[]\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter
net", "all"),[]
Underfull \hbox (badness 10000) in paragraph at lines 4591--4593
[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
[1956]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4650--4650
[]\T1/pcr/m/n/9 (prio <- sapply(as.vector(pNms), packageDescription, fields =
"Priority"))[]
[1957]
[1958]
[1959]
[1960]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4909--4909
[]\T1/pcr/m/n/9 toTitleCase("ensemble tool for predictions from species distri
bution models")[]
Overfull \hbox (128.58029pt too wide) in paragraph at lines 4913--4913
[]\T1/pcr/m/n/9 toTitleCase("a small fox is jumping") # "a Small Fox is .."
(the \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 a\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 may cha
nge)% i.e. BUG[]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 4917--4917
[]\T1/pcr/m/n/9 toTitleCase("asking -- \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 is a smal
l fox jumping?\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ") # ".. -- Is a Small ..." (fi
ne)[]
[1961]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5000--5000
[] \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry
run),[]
[1962]
[1963]
[1964]
Underfull \hbox (badness 10000) in paragraph at lines 5184--5187
[]\T1/ptm/m/n/10 optional char-ac-ter strings for the `[]\T1/pcr/m/n/10 Copyrig
ht[]\T1/ptm/m/n/10 ' and
Underfull \hbox (badness 6859) in paragraph at lines 5200--5205
[]\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory []\T1/pcr/m/n/10 po []\T1/
ptm/m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\
T1/ptm/m/n/10 ' are up-dated from
Underfull \hbox (badness 1184) in paragraph at lines 5208--5214
[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po
/\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T
he
Underfull \hbox (badness 2941) in paragraph at lines 5208--5214
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t
he pack-age are ex-am-ined to cre-ate a file
[1965]
[1966]
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[]\T1/pcr/m/n/9 parse_URI_reference(c("foo://example.com:8042/over/there?name=
ferret#nose",[]
[1967]
[1968]
[1969]
Underfull \hbox (badness 10000) in paragraph at lines 5513--5515
[]\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 vignetteEngine[][][][]\T1/ptm/m/n/10
, such as []\T1/pcr/m/n/10 "utils::Sweave" []\T1/ptm/m/n/10 or
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5542--5542
[] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F
ALSE,[]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 5543--5543
[] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr
ess = "xz",[]
Underfull \hbox (badness 3240) in paragraph at lines 5556--5559
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T
1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ',
Underfull \hbox (badness 1742) in paragraph at lines 5560--5570
[]\T1/pcr/m/n/10 "Package"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Version"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "Priority"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Depe
nds"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Imports"[]\T1/ptm/m/n/10 ,
[1970]
Underfull \hbox (badness 1127) in paragraph at lines 5598--5604
[]\T1/pcr/m/n/10 write_PACKAGES []\T1/ptm/m/n/10 scans the named di-rec-tory fo
r R pack-ages, ex-tracts in-for-ma-tion from
Underfull \hbox (badness 1635) in paragraph at lines 5598--5604
\T1/ptm/m/n/10 each pack-age's `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file
, and writes this in-for-ma-tion into the `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/1
0 ',
Underfull \hbox (badness 1571) in paragraph at lines 5626--5630
[]\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down-
load speed and time spent by
[1971]
Underfull \hbox (badness 2772) in paragraph at lines 5652--5657
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 PACKAGES.gz\T1/ptm/m/n/10 ' files. See [][][
]\T1/pcr/m/n/10 update_PACKAGES[][][] []\T1/ptm/m/n/10 for ef-fi-ciently up-dat
-ing ex-ist-ing
[1972]
[1973]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5790--5790
[] \T1/pcr/m/n/9 " stop(errorCondition(gettext(\TS1/pcr/m/n/9 '\T1/pcr/m/n
/9 needs Deep Thought\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ), class=\TS1/pcr/m/n/9 '\T1
/pcr/m/n/9 myError\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ))",[]
[1974]) (./utils-pkg.tex
Chapter 14.
Underfull \hbox (badness 1072) in paragraph at lines 47--52
[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[]
\T1/pcr/m/n/10 insertions[]\T1/ptm/m/n/10 ',
[1975]
[1976]
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[1978]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 260--260
[]\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with
these names[]
[1979]
[1980]
Underfull \hbox (badness 10000) in paragraph at lines 378--383
\T1/ptm/m/n/10 are []\T1/pcr/m/n/10 c("vertical", "horizontal", "cascade", "min
imize",
Underfull \hbox (badness 10000) in paragraph at lines 384--386
[]\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 list[][][] []\T1/ptm/m/n/10 of win-dow
han-dles, by de-fault pro-duced by
[1981]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 450--450
[]\T1/pcr/m/n/9 # This default is useful only in SDI mode: it will tile any F
irefox window[]
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[]\T1/pcr/m/n/9 .arrangeWindowsDefaults <- list(c("R", "all"), pattern = c("",
"Firefox"))[]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 469--469
[] \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No
", "Cancel"))),[]
[1982]
[1983]
[1984]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 691--691
[]\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l
ist(),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 692--692
[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 693--693
[]\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l
ist(),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 694--694
[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
[1985]
Underfull \hbox (badness 10000) in paragraph at lines 728--734
[]\T1/ptm/m/n/10 Functions []\T1/pcr/m/n/10 aspell_package_Rd_files[]\T1/ptm/m/
n/10 , []\T1/pcr/m/n/10 aspell_package_vignettes[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 4416) in paragraph at lines 728--734
[]\T1/pcr/m/n/10 aspell_package_R_files []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 a
spell_package_C_files []\T1/ptm/m/n/10 per-form spell check-
[1986]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 797--797
[] \T1/pcr/m/n/10 fields = getOption("available_packages_fie
lds"),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 802--802
[] \T1/pcr/m/n/10 str2logical(Sys.getenv("R_PACKAGES_CAC
HE_USER_DIR",[]
Underfull \hbox (badness 10000) in paragraph at lines 842--845
[][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 in-di-cat-ing if caching sh
ould hap-pen in \T1/ptm/b/n/10 tools\T1/ptm/m/n/10 '
[1987]
Underfull \hbox (badness 1552) in paragraph at lines 936--942
[]\T1/ptm/m/n/10 A char-ac-ter ma-trix with one row per pack-age, row names the
pack-age names and col-
[1988]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 963--963
[]\T1/pcr/m/n/9 db <- available.packages(repos = findCRANmirror("web"), filter
s = "duplicates")[]
[1989]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1065--1065
[]\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
NULL,
[1990]
[1991]
Underfull \hbox (badness 7649) in paragraph at lines 1139--1145
[][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 in-di-cat-ing if Bib-TeX co
de should be given ad-di-tion-ally;
Underfull \hbox (badness 5533) in paragraph at lines 1139--1145
\T1/ptm/m/n/10 cur-rently ap-plies only to []\T1/pcr/m/n/10 style = "citation"[
]\T1/ptm/m/n/10 . The de-fault for
Underfull \hbox (badness 4739) in paragraph at lines 1139--1145
\T1/ptm/m/n/10 the []\T1/pcr/m/n/10 print() []\T1/ptm/m/n/10 method de-pends on
the num-ber of (bib) en-tries and
Underfull \hbox (badness 1215) in paragraph at lines 1139--1145
\T1/ptm/m/n/10 For ex-am-ple, to see no Bib-TeX at all, you can change the de-f
ault by
Underfull \hbox (badness 10000) in paragraph at lines 1148--1150
[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1992]
Underfull \hbox (badness 10000) in paragraph at lines 1266--1269
[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org
/ wiki / Digital _ Object _
[1993]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1349--1349
[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
[1994]
[1995]
[1996]
[1997]
[1998]
[1999]
Underfull \hbox (badness 1859) in paragraph at lines 1758--1767
[]\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b
e quite large the com-
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\T1/ptm/m/n/10 mand []\T1/pcr/m/n/10 data.frame(x, y, z, monday, tuesday) []\T1
/ptm/m/n/10 never re-turns. Do not re-port that
[2000]
[2001]
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[] \T1/pcr/m/n/9 data = infert, family = b
inomial())))[]
[2002]
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[] \T1/pcr/m/n/10 md5sum = FALSE, digest = NULL, full.names = length(path)
> 1,[]
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[]\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[]
[2003]
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[]\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[]
[2004]
Underfull \hbox (badness 2277) in paragraph at lines 2113--2118
[]\T1/pcr/m/n/10 charClass []\T1/ptm/m/n/10 was added in \T1/phv/m/n/10 R \T1/p
tm/m/n/10 4.1.0. A less di-rect way to ex-am-ine char-ac-ter classes
[2005]
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[]\T1/pcr/m/n/9 cl <- c("alnum", "alpha", "blank", "digit", "graph", "punct",
"upper", "xdigit")[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2147--2147
[]\T1/pcr/m/n/9 X <- as.data.frame(X); row.names(X) <- sQuote(intToUtf8(x, mul
tiple = TRUE))[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2155--2155
[]\T1/pcr/m/n/9 ## How many printable characters are there? (Around 280,000 in
Unicode 13.)[]
[2006]
[2007]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2303--2303
[]\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
NULL,
[2008]
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[]\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
NULL,
[2009]
[2010]
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[]\T1/ptm/m/n/10 If the ob-ject re-turned by []\T1/pcr/m/n/10 citation() []\T1/
ptm/m/n/10 con-tains only one ref-er-ence, the as-so-ci-ated print
Underfull \hbox (badness 1400) in paragraph at lines 2481--2488
\T1/ptm/m/n/10 method shows both a text ver-sion and a Bib-TeX en-try for it. I
f a pack-age has more
[2011]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2564--2564
[]\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
NULL,[]
[2012]
[2013]
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[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 2724--2724
[]\T1/pcr/m/n/10 citEntry(entry, textVersion = NULL, header = NULL, footer = N
ULL, ...)
[2014]
Underfull \hbox (badness 1082) in paragraph at lines 2753--2757
[][][]\T1/pcr/m/n/10 citation[][][] []\T1/ptm/m/n/10 for more in-for-ma-tion ab
out cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file
s;
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard
}) has been already used, duplicate ignored
<to be read again>
\relax
l.2758 ... the Clipboard in MS Windows}{clipboard}
[2015]
[2016]
Underfull \hbox (badness 10000) in paragraph at lines 2882--2884
[]\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/
phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see
[2017]
[2018]
[2019]
[2020]
Underfull \hbox (badness 10000) in paragraph at lines 3103--3105
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[2021]
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[2024]
Underfull \hbox (badness 1762) in paragraph at lines 3396--3399
[]\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re
c-tory of the cur-rent work-ing di-rec-tory, set []\T1/pcr/m/n/10 package =
[2025]
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[]\T1/pcr/m/n/9 try(data(package = "rpart"), silent = TRUE) # list the data se
ts in the rpart package[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3485--3485
[]\T1/pcr/m/n/9 data(USArrests, "VADeaths") # load the data sets \TS1/pcr/m
/n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9
'\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[]
[2026]
Underfull \hbox (badness 2452) in paragraph at lines 3559--3562
[]\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class []\
T1/pcr/m/n/10 R_dataentry[]\T1/ptm/m/n/10 . Re-sources
[2027]
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[2031]
[2032]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 3987--3987
[] \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf
orm$r_arch, "stats.dll"))[]
[2033]
[2034]
Underfull \hbox (badness 4779) in paragraph at lines 4068--4073
[]\T1/ptm/m/n/10 Support for method []\T1/pcr/m/n/10 "libcurl" []\T1/ptm/m/n/10
was op-tional on Win-dows prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0: use
Underfull \hbox (badness 1072) in paragraph at lines 4131--4135
[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
the []\T1/pcr/m/n/10 quiet []\T1/ptm/m/n/10 ar-gu-ment and the
[2035]
Underfull \hbox (badness 7238) in paragraph at lines 4192--4197
[]\T1/ptm/m/n/10 For the []\T1/pcr/m/n/10 "libcurl" []\T1/ptm/m/n/10 and []\T1/
pcr/m/n/10 "curl" []\T1/ptm/m/n/10 meth-ods, prox-ies can be set \T1/ptm/m/it/1
0 via \T1/ptm/m/n/10 the en-vi-ron-
Underfull \hbox (badness 1337) in paragraph at lines 4192--4197
\T1/ptm/m/n/10 ment vari-ables []\T1/pcr/m/n/10 http_proxy []\T1/ptm/m/n/10 or
[]\T1/pcr/m/n/10 ftp_proxy[]\T1/ptm/m/n/10 . See [][]$\T1/pcr/m/n/10 https : /
/ curl . se / libcurl / c /
Underfull \hbox (badness 1184) in paragraph at lines 4207--4223
\T1/ptm/m/n/10 string con-tain-ing `[]\T1/pcr/m/n/10 "Schannel"[]\T1/ptm/m/n/10
'. If it does not, for ver-i-fi-ca-tion to be on the en-vi-ron-
[2036]
[2037]
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\T1/ptm/m/n/10 able at the repos-i-to-ries, or []\T1/pcr/m/n/10 NULL []\T1/ptm/
m/n/10 which makes an in-ter-nal call to
Underfull \hbox (badness 10000) in paragraph at lines 4357--4359
[]\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][][]\T1/pcr/m/n/10 do
wnload.file[][][] []\T1/ptm/m/n/10 and
[2038]
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[]\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c
har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of
[2041]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4627--4627
[] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[]
[2042]
Underfull \hbox (badness 1910) in paragraph at lines 4662--4669
\T1/ptm/m/n/10 is saved, then ini-tial-ized to a spec-i-fied state, the ex-am-p
le is run and
Underfull \hbox (badness 1655) in paragraph at lines 4662--4669
\T1/ptm/m/n/10 the (saved) state is re-stored. []\T1/pcr/m/n/10 setRNG = TRUE [
]\T1/ptm/m/n/10 sets the same state as
Underfull \hbox (badness 2846) in paragraph at lines 4662--4669
[]\T1/pcr/m/n/10 R CMD [][]check[][][] []\T1/ptm/m/n/10 does for run-ning a pac
k-age's ex-am-ples. This is cur-
Underfull \hbox (badness 3460) in paragraph at lines 4662--4669
\T1/ptm/m/n/10 rently equiv-a-lent to []\T1/pcr/m/n/10 setRNG = {RNGkind("defau
lt", "default",
Underfull \hbox (badness 1931) in paragraph at lines 4669--4676
[]\T1/ptm/m/n/10 logical (or []\T1/pcr/m/n/10 "default"[]\T1/ptm/m/n/10 ) in-di
-cat-ing if [][][]\T1/pcr/m/n/10 devAskNewPage[][][](ask = TRUE)
[2043]
[2044]
[2045]
[2046]
Underfull \hbox (badness 5939) in paragraph at lines 4922--4924
[]\T1/ptm/m/n/10 An en-try in []\T1/pcr/m/n/10 getOption("repos") []\T1/ptm/m/n
/10 named `[]\T1/pcr/m/n/10 CRAN[]\T1/ptm/m/n/10 ' which is not the de-fault
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[]\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[]
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pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format})
has been already used, duplicate ignored
<to be read again>
\relax
l.5136 ...mat Unordered and Ordered Lists}{format}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format.1}
) has been already used, duplicate ignored
<to be read again>
\relax
l.5136 ...mat Unordered and Ordered Lists}{format}
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[]\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing
to ex-ter-nal GUIs or to the
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[]\T1/ptm/m/n/10 External pointer ob-jects are com-pared as ref-er-ence ob-ject
s, cor-re-spond-ing to call-ing
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[]\T1/pcr/m/n/10 ## NB: The methods for \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 data.f
rame\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 and \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 array\
TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 are identical to the \TS1/pcr/m/n/10 '\T1/pcr/
m/n/10 matrix\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 one[]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 6205--6205
[]\T1/pcr/m/n/10 tail(x, n = 6L, keepnums = TRUE, addrownums, ...) # exported
as tail.matrix()[]
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Overfull \hbox (15.18042pt too wide) in paragraph at lines 6347--6347
[] \T1/pcr/m/n/9 ## BUT if I use "useAttrib(.)", this is *not* ok, when n i
s of length 2:[]
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[] \T1/pcr/m/n/9 ## --- because [i,j]-indexing of data frames *also* drops
"other" attributes ..[]
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 6558--6558
[] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[]
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[]\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 https : / / www . r-[]
project . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also
[2072]
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[]\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words
'. `Key-
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\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are
listed in file
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[]\T1/pcr/m/n/9 help.search("linear models") # In case you forgot how to fit
linear models[]
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[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-
Underfull \hbox (badness 10000) in paragraph at lines 6871--6880
\T1/ptm/m/n/10 dex, `\T1/ptm/m/sl/10 R_DOC_DIR\T1/pcr/m/n/10 /html/packages.htm
l\T1/ptm/m/n/10 ', which can be re-made by
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion
to search. See
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Underfull \hbox (badness 5175) in paragraph at lines 6949--6952
[]\T1/pcr/m/n/10 hsearch_db() []\T1/ptm/m/n/10 builds and caches the help searc
h database for sub-se-quent use by
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[]\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion `
Lock-ing' in the help for
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Underfull \hbox (badness 10000) in paragraph at lines 7276--7283
[]\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 means to use []\T1/pcr/m/n/10 c("Depends
", "Imports", "LinkingTo",
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\T1/pcr/m/n/10 "Suggests") []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pkgs []\T1/ptm
/m/n/10 and []\T1/pcr/m/n/10 c("Depends", "Imports",
Underfull \hbox (badness 1270) in paragraph at lines 7276--7283
\T1/pcr/m/n/10 "LinkingTo") []\T1/ptm/m/n/10 for added de-pen-den-cies: this in
-stalls all the pack-ages
Underfull \hbox (badness 1270) in paragraph at lines 7291--7301
\T1/ptm/m/n/10 for the `[]\T1/pcr/m/n/10 --configure-args[]\T1/ptm/m/n/10 ' fla
g in the call to []\T1/pcr/m/n/10 R CMD INSTALL[]\T1/ptm/m/n/10 . If
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[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
be passed to []\T1/pcr/m/n/10 R
Underfull \hbox (badness 4913) in paragraph at lines 7334--7338
\T1/pcr/m/n/10 CMD INSTALL []\T1/ptm/m/n/10 for a source pack-age in-stall. E.g
., []\T1/pcr/m/n/10 c("--html",
Underfull \hbox (badness 10000) in paragraph at lines 7334--7338
\T1/pcr/m/n/10 "--no-multiarch", "--no-test-load") []\T1/ptm/m/n/10 or, for ma-
cOS,
Underfull \hbox (badness 1424) in paragraph at lines 7343--7346
[]\T1/ptm/m/n/10 logical: if true, re-duce the amount of out-put. This is \T1/p
tm/m/it/10 not \T1/ptm/m/n/10 passed to
Underfull \hbox (badness 10000) in paragraph at lines 7356--7360
[]\T1/ptm/m/n/10 further ar-gu-ments to be passed to [][][]\T1/pcr/m/n/10 downl
oad.file[][][][]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is []\T1/pcr/m/n
/10 "both" []\T1/ptm/m/n/10 which means `use bi-nary if avail-
Underfull \hbox (badness 5175) in paragraph at lines 7424--7431
\T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there
are source pack-ages
Underfull \hbox (badness 1342) in paragraph at lines 7424--7431
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by
Underfull \hbox (badness 1087) in paragraph at lines 7432--7435
[]\T1/ptm/m/n/10 Using pack-ages with []\T1/pcr/m/n/10 type = "source" []\T1/pt
m/m/n/10 al-ways works pro-vided the pack-age con-tains no
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Underfull \hbox (badness 1314) in paragraph at lines 7511--7518
[]\T1/pcr/m/n/10 install.packages []\T1/ptm/m/n/10 needs to be able to com-pute
all the de-pen-den-cies of []\T1/pcr/m/n/10 pkgs []\T1/ptm/m/n/10 from
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Underfull \hbox (badness 10000) in paragraph at lines 7594--7599
[][][]\T1/pcr/m/n/10 update.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 download.pac
kages[][][][]\T1/ptm/m/n/10 ,
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[] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 7635--7635
[] \T1/pcr/m/n/10 str2logical(Sys.getenv("R_PACKAGES_CAC
HE_USER_DIR",[]
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Underfull \hbox (badness 10000) in paragraph at lines 7656--7659
[][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 in-di-cat-ing if caching sh
ould hap-pen in \T1/ptm/b/n/10 tools\T1/ptm/m/n/10 '
Underfull \hbox (badness 5133) in paragraph at lines 7660--7664
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each
pack-age's
Underfull \hbox (badness 1983) in paragraph at lines 7674--7677
[]\T1/pcr/m/n/10 installed.packages []\T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10
DESCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along
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[]\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
= "License")[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7726--7726
[]\T1/pcr/m/n/9 ## Keep packages that come with R (priority="high") and all ot
hers separate![]
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Underfull \hbox (badness 4132) in paragraph at lines 7852--7854
[]\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion
of []\T1/pcr/m/n/10 libtool []\T1/ptm/m/n/10 in-stalled at
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 8019--8019
[]\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h
ave defined?[]
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[]\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE)
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Underfull \hbox (badness 10000) in paragraph at lines 8202--8204
[]\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/
phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see
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[] \T1/pcr/m/n/10 methods(generic.function, class, all.names = FALSE, dropPa
th = FALSE)[]
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[] \T1/pcr/m/n/10 all.names = FALSE, dropPa
th = FALSE, useEnv = FALSE)[]
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[]\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if
Underfull \hbox (badness 10000) in paragraph at lines 8327--8329
[]\T1/ptm/m/n/10 typically the re-sult of []\T1/pcr/m/n/10 methods(..)[]\T1/ptm
/m/n/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of S3 class
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Underfull \hbox (badness 1859) in paragraph at lines 8559--8562
[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
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[]\T1/pcr/m/n/9 db4 <- news(Version == "4.0.0" & grepl("^BUG", Category) & gre
pl("PR#", Text),[]
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[]\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri
x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[]
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[]\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[]
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[]\T1/pcr/m/n/10 "B"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "KiB"[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 "MiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "GiB"[]\T1/ptm/m/n/1
0 , []\T1/pcr/m/n/10 "TiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "PiB"[]\T1/ptm/m/
n/10 ,
Underfull \hbox (badness 1331) in paragraph at lines 8796--8800
[]\T1/ptm/m/n/10 For all stan-dards, []\T1/pcr/m/n/10 units = "auto" []\T1/ptm/
m/n/10 is also al-lowed. If []\T1/pcr/m/n/10 standard =
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[]\T1/ptm/m/n/10 optionally a [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/
n/10 string with an en-cod-ing for an op-tional
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[] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica
tion", "Built"),[]
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[] \T1/pcr/m/n/10 tryFormats = c("%Y-%m-%d", "%Y/%m/%d", "%D", "%m/
%d/%y"),[]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 9064--9064
[] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f
ields=date.fields))[]
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Underfull \hbox (badness 10000) in paragraph at lines 9092--9094
[]\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 asDateBuilt()[]\T1/ptm/m/n/10 , a [][][]\
T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string as from
Underfull \hbox (badness 10000) in paragraph at lines 9106--9108
[]\T1/pcr/m/n/10 packageVersion() []\T1/ptm/m/n/10 is a con-ve-nience short-cut
, al-low-ing things like []\T1/pcr/m/n/10 if
Underfull \hbox (badness 1259) in paragraph at lines 9114--9119
[]\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the
given pack-age is found and can suc-cess-fully be read,
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[] \T1/pcr/m/n/9 identical(pu, packageDate("stats"))) # as "utils" an
d "stats" are[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9159--9159
[] \T1/pcr/m/n/9 # both \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 base R\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and "Built" at same time[]
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[]\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 "Status"[]\T1/ptm/m/n/10 , a fac-tor wit
h lev-els []\T1/pcr/m/n/10 c("ok", "upgrade",
Underfull \hbox (badness 10000) in paragraph at lines 9292--9295
[]\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 "Status"[]\T1/ptm/m/n/10 , a fac-tor wit
h lev-els []\T1/pcr/m/n/10 c("installed", "not
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[] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[]
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[] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<",
">"),[]
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[] \T1/pcr/m/n/9 "S original, <http://statwww.epfl.ch/davison/BMA/libr
ary.html>"),[]
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[]\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for
more dis-cus-sion of the
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the name of the help topic;
de-faults to
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[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[]
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[]\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[]
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 10958--10958
[]\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23
456 98 76 54[]
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[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
"no.loss"),[]
[2136]
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[] \T1/pcr/m/n/10 row.names, col.names, as.is = !stringsAsFactors, t
ryLogical = TRUE,[]
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[] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 11052--11052
[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[]
[2137]
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[]\T1/ptm/m/n/10 Using []\T1/pcr/m/n/10 row.names = NULL []\T1/ptm/m/n/10 force
s row num-ber-ing. Miss-ing or []\T1/pcr/m/n/10 NULL
Underfull \hbox (badness 2435) in paragraph at lines 11147--11151
[]\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 de-ter-m
in-ing if columns con-sist-ing en-tirely of []\T1/pcr/m/n/10 "F"[]\T1/ptm/m/n/1
0 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1824) in paragraph at lines 11147--11151
[]\T1/pcr/m/n/10 "FALSE"[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 "TRUE" []\T1/pt
m/m/n/10 should be con-verted to [][][]\T1/pcr/m/n/10 logical[][][][]\T1/ptm/m/
n/10 ; passed to
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Overfull \hbox (12.78088pt too wide) in paragraph at lines 11409--11409
[]\T1/pcr/m/n/10 readRegistry(key, hive = c("HLM", "HCR", "HCU", "HU", "HCC",
"HPD"),
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[] \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64-
bit"))[]
Underfull \hbox (badness 10000) in paragraph at lines 11417--11422
[]\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are
Underfull \hbox (badness 10000) in paragraph at lines 11417--11422
\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 HKEY_LOCAL_MACHINE[]\T1/ptm/m/n/10 , []\T1/
pcr/m/n/10 HKEY_CLASSES_ROOT[]\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 11417--11422
[]\T1/pcr/m/n/10 HKEY_CURRENT_USER[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 HKEY_USER
S[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 HKEY_CURRENT_CONFIG
[2141]
[2142]
[2143]
[2144]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 11649--11649
[] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0)))
[2145]
[2146]
[2147]
[2148]
Underfull \hbox (badness 2469) in paragraph at lines 11915--11919
[]\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2024). Ro-man nu-mer-als. Wikipedia
, The Free En-cy-clo-pe-dia.
Underfull \hbox (badness 10000) in paragraph at lines 11915--11919
[][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / w / index . php ? title
= Roman _ numerals & oldid =
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Overfull \hbox (25.98041pt too wide) in paragraph at lines 11933--11933
[]\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:7))) # + NA with a warni
ng for the last.[]
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[]\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in
{1,2,..,4999} :[]
[2150]
[2151]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 12092--12092
[]\T1/pcr/m/n/10 4. | \-base:::tryCatchOne(expr, names, parentenv, handler
s[[1L]])[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 12093--12093
[]\T1/pcr/m/n/10 5. | \-base:::doTryCatch(return(expr), name, parentenv,
handler)[]
[2152]
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[]\T1/ptm/m/n/10 The chap-ter on ``Tidy-ing and pro-fil-ing R code'' in `Writ-i
ng R Ex-ten-sions':
[2153]
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[]\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
= 0)
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[]\T1/ptm/m/n/10 If `[]\T1/pcr/m/n/10 --default-packages[]\T1/ptm/m/n/10 ' is n
ot used, then []\T1/pcr/m/n/10 Rscript []\T1/ptm/m/n/10 checks the en-vi-ron-me
nt vari-
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\T1/ptm/m/n/10 able []\T1/pcr/m/n/10 R_SCRIPT_DEFAULT_PACKAGES[]\T1/ptm/m/n/10
. If this is set, then it takes prece-dence over
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[]\T1/pcr/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr
aphics,stats -e \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 sessionInfo()\TS1/pcr/m/n/9 '[]
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[] \T1/pcr/m/n/10 restrict = c("functions", "descriptions", "news",
"Rfunctions",[]
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[] \T1/pcr/m/n/10 "Rmanuals", "READMEs", "views", "vig
nettes"),[]
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[] \T1/pcr/m/n/10 sortby = c("score", "date:late", "date:early", "s
ubject",[]
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[] \T1/pcr/m/n/10 "subject:descending", "size", "size:de
scending"),[]
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\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 score[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 date:
late []\T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first,
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\T1/ptm/m/n/10 der, []\T1/pcr/m/n/10 subject:descending []\T1/ptm/m/n/10 for re
-verse al-pha-bet-i-cal or-der, []\T1/pcr/m/n/10 size []\T1/ptm/m/n/10 or
[2158]
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[]\T1/pcr/m/n/9 fullquery <- RSiteSearch("lattice", restrict = c("vignettes","
Rfunctions"))[]
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[]\T1/ptm/m/n/10 Character string spec-i-fy-ing whether emacs style ([]\T1/pcr/
m/n/10 "etags"[]\T1/ptm/m/n/10 ) or vi style
[2159]
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p
tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software /
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[] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F
ALSE, ...)[]
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[]\T1/ptm/m/n/10 The de-fault for []\T1/pcr/m/n/10 stylepath []\T1/ptm/m/n/10 i
s now taken from the en-vi-ron-ment vari-able
[2163]
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[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
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[]\T1/ptm/m/n/10 The use of fancy quotes (see [][][]\T1/pcr/m/n/10 sQuote[][][]
[]\T1/ptm/m/n/10 ) can cause prob-lems when set-ting \T1/phv/m/n/10 R \T1/ptm/m
/n/10 out-put in
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[] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[]
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[]\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func-
tions can be ex-e-cuted. If
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[]\T1/ptm/m/n/10 The file `\T1/pcr/m/n/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ures
the R GUI ([]\T1/pcr/m/n/10 Rgui[]\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows
and
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[]\T1/ptm/m/n/10 At the time of writ-ing `\T1/pcr/m/n/10 Rdevga\T1/ptm/m/n/10 '
con-fig-ured the map-ping of font num-bers to fonts, and
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[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
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[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
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[]\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at
end of report[]
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[]\T1/ptm/m/n/10 Repository `[]\T1/pcr/m/n/10 CRAN[]\T1/ptm/m/n/10 ' is treated
spe-cially: the value is taken from the cur-rent set-ting of
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[]\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf
fix))
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[]\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t
o the Win-dows API call
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[]\T1/pcr/m/n/10 getSrcFilename []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 getSrcDir
ectory []\T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file-
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Overfull \hbox (42.78088pt too wide) in paragraph at lines 14080--14080
[] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
TRUE, ...))[]
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[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
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[][][]\T1/pcr/m/n/10 options[][][]("width")[]\T1/ptm/m/n/10 ; note that this ha
s only a weak ef-fect, un-less
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[]\T1/ptm/m/n/10 (see [][][]\T1/pcr/m/n/10 options[][][][]\T1/ptm/m/n/10 ) whic
h de-faults to []\T1/pcr/m/n/10 "no" []\T1/ptm/m/n/10 for back com-pat-i-bil-it
y rea-sons;
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[]\T1/ptm/m/n/10 numeric or []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 as by de-fau
lt, de-ter-min-ing the []\T1/pcr/m/n/10 nlines []\T1/ptm/m/n/10 ar-gu-ment to
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[]\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
of binary numbers[]
[2182]
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[]\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo
ng" non-ASCII:[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 14220--14220
[]\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of 2 in order to se
e 1 (in UTF-8!):[]
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[]\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N)))
# "1 is 1" here[]
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[]\T1/ptm/m/n/10 Options other than []\T1/pcr/m/n/10 memory = "none" []\T1/ptm/
m/n/10 ap-ply only to files pro-duced by
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[]\T1/ptm/m/n/10 The chap-ter on `Tidy-ing and pro-fil-ing R code' in `Writ-ing
R Ex-ten-sions':
[2186]
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[]\T1/ptm/m/n/10 further ar-gu-ments passed to the driver's setup func-tion. Se
e
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[][][]\T1/pcr/m/n/10 RweaveLatexSetup[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/
m/n/10 RtangleSetup[][][][]\T1/ptm/m/n/10 , re-spec-tively, for the ar-gu-
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 syntax = NULL []\T1/ptm/m/n/10 (the de-fau
lt) then the avail-able syn-tax ob-jects are con-sulted in
Underfull \hbox (badness 6252) in paragraph at lines 14544--14551
\T1/ptm/m/n/10 turn, and se-lected if their []\T1/pcr/m/n/10 extension []\T1/pt
m/m/n/10 com-po-nent matches (as a reg-exp) the file
Underfull \hbox (badness 4556) in paragraph at lines 14544--14551
\T1/ptm/m/n/10 name. Ob-jects []\T1/pcr/m/n/10 SweaveSyntaxNoweb []\T1/ptm/m/n/
10 (with []\T1/pcr/m/n/10 extension = "[.][rsRS]nw$"[]\T1/ptm/m/n/10 ) and
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\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `[]\T1/pcr/m/n/10 -h[]\T1/ptm/m/
n/10 ' (fol-low sym-bolic links, also `[]\T1/pcr/m/n/10 -L[]\T1/ptm/m/n/10 ' on
some plat-forms),
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\T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 --acls[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 --
exclude-backups[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 --exclude-vcs[]\T1/ptm/m/n
/10 ' (and sim-i-lar) and on Win-dows
[2190]
Underfull \hbox (badness 1622) in paragraph at lines 14716--14723
[]\T1/ptm/m/n/10 A con-ve-nient and ro-bust way to set op-tions for GNU []\T1/p
cr/m/n/10 tar []\T1/ptm/m/n/10 is via en-vi-ron-ment vari-able
[2191]
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[]\T1/ptm/m/n/10 When ar-gu-ment []\T1/pcr/m/n/10 tar []\T1/ptm/m/n/10 is set t
o the com-mand []\T1/pcr/m/n/10 tar []\T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment
vari-able
[2192]
Underfull \hbox (badness 10000) in paragraph at lines 14879--14882
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f
ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / pubs .
Underfull \hbox (badness 10000) in paragraph at lines 14879--14882
\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _ 92 _
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Overfull \hbox (6.78088pt too wide) in paragraph at lines 15503--15503
[] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
...),[]
[2201]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 15509--15509
[] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
...),[]
Underfull \hbox (badness 4660) in paragraph at lines 15546--15550
\T1/ptm/m/n/10 able at the repos-i-to-ries, or []\T1/pcr/m/n/10 NULL []\T1/ptm/
m/n/10 which makes an in-ter-nal call to
Underfull \hbox (badness 1694) in paragraph at lines 15560--15564
[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][][]\T1/pcr/m/n/10 ins
talled.packages[][][](lib.loc =
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[]\T1/ptm/m/n/10 Arguments such as []\T1/pcr/m/n/10 destdir []\T1/ptm/m/n/10 an
d []\T1/pcr/m/n/10 dependencies []\T1/ptm/m/n/10 to be
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\T1/ptm/m/n/10 passed to [][][]\T1/pcr/m/n/10 install.packages[][][] []\T1/ptm/
m/n/10 and []\T1/pcr/m/n/10 ignore_repo_cache[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 15566--15571
[]\T1/pcr/m/n/10 max_repo_cache_age []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 noCac
he []\T1/ptm/m/n/10 to [][][]\T1/pcr/m/n/10 available.packages[][][]
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[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
in-stall. See
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Underfull \hbox (badness 10000) in paragraph at lines 15602--15607
[]\T1/pcr/m/n/10 available = NULL []\T1/ptm/m/n/10 make a call to []\T1/pcr/m/n
/10 available.packages(contriburl =
Underfull \hbox (badness 1226) in paragraph at lines 15602--15607
\T1/pcr/m/n/10 contriburl, method = method) []\T1/ptm/m/n/10 and hence by de-fa
ult fil-ters on \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion, OS type
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[]\T1/ptm/m/n/10 Take care when us-ing []\T1/pcr/m/n/10 dependencies []\T1/ptm/
m/n/10 (passed to [][][]\T1/pcr/m/n/10 install.packages[][][][]\T1/ptm/m/n/10 )
with
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[][][]\T1/pcr/m/n/10 install.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n
/10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 download.pa
ckages[][][][]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 ## Not run: url.show("https://www.stats.ox.ac.uk/pub/datasets/
csb/ch3a.txt")
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[][][]\T1/pcr/m/n/10 browseVignettes[][][] []\T1/ptm/m/n/10 for an HTML-based v
i-gnette browser; [][][]\T1/pcr/m/n/10 RShowDoc[][][]("\T1/ptm/m/sl/10 basename
\T1/pcr/m/n/10 ",
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[]\T1/pcr/m/n/9 ## Note that \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 package = *\TS1/pcr
/m/n/9 ' \T1/pcr/m/n/9 is much faster in the case of many installed packages:[]
[2208]
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[] \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d
ata = DAT)))[]
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[] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal),
data = DD)))[]
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[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i
s se-lected, or
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[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 winMenuDel []\T1/ptm/m/n/10 func-tion wil
l delete a menu and all of its items and sub-menus.
[2212]
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[]\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
" ",
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[]\T1/ptm/m/n/10 arguments to []\T1/pcr/m/n/10 write.table[]\T1/ptm/m/n/10 : []
\T1/pcr/m/n/10 append[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 col.names[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 sep[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 dec []\T1/ptm/m/n
/10 and
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[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion e.g. []\T1/pcr/m/n/10 file =
[2215]
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[2217])
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[2220] (./KernSmooth-pkg.tex
Chapter 15.
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[]\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE)
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Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518
[]\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
= 0.05,
[2227]
[2228]
[2229]
[2230]) (./MASS-pkg.tex
Chapter 16.
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[]\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b
eav2$hours/24))[]
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pdfTeX warning (ext4): destination with the same identifier (name{Rfn.confint.g
lm}) has been already used, duplicate ignored
<to be read again>
\relax
l.1477 ...{confint.glm}{confint-MASS}{confint.glm}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.confint.n
ls}) has been already used, duplicate ignored
<to be read again>
\relax
l.1478 ...{confint.nls}{confint-MASS}{confint.nls}
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[]\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq",
"F"),[]
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[]\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq",
"F"),[]
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[]\T1/ptm/m/n/10 further ar-gu-ments for []\T1/pcr/m/n/10 plot []\T1/ptm/m/n/10
and graph-i-cal pa-ram-e-ters. Note that
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[]\T1/pcr/m/n/10 "gamma"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "geometric"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "log-normal"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lo
gnormal"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 "logistic"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "negative binomi
al"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "normal"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n
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[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
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[] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[]
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[]\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
"exponential")[]
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[]\T1/ptm/m/n/10 The va-ri-ety of bar-ley ([]\T1/pcr/m/n/10 "manchuria"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "svansota"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "velv
et"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "trebi" []\T1/ptm/m/n/10 and
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[] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
...)[]
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[]\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model
= FALSE,
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[]\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE)
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[]\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/
10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log")
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l.6085 ...sical N, P, K Factorial Experiment}{npk}
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[] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[]
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[] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[]
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[] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[]
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[]\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea
s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c
mr/m/n/10 ) =
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[]\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[]
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[]\T1/ptm/m/n/10 the di-men-sion of the space to be used. If this is less than
[]\T1/pcr/m/n/10 min(p,
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[]\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[]
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[] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[]
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l.7513 ... for Profiling glm Objects}{profile.glm}
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[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
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[] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
NULL)[]
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[]\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if []\T1/pcr/m
/n/10 NA[]\T1/ptm/m/n/10 s are found. The
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[]\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[]
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[]\T1/ptm/m/n/10 ``Fold your arms! Which is on top'' (Fac-tor, with lev-els []\
T1/pcr/m/n/10 "R on L"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "L on R"[]\T1/ptm/m/n
/10 ,
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[]\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els []\T1/pcr/m/n/
10 "Heavy"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Regul" []\T1/ptm/m/n/10 (reg-u-l
arly),
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[]\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub
le.eps^0.25)
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[]\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[]
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[]\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[]
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[]\T1/ptm/m/n/10 The orig-i-nal data are avail-able at [][]$\T1/pcr/m/n/10 http
s : / / lib . stat . cmu . edu / datasets / 1993 .
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[2376]) (./Matrix-pkg.tex
Chapter 17.
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[]\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec
t to change, and if you
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\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
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[]\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o
wn code. Please con-tact us
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[]\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm
/m/n/10 ob-jects; here, when the first is
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\T1/ptm/m/n/10 an []\T1/pcr/m/n/10 "[][]abIndex[][][]" []\T1/ptm/m/n/10 vec-tor
, these ar-gu-ments will be con-cate-nated to a new
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l.182 ...{all.equal}{all.equal-methods}{all.equal}
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[]\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing
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[]\T1/ptm/m/n/10 There are more meth-ods, no-tably also for []\T1/pcr/m/n/10 "[
][]sparseVector[][][]"[]\T1/ptm/m/n/10 's, see
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[]\T1/ptm/m/n/10 optional ar-gu-ments passed to the de-fault method for generic
func-tion
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[] \T1/pcr/m/n/9 band(sm5, -1, 1)# "dsyMatrix": symmetric band preserves sym
metry property[]
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[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class
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[][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/
m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc
r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse
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[]\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[]
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[]\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[]
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[]\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20, 1), rpois(20, 3))[
c(1:3, 2:3, 3:2)],[]
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[]\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Fast version of Matrix :: .bd
iag() -- for the case of *many* (k x k) matrices:[]
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[]\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(<mat1>, <mat
2>, ....., <mat_N>) where each mat_j is a k x k \TS1/pcr/m/n/9 '\T1/pcr/m/n/9
matrix\TS1/pcr/m/n/9 '[]
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[]\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @return a sparse (N*k x N*k)
matrix of class \code{"\linkS4class{dgCMatrix}"}.[]
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[] \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 i :\TS1/pcr/m/n/9 ' \
T1/pcr/m/n/9 maybe there\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s a faster way (w/o matri
x indexing), but elegant?[]
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[] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len(
N), each=k)]),[]
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[]\T1/pcr/m/n/9 L. <- L; L.[1:2,1] <- TRUE; L.@x[1:2] <- FALSE; L. # has "zero
s" to drop0()[]
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[]\T1/pcr/m/n/10 new("pBunchKaufman", ...)[]\T1/ptm/m/n/10 , but they are more
typ-i-cally ob-tained as the value of
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[]\T1/pcr/m/n/10 signature(from = "pBunchKaufman", to = "dtpMatrix")[]\T1/ptm/m
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[]\T1/pcr/m/n/10 signature(from = "p?BunchKaufman", logarithm =
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[]\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m
atrix"), ...)[]
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[]\T1/ptm/m/n/10 An ob-ject rep-re-sent-ing the fac-tor-iza-tion, in-her-it-ing
from vir-tual class
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[]\T1/pcr/m/n/9 stopifnot(all.equal(as(A, "matrix"), as(Reduce(\TS1/cmtt/m/n/9
`\T1/pcr/m/n/9 %*%\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 , e.bk.A), "matrix")))[]
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l.1185 ... on cbind2/rbind2}{cbind2.Rdash.methods}
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[]\T1/ptm/m/n/10 Our class def-i-ni-tion help pages men-tion-ing []\T1/pcr/m/n/
10 cbind2() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 rbind2() []\T1/ptm/m/n/10 met
h-ods:
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[]\T1/ptm/m/n/10 The im-ple-men-ta-tion of class []\T1/pcr/m/n/10 CHMfactor []\
T1/ptm/m/n/10 is based on CHOLMOD's C-level
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[]\T1/pcr/m/n/10 signature(from = "CHMfactor", logarithm = "logical")[]\T1/ptm/
m/n/10 : be-
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[]\T1/pcr/m/n/10 signature(update = ., C = ., object = "CHMfactor")[]\T1/ptm/m/
n/10 : see
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[]\T1/ptm/m/n/10 The CHOLMOD source code; see [][]$\T1/pcr/m/n/10 https : / / g
ithub . com / DrTimothyAldenDavis /
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\T1/pcr/m/n/10 SuiteSparse$[][]\T1/ptm/m/n/10 , no-tably the header file `\T1/p
cr/m/n/10 CHOLMOD/Include/cholmod.h\T1/ptm/m/n/10 ' defin-ing
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[]\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m
atrix"), ...)[]
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[] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(list(
NULL), dn[2L]),[]
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[] \T1/pcr/m/n/9 ae2(A[ch.A@perm + 1L, ch.A@perm + 1L], with(e.ch.A, L1 %*%
D %*% L1.))[]
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[] \T1/pcr/m/n/9 ae2(A[ch.A@perm + 1L, ch.A@perm + 1L], with(E.ch.A, L %*%
L. ))[]
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[]\T1/pcr/m/n/9 u2 <- update(ch.A, t(M), mult = sqrt(2)) # updating with cross
prod(M), not M[]
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\T1/pcr/m/n/10 double / dpstrf . f$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 htt
ps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and
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[]\T1/ptm/m/n/10 The CHOLMOD source code; see [][]$\T1/pcr/m/n/10 https : / / g
ithub . com / DrTimothyAldenDavis /
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of length []\T1/pcr/m/n/10 n*n []\T1/ptm/m/
n/10 ([]\T1/pcr/m/n/10 Cholesky[]\T1/ptm/m/n/10 ) or []\T1/pcr/m/n/10 n*(n+1)/2
[]\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 pCholesky[]\T1/ptm/m/n/10 ), where
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[]\T1/ptm/m/n/10 Class [][][]\T1/pcr/m/n/10 CholeskyFactorization[][][][]\T1/pt
m/m/n/10 , di-rectly. Class [][][]\T1/pcr/m/n/10 MatrixFactorization[][][][]\T1
/ptm/m/n/10 , by class
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[]\T1/ptm/m/n/10 Objects can be gen-er-ated di-rectly by calls of the form []\T
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0 : re-turns a
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[]\T1/pcr/m/n/10 signature(from = "p?Cholesky", logarithm = "logical")[]\T1/ptm
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ps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and
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[]\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m
atrix"), ...)[]
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[] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(list(
NULL), dn[2L]),[]
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[]\T1/ptm/m/n/10 a [][]fi-nite[][][] num-ber. The ma-trix that is fac-tor-ized
is []\T1/pcr/m/n/10 A + Imult *
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\T1/pcr/m/n/10 - diag(abs(A))) []\T1/ptm/m/n/10 en-sures that []\T1/pcr/m/n/10
A + Imult * diag(nrow(A)) []\T1/ptm/m/n/10 is di-
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[]\T1/ptm/m/n/10 An ob-ject rep-re-sent-ing the fac-tor-iza-tion, in-her-it-ing
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ps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and
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[]\T1/ptm/m/n/10 The CHOLMOD source code; see [][]$\T1/pcr/m/n/10 https : / / g
ithub . com / DrTimothyAldenDavis /
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\T1/pcr/m/n/10 SuiteSparse$[][]\T1/ptm/m/n/10 , no-tably the header file `\T1/p
cr/m/n/10 CHOLMOD/Include/cholmod.h\T1/ptm/m/n/10 ' defin-ing
[2406]
[2407]
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[] \T1/pcr/m/n/9 list(simpl1 = Cholesky(A4, perm = TRUE, super = FALSE, L
DL = TRUE),[]
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[] \T1/pcr/m/n/9 simpl0 = Cholesky(A4, perm = TRUE, super = FALSE, L
DL = FALSE),[]
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[] \T1/pcr/m/n/9 super0 = Cholesky(A4, perm = TRUE, super = TRUE
)),[]
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[] \T1/pcr/m/n/9 list(simpl1 = Cholesky(A4, perm = FALSE, super = FALSE, L
DL = TRUE),[]
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[] \T1/pcr/m/n/9 simpl0 = Cholesky(A4, perm = FALSE, super = FALSE, L
DL = FALSE),[]
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[] \T1/pcr/m/n/9 super0 = Cholesky(A4, perm = FALSE, super = TRUE
)))[]
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[]\T1/pcr/m/n/9 rapply2 <- function(object, f, ...) rapply(object, f, , , how
= "list", ...)[]
Underfull \vbox (badness 10000) has occurred while \output is active
[2408]
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[] \T1/pcr/m/n/9 x = c(1, 6, 38, 10, 60, 103, -4, 6, -32, -247, -2, -
16, -128, -2, -67))[]
Underfull \vbox (badness 10000) has occurred while \output is active
[2409]
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[] \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4), j=c(2:4,1), x = 2,
dimnames=dns))[]
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[] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
dimnames=dns))[]
[2410]
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[] \T1/pcr/m/n/9 a. <- sparseMatrix(i=4:1, j=1:4, dimnames=list(n4, n4), repr
="T") # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[]
[2411]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colMeans}
) has been already used, duplicate ignored
<to be read again>
\relax
l.2696 ...asA{colMeans}{colSums-methods}{colMeans}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colSums})
has been already used, duplicate ignored
<to be read again>
\relax
l.2704 \aliasA{colSums}{colSums-methods}{colSums}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowMeans}
) has been already used, duplicate ignored
<to be read again>
\relax
l.2711 ...asA{rowMeans}{colSums-methods}{rowMeans}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowSums})
has been already used, duplicate ignored
<to be read again>
\relax
l.2719 \aliasA{rowSums}{colSums-methods}{rowSums}
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i
n-her-it-ing from
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\T1/ptm/m/n/10 class [][][]\T1/pcr/m/n/10 sparseVector[][][][]\T1/ptm/m/n/10 .
Only ap-pli-ca-ble when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 is in-her-it-ing fr
om a
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[][][]\T1/pcr/m/n/10 dimnames[][][](x) []\T1/ptm/m/n/10 are only kept (as [][][
]\T1/pcr/m/n/10 names[][][](v)[]\T1/ptm/m/n/10 ) when the re-sult-ing []\T1/pcr
/m/n/10 v []\T1/ptm/m/n/10 is [][][]\T1/pcr/m/n/10 numeric[][][][]\T1/ptm/m/n/1
0 , since
[2412]
[2413]
Underfull \hbox (badness 3547) in paragraph at lines 2888--2891
[]\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10
, the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when
[2414]
[2415]
[2416]
[2417]
[2418]
Underfull \hbox (badness 10000) in paragraph at lines 3290--3293
[]\T1/pcr/m/n/10 signature(from = "denseLU", logarithm = "logical")[]\T1/ptm/m/
n/10 : com-
[2419]
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[]\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m
atrix"), ...)[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 3352--3352
[] \T1/pcr/m/n/9 new( "pMatrix", Dim = c(n, n), Dimnames = c(dn[
1L], list(NULL)),[]
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[] \T1/pcr/m/n/9 new("dtrMatrix", Dim = c(n, n), Dimnames = list(
NULL, NULL),[]
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[] \T1/pcr/m/n/9 new("dtrMatrix", Dim = c(n, n), Dimnames = c(lis
t(NULL), dn[2L]),[]
[2420]
Underfull \hbox (badness 7379) in paragraph at lines 3486--3488
[]\T1/pcr/m/n/10 signature(x = "dgCMatrix")[]\T1/ptm/m/n/10 : com-putes the LU
de-com-po-si-tion of a square
[2421]
[2422]
[2423]
Underfull \hbox (badness 4846) in paragraph at lines 3707--3711
[]\T1/ptm/m/n/10 Note that both []\T1/pcr/m/n/10 new(.) []\T1/ptm/m/n/10 and []
[][]\T1/pcr/m/n/10 spMatrix[][][] []\T1/ptm/m/n/10 con-struc-tors for []\T1/pcr
/m/n/10 "dgTMatrix" []\T1/ptm/m/n/10 (and other
Underfull \hbox (badness 2717) in paragraph at lines 3712--3716
[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can be stored in
more than one pos-si-ble
[2424]
Underfull \hbox (badness 5231) in paragraph at lines 3757--3762
[]\T1/ptm/m/n/10 Construct a for-mally di-ag-o-nal [][][]\T1/pcr/m/n/10 Matrix[
][][][]\T1/ptm/m/n/10 , i.e., an ob-ject in-her-it-ing from vir-tual class
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[]\T1/pcr/m/n/10 .sparseDiagonal(n, x = NULL, uplo = "U", shape = "t", unitri
= TRUE, kind, cols)[]
[2425]
Underfull \hbox (badness 10000) in paragraph at lines 3824--3827
[]\T1/pcr/m/n/10 .trDiagonal() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 .symDiagon
al() []\T1/ptm/m/n/10 are sim-ple wrap-pers, for
Underfull \hbox (badness 6792) in paragraph at lines 3824--3827
[]\T1/pcr/m/n/10 .sparseDiagonal(shape = "t") []\T1/ptm/m/n/10 and []\T1/pcr/m/
n/10 .sparseDiagonal(shape = "s")[]\T1/ptm/m/n/10 , re-spec-
[2426]
Underfull \hbox (badness 3646) in paragraph at lines 3901--3904
[]\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 dimnames[][][][]\T1/ptm/m/n/10 , a []
[][]\T1/pcr/m/n/10 list[][][][]\T1/ptm/m/n/10 , see the [][][]\T1/pcr/m/n/10 Ma
trix[][][] []\T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally
Underfull \hbox (badness 6542) in paragraph at lines 3936--3940
[]\T1/pcr/m/n/10 signature(x = "diagonalMatrix")[]\T1/ptm/m/n/10 : all these gr
oup meth-ods re-turn a
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[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")[]\T1/ptm/m/n/10
: the re-sult is from class
[2427]
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[]\T1/pcr/m/n/10 (object = "diagonalMatrix")[]\T1/ptm/m/n/10 : Re-turns an ob-j
ect of S3 class
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[][][]\T1/pcr/m/n/10 Diagonal[][][]() []\T1/ptm/m/n/10 as con-struc-tor of thes
e ma-tri-ces, and [][][]\T1/pcr/m/n/10 isDiagonal[][][][]\T1/ptm/m/n/10 . [][][
]\T1/pcr/m/n/10 ddiMatrix[][][] []\T1/ptm/m/n/10 and
[2428]
[2429]
[2430]
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[]\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")[]\T1/ptm/m/n/10 :
this group con-tains
[2431]
[2432]
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[]\T1/pcr/m/n/9 stopifnot(all.equal(S9p0, S9p))# same as as default, but diffe
rent from the random one[]
[2433]
Underfull \hbox (badness 2469) in paragraph at lines 4474--4477
[]\T1/pcr/m/n/10 signature(x = "dpoMatrix")[]\T1/ptm/m/n/10 : Re-turns the [][]
[]\T1/pcr/m/n/10 determinant[][][] []\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 x[]\T1/
ptm/m/n/10 , via
[2434]
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[]\T1/ptm/m/n/10 Currently the va-lid-ity meth-ods for these classes such as
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[][][]\T1/pcr/m/n/10 getValidity[][][](getClass("dpoMatrix")) []\T1/ptm/m/n/10
for ef-fi-ciency rea-sons only check the di-
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\T1/pcr/m/n/10 error=identity), "error") []\T1/ptm/m/n/10 . In-deed, when \T1/p
tm/m/it/10 co-erc-ing \T1/ptm/m/n/10 to these classes, a ver-sion
Underfull \hbox (badness 1590) in paragraph at lines 4503--4512
\T1/ptm/m/n/10 of [][][]\T1/pcr/m/n/10 Cholesky[][][]() []\T1/ptm/m/n/10 or [][
][]\T1/pcr/m/n/10 chol[][][]() []\T1/ptm/m/n/10 is typ-i-cally used, e.g., see
[]\T1/pcr/m/n/10 selectMethod("coerce",
Underfull \hbox (badness 6675) in paragraph at lines 4559--4566
[]\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 Matrix[][][][]\T1/ptm/m/n/10 , typ-i-ca
lly in-her-it-ing from vir-tual class [][][]\T1/pcr/m/n/10 sparseMatrix[][][][]
\T1/ptm/m/n/10 .
Underfull \hbox (badness 6493) in paragraph at lines 4559--4566
[][][]\T1/pcr/m/n/10 denseMatrix[][][] []\T1/ptm/m/n/10 and tra-di-tional vec-t
ors and ma-tri-ces are co-erced to
[2435]
Underfull \hbox (badness 10000) in paragraph at lines 4574--4582
[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing if the re-sult must in-herit from vi
r-tual class
Underfull \hbox (badness 1365) in paragraph at lines 4574--4582
[][][]\T1/pcr/m/n/10 CsparseMatrix[][][][]\T1/ptm/m/n/10 . If []\T1/pcr/m/n/10
FALSE []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 in-her-its from
[][][]\T1/pcr/m/n/10 RsparseMatrix[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4597--4600
[]\T1/ptm/m/n/10 Function [][][]\T1/pcr/m/n/10 sparseMatrix[][][][]\T1/ptm/m/n/
10 , for con-struct-ing ob-jects in-her-it-ing from vir-tual class
[2436]
Underfull \hbox (badness 10000) in paragraph at lines 4641--4645
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10
new("dsCMatrix", ...) []\T1/ptm/m/n/10 or
Underfull \hbox (badness 2103) in paragraph at lines 4641--4645
[]\T1/pcr/m/n/10 new("dsTMatrix", ...)[]\T1/ptm/m/n/10 , or au-to-mat-i-cally v
ia e.g., []\T1/pcr/m/n/10 as(*, "symmetricMatrix")[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1571) in paragraph at lines 4691--4694
[]\T1/pcr/m/n/10 signature(x = "dsCMatrix", pivot = "logical")[]\T1/ptm/m/n/10
: Re-turns (and stores) the
[2437]
[2438]
Underfull \hbox (badness 1221) in paragraph at lines 4834--4837
[]\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "dMatrix"[]\T1/ptm/m/n/10 , by class []
\T1/pcr/m/n/10 "dsparseMatrix"[]\T1/ptm/m/n/10 ; class []\T1/pcr/m/n/10 "sparse
Matrix"[]\T1/ptm/m/n/10 , by classes
Underfull \hbox (badness 1400) in paragraph at lines 4844--4847
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")[]\T1/ptm/m/n/10
: if []\T1/pcr/m/n/10 uplo ==
[2439]
Underfull \hbox (badness 10000) in paragraph at lines 4896--4898
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10
new("dsyMatrix", ...) []\T1/ptm/m/n/10 or
Underfull \hbox (badness 1365) in paragraph at lines 4932--4935
[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")[]\T1/ptm/m/n/10
, or []\T1/pcr/m/n/10 x = "dsyMatrix"
[2440]
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[]\T1/pcr/m/n/9 stopifnot(all(S1 == S2)) # equal "seen as matrix", but differ
internally :[]
[2441]
[2442]
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[]\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim
= c(5L, 5L),[]
Underfull \hbox (badness 3635) in paragraph at lines 5139--5143
[]\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ddenseMatrix"[]\T1/ptm/m/n/10 , di-rec
tly. Class []\T1/pcr/m/n/10 "triangularMatrix"[]\T1/ptm/m/n/10 , di-rectly. Cla
ss
Underfull \hbox (badness 10000) in paragraph at lines 5148--5151
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")[]\T1/ptm/m/n/10 :
Ma-trix mul-ti-pli-ca-tion;
Underfull \hbox (badness 10000) in paragraph at lines 5151--5155
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")[]\T1/ptm/m/n
/10 : the
[2443]
[2444]
[2445]
[2446]
Underfull \hbox (badness 10000) in paragraph at lines 5399--5401
[]\T1/ptm/m/n/10 a ma-trix fac-tor-iza-tion, typ-i-cally in-her-it-ing from vir
-tual class
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[] \T1/pcr/m/n/10 all.equal(as(x, "matrix"), as(Reduce(\TS1/cmtt/m/n/10 `\T
1/pcr/m/n/10 %*%\TS1/cmtt/m/n/10 `\T1/pcr/m/n/10 , expand2(y)), "matrix"))
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[] []
[2447]
Underfull \hbox (badness 7064) in paragraph at lines 5477--5494
[]\T1/pcr/m/n/10 signature(x = "p?BunchKaufman")[]\T1/ptm/m/n/10 : ex-pands the
fac-tor-iza-tion $\OML/cmm/m/it/10 A \OT1/cmr/m/n/10 =
Underfull \hbox (badness 3000) in paragraph at lines 5506--5513
[]\T1/pcr/m/n/10 signature(x = "denseLU")[]\T1/ptm/m/n/10 : ex-pands the fac-to
r-iza-tion $\OML/cmm/m/it/10 A \OT1/cmr/m/n/10 = \OML/cmm/m/it/10 P[]LU$ \T1/pt
m/m/n/10 as
Underfull \hbox (badness 2735) in paragraph at lines 5522--5529
[]\T1/pcr/m/n/10 signature(x = "CHMfactor")[]\T1/ptm/m/n/10 : as []\T1/pcr/m/n/
10 expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/pcr/m/n/10 list(P, L)[]\T1/p
tm/m/n/10 .
Underfull \hbox (badness 1337) in paragraph at lines 5529--5544
[]\T1/pcr/m/n/10 signature(x = "sparseLU")[]\T1/ptm/m/n/10 : as []\T1/pcr/m/n/1
0 expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/pcr/m/n/10 list(P, L, U,
Underfull \hbox (badness 2680) in paragraph at lines 5529--5544
\T1/pcr/m/n/10 Q)[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 expand(x)[["Q"]] []\T1/ptm
/m/n/10 and []\T1/pcr/m/n/10 expand2(x)[["P2."]] []\T1/ptm/m/n/10 rep-re-sent t
he same per-
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\T1/ptm/m/n/10 mu-ta-tion ma-trix $\OML/cmm/m/it/10 P[]$ \T1/ptm/m/n/10 but hav
e op-po-site []\T1/pcr/m/n/10 margin []\T1/ptm/m/n/10 slots and in-verted []\T1
/pcr/m/n/10 perm []\T1/ptm/m/n/10 slots.
Underfull \hbox (badness 2073) in paragraph at lines 5544--5549
[]\T1/pcr/m/n/10 signature(x = "denseLU")[]\T1/ptm/m/n/10 : as []\T1/pcr/m/n/10
expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/pcr/m/n/10 list(L, U, P)[]\T1/
ptm/m/n/10 .
[2448]
[2449]
[2450]
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[]\T1/pcr/m/n/9 str(pores <- readMM(system.file("external/pores_1.mtx", packag
e = "Matrix")))[]
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[]\T1/pcr/m/n/9 str(utm <- readHB(system.file("external/utm300.rua" , packag
e = "Matrix")))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5754--5754
[]\T1/pcr/m/n/9 str(lundA <- readMM(system.file("external/lund_a.mtx" , packag
e = "Matrix")))[]
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[]\T1/pcr/m/n/9 str(lundA <- readHB(system.file("external/lund_a.rsa" , packag
e = "Matrix")))[]
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[]\T1/pcr/m/n/9 ## https://math.nist.gov/MatrixMarket/data/Harwell-Boeing/coun
terx/counterx.htm[]
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[]\T1/pcr/m/n/9 str(jgl <- readMM(system.file("external/jgl009.mtx" , packag
e = "Matrix")))[]
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[]\T1/pcr/m/n/9 u. <- url("https://www.cise.ufl.edu/research/sparse/RB/Boeing/
msc00726.tar.gz")[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5768--5768
[]\T1/pcr/m/n/9 ## Store as MatrixMarket (".mtx") file, here inside temporary
dir./folder:[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5771--5771
[]\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of
the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[]
[2451]
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[]\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume
nts to sparseMatrix():[]
[2452]
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[] \T1/pcr/m/n/9 all.equal(facmul(x, nm, y, trans = TRUE, left = TRUE),
crossprod(L, y))[]
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[] \T1/pcr/m/n/9 all.equal(facmul(x, nm, y, trans = TRUE, left = FALSE), t
crossprod(y, L))[]
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[]\T1/pcr/m/n/10 .diag2dense(from, kind = ".", shape = "t", packed = FALSE, up
lo = "U")[]
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[]\T1/pcr/m/n/10 .m2dense(from, class = ".ge", uplo = "U", diag = "N", trans =
FALSE)[]
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[]\T1/pcr/m/n/10 .diag2sparse(from, kind = ".", shape = "t", repr = "C", uplo
= "U")[]
[2453]
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[]\T1/pcr/m/n/10 .m2sparse(from, class = ".gC", uplo = "U", diag = "N", trans
= FALSE)[]
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[]\T1/ptm/m/n/10 a string in []\T1/pcr/m/n/10 c("trace", "sumLog", "prod", "min
", "max",
[2454]
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[][]\T1/pcr/m/n/10 .solve.dgC.*(a, b)[]\T1/ptm/b/n/10 : []\T1/pcr/m/n/10 .solv
e.dgC.lu(a, b) []\T1/ptm/m/n/10 needs a square ma-trix []\T1/pcr/m/n/10 a[]\T1/
ptm/m/n/10 .
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[]\T1/pcr/m/n/10 .solve.dgC.qr(a, b) []\T1/ptm/m/n/10 needs a ``long'' ma-trix
[]\T1/pcr/m/n/10 a[]\T1/ptm/m/n/10 , with []\T1/pcr/m/n/10 nrow(a) >= ncol(a)[]
\T1/ptm/m/n/10 .
[2455]
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[][]\T1/pcr/m/n/10 .updateCHMfactor(object, parent, mult)[]\T1/ptm/b/n/10 : []
\T1/pcr/m/n/10 .updateCHMfactor []\T1/ptm/m/n/10 up-
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\T1/ptm/m/n/10 dates []\T1/pcr/m/n/10 object []\T1/ptm/m/n/10 with the re-sult
of Cholesky fac-tor-iz-ing []\T1/pcr/m/n/10 F(parent) + mult[1] *
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\T1/pcr/m/n/10 diag(nrow(parent))[]\T1/ptm/m/n/10 , i.e., []\T1/pcr/m/n/10 F(pa
rent) []\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 mult[1] []\T1/ptm/m/n/10 times the
iden-tity ma-trix,
[2456]
[2457]
[2458]
[2459]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.image}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.6399 \aliasA{image}{image-methods}{image}
[2460]
[2461]
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[]\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][
][]\T1/pcr/m/n/10 dgTMatrix[][][] []\T1/ptm/m/n/10 class. Use
Overfull \hbox (47.58038pt too wide) in paragraph at lines 6514--6514
[]\T1/pcr/m/n/9 stopifnot(!is.null(leg <- imgC$legend), is.list(leg$right)) #
failed for 2 days ..[]
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[]\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col
/row) indices:[]
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[] \T1/pcr/m/n/9 I2 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE,
border.col=NA)[]
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[] \T1/pcr/m/n/9 I3 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd
=2, border.col=NA)[]
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[]\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor
der.col = adjustcolor("skyblue", 1/2))[]
[2462]
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[]\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a
nti-aliasing[]
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[] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[]
[2463]
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[]\T1/pcr/m/n/10 signature(x = "indMatrix", y = "Matrix") []\T1/ptm/m/n/10 and
oth-ers listed by
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[]\T1/pcr/m/n/10 showMethods("%*%", classes = "indMatrix")[]\T1/ptm/m/n/10 : ma
-trix prod-ucts im-ple-mented
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[]\T1/pcr/m/n/10 signature(from = "numeric", to = "indMatrix")[]\T1/ptm/m/n/10
: sup-port-ing typ-i-cal
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[]\T1/pcr/m/n/10 signature(from = "list", to = "indMatrix")[]\T1/ptm/m/n/10 : s
up-port-ing []\T1/pcr/m/n/10 indMatrix
[2464]
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[]\T1/pcr/m/n/10 signature(x = "indMatrix")[]\T1/ptm/m/n/10 : row and
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[]\T1/pcr/m/n/10 signature(X = "indMatrix", Y = "indMatrix")[]\T1/ptm/m/n/10 :
Kro-necker prod-uct of
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[]\T1/ptm/m/n/10 Fabian Scheipl at `\T1/pcr/m/n/10 uni-muenchen.de\T1/ptm/m/n/1
0 ', build-ing on the ex-ist-ing class [][][]\T1/pcr/m/n/10 pMatrix[][][] []\T1
/ptm/m/n/10 af-ter
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\T1/ptm/m/n/10 a nice hike's con-ver-sa-tion with Mar-tin Maech-ler. Meth-ods f
or [][][]\T1/pcr/m/n/10 crossprod[][][](x, y) []\T1/ptm/m/n/10 and
[2465]
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[]\T1/ptm/m/n/10 an in-te-ger off-set, in-di-cat-ing that the re-sult should be
a per-mu-ta-tion of
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[]\T1/pcr/m/n/10 invertPerm(p) []\T1/ptm/m/n/10 re-turns an in-te-ger vec-tor o
f length []\T1/pcr/m/n/10 length(p) []\T1/ptm/m/n/10 such that
Underfull \hbox (badness 4441) in paragraph at lines 6837--6841
[]\T1/pcr/m/n/10 p[invertPerm(p)] []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 invertP
erm(p)[p] []\T1/ptm/m/n/10 are both []\T1/pcr/m/n/10 seq_along(p)[]\T1/ptm/m/n/
10 , i.e., the
[2466]
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[]\T1/pcr/m/n/9 ## Product of transpositions (1 2)(2 1)(4 3)(6 8)(10 1) = (3 4
)(6 8)(1 10)[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.anyNA}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.6888 \aliasA{anyNA}{is.na-methods}{anyNA}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.finite
}) has been already used, duplicate ignored
<to be read again>
\relax
l.6895 ...asA{is.finite}{is.na-methods}{is.finite}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.infini
te}) has been already used, duplicate ignored
<to be read again>
\relax
l.6903 ...is.infinite}{is.na-methods}{is.infinite}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.na}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.6911 \aliasA{is.na}{is.na-methods}{is.na}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.nan})
has been already used, duplicate ignored
<to be read again>
\relax
l.6918 \aliasA{is.nan}{is.na-methods}{is.nan}
[2467]
[2468]
[2469]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.isSymmetr
ic}) has been already used, duplicate ignored
<to be read again>
\relax
l.7077 ...etric}{isSymmetric-methods}{isSymmetric}
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[]\T1/pcr/m/n/10 isSymmetric(object, checkDN = TRUE, tol = 100 * .Machine$doub
le.eps, tol1 = 8 * tol, ...)[]
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[]\T1/pcr/m/n/10 isSymmetric(object, checkDN = TRUE, tol = 100 * .Machine$doub
le.eps, ...)[]
[2470]
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[]\T1/pcr/m/n/9 isSymmetric(as(M, "generalMatrix")) # still symmetric, even if
not "formally"[]
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[]\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs = TRUE) # includes S3 g
eneric from base[]
[2471]
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[]\T1/pcr/m/n/9 isTriangular(as(M, "generalMatrix")) # still triangular, even
if not "formally"[]
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[]\T1/pcr/m/n/10 KhatriRao(X, Y = X, FUN = "*", sparseY = TRUE, make.dimnames
= FALSE)
[2472]
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[]\T1/pcr/m/n/9 stopifnot(all(K1 <- KhatriRao(nd, zm) == 0), identical(dim(K1)
, c(12L, 4L)),[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7372--7372
[] \T1/pcr/m/n/9 all(K2 <- KhatriRao(zm, nd) == 0), identical(dim(K2)
, c(12L, 4L)))[]
[2473]
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[] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), d
imnames(Kmd)))[]
[2474]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.kronecker
}) has been already used, duplicate ignored
<to be read again>
\relax
l.7453 ...kronecker}{kronecker-methods}{kronecker}
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[]\T1/pcr/m/n/10 ldenseMatrix []\T1/ptm/m/n/10 is the vir-tual class of all den
se \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2475]
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[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-call
y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2476
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.*,ndiMatr
ix,Matrix.Rdash.method}) has been already used, duplicate ignored
<argument> ...shipout:D \box_use:N \l_shipout_box
\__shipout_drop_firstpage_...
l.7691 C
lass \code{"\LinkA{sparseMatrix}{sparseMatrix.Rdash.class}"}, by cla...
]
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[]\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ldenseMatrix"[]\T1/ptm/m/n/10 , di-rec
tly. Class []\T1/pcr/m/n/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/
10 "ldenseMatrix"[]\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 7738--7743
\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "denseMatrix"[]\T1/ptm/m/n/10 , by class
[]\T1/pcr/m/n/10 "ldenseMatrix"[]\T1/ptm/m/n/10 . Class []\T1/pcr/m/n/10 "Matri
x"[]\T1/ptm/m/n/10 , by class
Underfull \hbox (badness 10000) in paragraph at lines 7746--7749
[]\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n
/10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/
10 ); use, e.g.,
[2477]
Underfull \hbox (badness 10000) in paragraph at lines 7804--7814
[]\T1/pcr/m/n/10 lsTMatrix[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 ltTMatrix[]\T
1/ptm/m/n/10 ) or in com-pressed column-oriented form (class
Underfull \hbox (badness 1242) in paragraph at lines 7804--7814
[][][]\T1/pcr/m/n/10 CsparseMatrix[][][][]\T1/ptm/m/n/10 , sub-classes []\T1/pc
r/m/n/10 lgCMatrix[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lsCMatrix[]\T1/ptm/m/n/10
, and []\T1/pcr/m/n/10 ltCMatrix[]\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\
T1/ptm/m/n/10 --in
[2478]
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[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cal
ly equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2479]
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[]\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n
/10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/
10 ; use, e.g.,
[2480]
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[]\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n
/10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/
10 ; use, e.g.,
[2481]
[2482]
[2483]
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[]\T1/ptm/m/n/10 vector of all non-zero en-tries of []\T1/pcr/m/n/10 x[]\T1/ptm
/m/n/10 ; ex-ists \T1/ptm/b/n/10 only \T1/ptm/m/n/10 when []\T1/pcr/m/n/10 as(x
,
Underfull \hbox (badness 1490) in paragraph at lines 8292--8294
[]\T1/pcr/m/n/10 mat2triplet() []\T1/ptm/m/n/10 is con-cep-tu-ally the \T1/ptm/
m/it/10 in-verse \T1/ptm/m/n/10 func-tion of [][][]\T1/pcr/m/n/10 spMatrix[][][
] []\T1/ptm/m/n/10 and (one case of)
[2484]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rpcent.*
.Rpcent.}) has been already used, duplicate ignored
<to be read again>
\relax
l.8313 ...*\%}{matmult-methods}{.Rpcent.*.Rpcent.}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.crossprod
}) has been already used, duplicate ignored
<to be read again>
\relax
l.8387 ...A{crossprod}{matmult-methods}{crossprod}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tcrosspro
d}) has been already used, duplicate ignored
<to be read again>
\relax
l.8463 ...tcrossprod}{matmult-methods}{tcrossprod}
Underfull \hbox (badness 1881) in paragraph at lines 8549--8555
\T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][][]\T1/
pcr/m/n/10 t[][][](.)[]\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn
[2485]
Underfull \hbox (badness 10000) in paragraph at lines 8618--8621
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")[]\T1/ptm/m/n/10 :
Ma-trix mul-ti-pli-ca-tion;
Underfull \hbox (badness 10000) in paragraph at lines 8621--8626
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and
other sig-na-tures (use
Underfull \hbox (badness 3557) in paragraph at lines 8621--8626
[]\T1/pcr/m/n/10 showMethods("%*%", class="dtrMatrix")[]\T1/ptm/m/n/10 ): ma-tr
ix mul-ti-pli-ca-tion. Mul-ti-
Underfull \hbox (badness 6608) in paragraph at lines 8626--8630
\T1/ptm/m/n/10 sig-na-tures, use []\T1/pcr/m/n/10 showMethods("crossprod", clas
s = "dgeMatrix")[]\T1/ptm/m/n/10 , ma-trix
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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and
other sig-na-
[2486]
[2487]
[2488]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det}) has
been already used, duplicate ignored
<to be read again>
\relax
l.8859 \aliasA{det}{Matrix-class}{det}
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[]\T1/pcr/m/n/10 signature(x = "Matrix", value = "list")[]\T1/ptm/m/n/10 : set
the []\T1/pcr/m/n/10 dimnames []\T1/ptm/m/n/10 to a
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[2489]
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[]\T1/pcr/m/n/10 signature(from = "ANY", to = "Matrix")[]\T1/ptm/m/n/10 : This
re-lies on a cor-rect
[2490]
[2491]
Underfull \hbox (badness 10000) in paragraph at lines 9128--9132
[]\T1/pcr/m/n/10 CholeskyFactorization[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Bunch
KaufmanFactorization[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 signature(x = "MatrixFactorization", logarithm =
Underfull \hbox (badness 10000) in paragraph at lines 9168--9171
[]\T1/pcr/m/n/10 signature(obj = "MatrixFactorization")[]\T1/ptm/m/n/10 : re-tu
rns []\T1/pcr/m/n/10 obj []\T1/ptm/m/n/10 with
Underfull \hbox (badness 3019) in paragraph at lines 9177--9180
[]\T1/ptm/m/n/10 Classes ex-tend-ing []\T1/pcr/m/n/10 CholeskyFactorization[]\T
1/ptm/m/n/10 , namely [][][]\T1/pcr/m/n/10 Cholesky[][][][]\T1/ptm/m/n/10 , [][
][]\T1/pcr/m/n/10 pCholesky[][][][]\T1/ptm/m/n/10 , and
[2492]
Underfull \hbox (badness 10000) in paragraph at lines 9181--9183
[]\T1/ptm/m/n/10 Classes ex-tend-ing []\T1/pcr/m/n/10 BunchKaufmanFactorization
[]\T1/ptm/m/n/10 , namely [][][]\T1/pcr/m/n/10 BunchKaufman[][][] []\T1/ptm/m/n
/10 and
Underfull \hbox (badness 10000) in paragraph at lines 9196--9199
[]\T1/ptm/m/n/10 Generic func-tions [][][]\T1/pcr/m/n/10 expand1[][][] []\T1/pt
m/m/n/10 and [][][]\T1/pcr/m/n/10 expand2[][][] []\T1/ptm/m/n/10 for con-struct
-ing ma-trix fac-tors from
Underfull \hbox (badness 1062) in paragraph at lines 9225--9228
[]\T1/pcr/m/n/10 ndenseMatrix []\T1/ptm/m/n/10 is the vir-tual class of all den
se \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
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[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-call
y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2493]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if []\T1/pcr/m/n/10 X <- (X + t(X))/2 []
\T1/ptm/m/n/10 should be done, af-ter []\T1/pcr/m/n/10 X <-
[2494]
[2495]
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[] \T1/pcr/m/n/9 all.equal(n.A.m, unname(as.matrix(n.A$mat)), tolerance = 1e
-15)# seen rel.d.= 1.46e-16[]
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[]\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a
ll in this example[]
[2496]
Underfull \hbox (badness 2635) in paragraph at lines 9510--9515
[]\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ndenseMatrix"[]\T1/ptm/m/n/10 , di-rec
tly. Class []\T1/pcr/m/n/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/
10 "ndenseMatrix"[]\T1/ptm/m/n/10 .
Underfull \hbox (badness 4229) in paragraph at lines 9510--9515
\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "denseMatrix"[]\T1/ptm/m/n/10 , by class
[]\T1/pcr/m/n/10 "ndenseMatrix"[]\T1/ptm/m/n/10 . Class []\T1/pcr/m/n/10 "Matri
x"[]\T1/ptm/m/n/10 , by class
Underfull \hbox (badness 10000) in paragraph at lines 9518--9521
[]\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n
/10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/
10 ); use, e.g.,
[2497]
Underfull \hbox (badness 2521) in paragraph at lines 9586--9592
[]\T1/pcr/m/n/10 signature(from = "matrix", to = "nMatrix")[]\T1/ptm/m/n/10 : N
ote that these co-er-cions
[2498]
Underfull \hbox (badness 1867) in paragraph at lines 9699--9701
[]\T1/ptm/m/n/10 fast sim-
[2499]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.norm}) ha
s been already used, duplicate ignored
<to be read again>
\relax
l.9741 \aliasA{norm}{norm-methods}{norm}
[2500]
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[]\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x) ## 8 x 10
"dgCMatrix"[]
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[]\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
"dsCMatrix"[]
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[]\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
"dtCMatrix"[]
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[]\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][][]\T1/pcr/m/n
/10 TsparseMatrix[][][][]\T1/ptm/m/n/10 , sub-classes []\T1/pcr/m/n/10 ngTMatri
x[]\T1/ptm/m/n/10 ,
[2501]
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[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cal
ly equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2502]
Underfull \hbox (badness 10000) in paragraph at lines 10034--10037
[]\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n
/10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/
10 ; use, e.g.,
[2503]
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[]\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n
/10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/
10 ; use, e.g.,
[2504]
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[]\T1/ptm/m/n/10 typically a []\T1/pcr/m/n/10 "packedMatrix"[]\T1/ptm/m/n/10 ,
though
[2505]
[2506]
[2507]
Underfull \hbox (badness 10000) in paragraph at lines 10386--10389
[]\T1/pcr/m/n/10 signature(x = "pMatrix", y = "Matrix") []\T1/ptm/m/n/10 and ot
h-ers listed by
Underfull \hbox (badness 8189) in paragraph at lines 10386--10389
[]\T1/pcr/m/n/10 showMethods("%*%", classes = "pMatrix")[]\T1/ptm/m/n/10 : ma-t
rix prod-ucts im-ple-mented
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[]\T1/pcr/m/n/10 signature(from = "numeric", to = "pMatrix")[]\T1/ptm/m/n/10 :
sup-port-ing typ-i-cal
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[]\T1/pcr/m/n/10 signature(a = "pMatrix", b = "missing")[]\T1/ptm/m/n/10 : the
in-verse per-mu-ta-tion ma-trix,
[2508]
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[] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD
iag = TRUE,[]
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[]\T1/pcr/m/n/10 printSpMatrix(x, digits = NULL, maxp = max(100L, getOption("m
ax.print")),[]
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[] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 10476--10476
[]\T1/pcr/m/n/10 printSpMatrix2(x, digits = NULL, maxp = max(100L, getOption("
max.print")),[]
[2509]
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[] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[]
Underfull \hbox (badness 3989) in paragraph at lines 10502--10512
[]\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of []
\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 should
Underfull \hbox (badness 10000) in paragraph at lines 10502--10512
\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2510]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr}) has
been already used, duplicate ignored
<to be read again>
\relax
l.10604 \aliasA{qr}{qr-methods}{qr}
[2511]
[2512]
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[] \T1/pcr/m/n/9 all.equal(qr.coef(qr.A1, b), drop(solve(crossprod(A1), cro
ssprod(A1, b))))[]
[2513]
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[] \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 qr.coef\TS1/pcr/m/n/9 ' \
T1/pcr/m/n/9 computes unique least squares solution of "nearby" problem[]
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[] \T1/pcr/m/n/9 ## Z x = b for some full rank Z ~ A, currently without war
ning {FIXME} ![]
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[]\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m
atrix"), ...)[]
Underfull \vbox (badness 10000) has occurred while \output is active
[2514]
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[]\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of [][][]\T1/pcr/m/n/10
qr[][][](x, tol,
Underfull \hbox (badness 10000) in paragraph at lines 10865--10868
[]\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense []\T1/pcr/m/n/10 x[]\
T1/ptm/m/n/10 , it cor-re-sponds to
[2515]
[2516]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 10962--10962
[]\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/
n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale
free"[]
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[]\T1/pcr/m/n/9 sapply(meths, function(.m.) rankMatrix(M15, method = .m., tol
= 1e-7)) # all 14[]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 10985--10985
[]\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L))) # war
ning+ ~1.5 sec (2013)[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 10986--10986
[]\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con
siderably faster![]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.11005 \aliasA{rcond}{rcond-methods}{rcond}
[2517]
[2518]
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[]\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
have full rank[]
[2519]
[2520]
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\T1/ptm/m/n/10 dices, if not []\T1/pcr/m/n/10 symmetric [][]sample.int[][][](nr
ow*ncol, nnz)[]\T1/ptm/m/n/10 , then---if []\T1/pcr/m/n/10 rand.x []\T1/ptm/m/n
/10 is not
[2521]
[2522]
Underfull \hbox (badness 5147) in paragraph at lines 11444--11447
[]\T1/ptm/m/n/10 Class [][][]\T1/pcr/m/n/10 SchurFactorization[][][][]\T1/ptm/m
/n/10 , di-rectly. Class [][][]\T1/pcr/m/n/10 MatrixFactorization[][][][]\T1/pt
m/m/n/10 , by class
[2523]
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[]\T1/pcr/m/n/10 signature(from = "Schur", logarithm = "logical")[]\T1/ptm/m/n/
10 : com-putes
[2524]
[2525]
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[] \T1/pcr/m/n/9 all.equal(e1, e3[order(Mod(e3), decreasing = TRUE)], toler
ance = 1e-13)[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solve}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.11633 \aliasA{solve}{solve-methods}{solve}
[2526]
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[]\T1/pcr/m/n/10 solve(a, b, system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "
D", "P", "Pt"), ...)[]
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[]\T1/ptm/m/n/10 a vec-tor, [][][]\T1/pcr/m/n/10 sparseVector[][][][]\T1/ptm/m/
n/10 , ma-trix, or [][][]\T1/pcr/m/n/10 Matrix[][][] []\T1/ptm/m/n/10 sat-is-fy
-ing []\T1/pcr/m/n/10 NROW(b) ==
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[]\T1/ptm/m/n/10 Methods for dense []\T1/pcr/m/n/10 a []\T1/ptm/m/n/10 are buil
t on 14 LA-PACK rou-tines: class []\T1/pcr/m/n/10 d..Matrix[]\T1/ptm/m/n/10 , w
here
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[]\T1/ptm/m/n/10 Methods for sparse []\T1/pcr/m/n/10 a []\T1/ptm/m/n/10 are bui
lt on CXS-parse rou-tines []\T1/pcr/m/n/10 cs_lsolve[]\T1/ptm/m/n/10 , []\T1/pc
r/m/n/10 cs_usolve[]\T1/ptm/m/n/10 , and
[2527]
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[]\T1/pcr/m/n/9 image(ia0 <- solve(a, tol = 0)) # checker board, dense [but re
ally, a is singular!][]
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[] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on
[FIXME ??] only[]
[2528]
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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, from a for-mu
la and data frame
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[] \T1/pcr/m/n/10 drop.unused.levels = TRUE, repr = c("C", "R", "T"), giveC
sparse)[]
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[] \T1/pcr/m/n/10 drop.unused.levels = TRUE, repr = c("C", "R", "T"), giveC
sparse,[]
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[]\T1/ptm/m/n/10 a data frame cre-ated with [][][]\T1/pcr/m/n/10 model.frame[][
][][]\T1/ptm/m/n/10 . If an-other sort of ob-ject,
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[]\T1/ptm/m/n/10 character string or []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or
(co-er-ca-ble to)
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[]\T1/pcr/m/n/10 "[][]sparseMatrix[][][]"[]\T1/ptm/m/n/10 , spec-i-fy-ing the c
on-trasts to be ap-plied to the
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[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for
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[]\T1/pcr/m/n/10 sparse.model.matrix []\T1/ptm/m/n/10 has been changed to []\T1
/pcr/m/n/10 FALSE[]\T1/ptm/m/n/10 , 2010-07, for
[2529]
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[][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/
m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc
r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse
Underfull \hbox (badness 3291) in paragraph at lines 12008--12013
[]\T1/pcr/m/n/10 model.Matrix(sparse = TRUE) []\T1/ptm/m/n/10 from pack-age [][
]\T1/ptm/b/n/10 Ma-trix-Mod-els[][] \T1/ptm/m/n/10 may be nowa-days be
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\T1/ptm/m/n/10 prefer-able to []\T1/pcr/m/n/10 sparse.model.matrix[]\T1/ptm/m/n
/10 , as []\T1/pcr/m/n/10 model.Matrix []\T1/ptm/m/n/10 re-turns an ob-ject of
class
[2530]
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[] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M)
== c(0, 0),[]
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[] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M)
== c(3, 0),[]
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[] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
== c(0,12),[]
[2531]
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[]\T1/pcr/m/n/10 signature(from = "sparseLU", logarithm = "logical")[]\T1/ptm/m
/n/10 : com-
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[]\T1/pcr/m/n/9 A <- as(readMM(system.file("external", "pores_1.mtx", package
= "Matrix")),[]
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[]\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m
atrix"), ...)[]
[2532]
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[] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(dn[1L
], list(NULL)),[]
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[] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(list(
NULL), dn[2L]),[]
Underfull \hbox (badness 10000) in paragraph at lines 12214--12216
[]\T1/ptm/m/n/10 This in-ter-face is rec-om-mended over di-rect con-struc-tion
via calls such as
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12221--12221
[] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 =
TRUE,[]
[2533]
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\T1/ptm/m/n/10 of the sparse ma-trix re-sult, i.e., spec-i-fy-ing one of the vi
r-tual classes
[2534]
Underfull \hbox (badness 10000) in paragraph at lines 12348--12351
[]\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][][]\T1/pcr/m/n/10 xtabs[][][
](*, sparse=TRUE)[]\T1/ptm/m/n/10 , for sparse ta-bles and
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[]\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x)) ## 8 x 10
"dgCMatrix"[]
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[]\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
"dsCMatrix"[]
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[]\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
"dtCMatrix"[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12371--12371
[]\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims
= c(10,20)))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12374--12374
[]\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[]
[2535]
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[]\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
if necessary:[]
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[]\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x =
1:6, dimnames = dn)[]
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[]\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep
resentations.[]
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[] \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack
age = "SparseM"))) {[]
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[] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
X@dimension)[]
[2536]
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[]\T1/pcr/m/n/10 (x = "sparseMatrix", logarithm=TRUE)[]\T1/ptm/m/n/10 : [][][]\
T1/pcr/m/n/10 determinant[][][]() []\T1/ptm/m/n/10 meth-ods
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[][][]\T1/pcr/m/n/10 sparseMatrix[][][][]\T1/ptm/m/n/10 , and its ref-er-ences,
such as [][][]\T1/pcr/m/n/10 xtabs[][][](*, sparse=TRUE)[]\T1/ptm/m/n/10 , or
[2537]
[2538]
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[]\T1/pcr/m/n/10 signature(from = "sparseQR", logarithm = "logical")[]\T1/ptm/m
/n/10 : com-
[2539]
Underfull \hbox (badness 3229) in paragraph at lines 12816--12820
[]\T1/ptm/m/n/10 The many aux-il-iary func-tions for QR fac-tor-iza-tions: [][]
[]\T1/pcr/m/n/10 qr.Q[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 qr.R[][][][]
\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 qr.X[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc
r/m/n/10 qr.coef[][][][]\T1/ptm/m/n/10 ,
[2540]
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[]\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m
atrix"), ...)[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 12864--12864
[] \T1/pcr/m/n/9 new("pMatrix", Dim = c(m, m), Dimnames = c(dn[1L
], list(NULL)),[]
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[] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(list(
NULL), dn[2L]),[]
Underfull \vbox (badness 10000) has occurred while \output is active
[2541]
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[] \T1/pcr/m/n/9 ae2(qrc <- qr.coef (qr.A, b), with(e.qr.A, solve(R1 %*% P
2., t(qrQ)) %*% b))[]
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[]\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case
a
[2542]
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[]\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class []\T1/pcr/m/
n/10 "sparseVector" []\T1/ptm/m/n/10 has the five ac-
Underfull \hbox (badness 3679) in paragraph at lines 13044--13050
\T1/ptm/m/n/10 tual daugh-ter classes []\T1/pcr/m/n/10 "dsparseVector"[]\T1/ptm
/m/n/10 , []\T1/pcr/m/n/10 "isparseVector"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "
lsparseVector"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") []\T1/ptm/m/
n/10 co-erces sparse
[2543]
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[]\T1/pcr/m/n/10 (x = "nsparseVector")[]\T1/ptm/m/n/10 : re-turn [][][]\T1/pcr/
m/n/10 logical[][][] []\T1/ptm/m/n/10 or
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[][][]\T1/pcr/m/n/10 sparseVector[][][]() []\T1/ptm/m/n/10 for friendly con-str
uc-tion of sparse vec-tors (apart from []\T1/pcr/m/n/10 as(*,
[2544]
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[2545]
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[]\T1/pcr/m/n/10 spMatrix(nrow, ncol, i = integer(0L), j = integer(0L), x = do
uble(0L))
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[][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) []\T1/ptm/m/n/10 for the more
usual con-struc-tor of such ma-tri-ces. Then,
[2546]
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}) has been already used, duplicate ignored
<to be read again>
\relax
l.13316 ...\Rdash{}}{subassign-methods}{[<.Rdash.}
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[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2547]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.[}) has b
een already used, duplicate ignored
<to be read again>
\relax
l.13450 \aliasA{[}{subscript-methods}{[}
[2548]
Underfull \hbox (badness 2591) in paragraph at lines 13585--13590
\T1/ptm/m/n/10 Classes [][][]\T1/pcr/m/n/10 triangularMatrix[][][][]\T1/ptm/m/n
/10 , and, e.g., [][][]\T1/pcr/m/n/10 dsyMatrix[][][] []\T1/ptm/m/n/10 for nu-m
eric \T1/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or
[2549]
Underfull \hbox (badness 2057) in paragraph at lines 13661--13663
[]\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe
r-ent ma-trix classes, use e.g.,
Underfull \hbox (badness 6396) in paragraph at lines 13670--13674
[]\T1/pcr/m/n/10 symmpart(x) []\T1/ptm/m/n/10 re-turns a sym-met-ric ma-trix, i
n-her-it-ing from [][][]\T1/pcr/m/n/10 symmetricMatrix[][][] []\T1/ptm/m/n/10 o
r
[2550]
Underfull \hbox (badness 7722) in paragraph at lines 13675--13680
[]\T1/pcr/m/n/10 skewpart(x) []\T1/ptm/m/n/10 re-turns a skew-symmetric ma-trix
, in-her-it-ing from [][][]\T1/pcr/m/n/10 generalMatrix[][][][]\T1/ptm/m/n/10 ,
[2551]
Underfull \hbox (badness 6641) in paragraph at lines 13752--13755
[]\T1/ptm/m/n/10 Currently, [][][]\T1/pcr/m/n/10 Schur[][][][]\T1/ptm/m/n/10 ,
[][][]\T1/pcr/m/n/10 isSymmetric[][][] []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 as
() []\T1/ptm/m/n/10 (i.e. [][][]\T1/pcr/m/n/10 coerce[][][][]\T1/ptm/m/n/10 ) h
ave meth-ods with
Underfull \hbox (badness 5133) in paragraph at lines 13788--13792
[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 "TsparseMatrix" []\T1/ptm/m/n/10 class is
the vir-tual class of all sparse ma-tri-ces coded in
Underfull \hbox (badness 2818) in paragraph at lines 13788--13792
\T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c
re-ated from it. See
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[2553]
Underfull \hbox (badness 1668) in paragraph at lines 13915--13918
[][][]\T1/pcr/m/n/10 pack[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 unpac
k[][][][]\T1/ptm/m/n/10 ; its vir-tual "com-ple-ment" []\T1/pcr/m/n/10 "[][]pac
kedMatrix[][][]"[]\T1/ptm/m/n/10 ; its proper sub-classes
[2554]
Underfull \hbox (badness 10000) in paragraph at lines 14026--14032
[]\T1/ptm/m/n/10 GAL lat-tice file `\T1/pcr/m/n/10 usc_q.GAL\T1/ptm/m/n/10 ' (r
e-trieved in 2008 from
[2555]
[2556]
[2557]) (./boot-pkg.tex
[2558]
Chapter 18.
[2559]
[2560]
[2561]
[2562]
[2563]
[2564]
[2565]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 532--532
[]\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"),
[2566]
Underfull \hbox (badness 1325) in paragraph at lines 570--577
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r
e-quired. Pos-si-ble
Underfull \hbox (badness 1275) in paragraph at lines 585--590
[]\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m
ulti-sample prob-
[2567]
[2568]
[2569]
Underfull \hbox (badness 1881) in paragraph at lines 826--828
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
Underfull \hbox (badness 6493) in paragraph at lines 853--857
[][][]\T1/pcr/m/n/10 boot.array[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 bo
ot.ci[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 censboot[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 empinf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 j
ack.after.boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 tilt.boot[][][][]\T
1/ptm/m/n/10 ,
[2570]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 887--887
[]\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt,
data = nuke)[]
Underfull \vbox (badness 10000) has occurred while \output is active
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[2573]
Underfull \hbox (badness 1496) in paragraph at lines 1084--1093
[]\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari-
ance of the
Underfull \hbox (badness 2005) in paragraph at lines 1084--1093
\T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i
n-ter-vals. If it
Underfull \hbox (badness 2343) in paragraph at lines 1084--1093
\T1/ptm/m/n/10 is not sup-plied and []\T1/pcr/m/n/10 length(index) []\T1/ptm/m/
n/10 is 2 then []\T1/pcr/m/n/10 var.t0 []\T1/ptm/m/n/10 de-faults to
Underfull \hbox (badness 2150) in paragraph at lines 1105--1111
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
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[2575]
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[2577]
Underfull \hbox (badness 1571) in paragraph at lines 1445--1447
[]\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An
al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis-
[2578]
[2579]
[2580]
[2581]
[2582]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1738--1738
[]\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2),
[2583]
[2584]
[2585]
Underfull \vbox (badness 10000) has occurred while \output is active
[2586]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 2013--2013
[]\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
+ strata(ulcer),[]
[2587]
Underfull \hbox (badness 6268) in paragraph at lines 2084--2086
[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
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[2590]
Underfull \hbox (badness 1565) in paragraph at lines 2338--2343
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori
g-i-nal data set
[2591]
Underfull \hbox (badness 4595) in paragraph at lines 2363--2368
\T1/ptm/m/n/10 are passed un-changed ev-ery time []\T1/pcr/m/n/10 boot.out$stat
istic []\T1/ptm/m/n/10 is called.
Underfull \hbox (badness 1881) in paragraph at lines 2432--2434
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
Underfull \hbox (badness 2057) in paragraph at lines 2440--2441
[][][]\T1/pcr/m/n/10 boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 empinf[]
[][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 k3.linear[][][][]\T1/ptm/m/n/10 , [
][][]\T1/pcr/m/n/10 linear.approx[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
saddle.distn[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 smooth.spline[][][][]
\T1/ptm/m/n/10 ,
[2592]
[2593]
Underfull \hbox (badness 1077) in paragraph at lines 2536--2540
[]\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of []\T1/pcr/m
/n/10 n/((n-1)*(n-2)) []\T1/ptm/m/n/10 where []\T1/pcr/m/n/10 n []\T1/ptm/m/n/1
0 is the sam-ple
Underfull \hbox (badness 1112) in paragraph at lines 2536--2540
\T1/ptm/m/n/10 size, if []\T1/pcr/m/n/10 unbiased []\T1/ptm/m/n/10 is []\T1/pcr
/m/n/10 FALSE []\T1/ptm/m/n/10 then a mul-ti-plier of []\T1/pcr/m/n/10 1/n []\T
1/ptm/m/n/10 is used. This is mul-ti-plied by
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[2595]
[2596]
[2597]
[2598]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2895--2895
[]\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t
= 25,
Overfull \hbox (18.78088pt too wide) in paragraph at lines 2897--2897
[]\T1/pcr/m/n/10 EL.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t
= 25,[]
[2599]
[2600]
[2601]
Underfull \hbox (badness 3861) in paragraph at lines 3105--3108
[][][]\T1/pcr/m/n/10 boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 boot.arr
ay[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 boot.ci[][][][]\T1/ptm/m/n/10 ,
[][][]\T1/pcr/m/n/10 control[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 jack
.after.boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 linear.approx[][][][]\
T1/ptm/m/n/10 ,
[2602]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3158--3158
[]\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat))
[2603]
[2604]
[2605]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3378--3378
[]\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling
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[2607]
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[2609]
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[2611]
[2612]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3838--3838
[] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
= NULL)[]
[2613]
[2614]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3977--3977
[]\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
grav.z0[3])[]
[2615]
[2616]
[2617]
[2618]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4259--4259
[]\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz
e data as in
[2619]
[2620]
Underfull \hbox (badness 10000) in paragraph at lines 4362--4364
[]\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o
f
Underfull \hbox (badness 1430) in paragraph at lines 4371--4375
\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 t0 []\T1/ptm/m/n/10 is sup-plied but nei-the
r []\T1/pcr/m/n/10 t []\T1/ptm/m/n/10 nor []\T1/pcr/m/n/10 L []\T1/ptm/m/n/10 a
re sup-plied then []\T1/pcr/m/n/10 t0 []\T1/ptm/m/n/10 is set to
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[2629]
Underfull \hbox (badness 3000) in paragraph at lines 4959--4962
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put
of a call to
[2630]
[2631]
[2632]
[2633]
Underfull \hbox (badness 2293) in paragraph at lines 5238--5241
[]\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the
boot-strap
Underfull \hbox (badness 1668) in paragraph at lines 5238--5241
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2634]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5317--5317
[]\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[]
[2635]
[2636]
[2637]
[2638]
[2639]
[2640]
[2641]
[2642]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5866--5866
[]\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][]
[2643]
Underfull \hbox (badness 1127) in paragraph at lines 5988--6006
[]\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less
than []\T1/pcr/m/n/10 min(alpha)/10[]\T1/ptm/m/n/10 , then
[2644]
Underfull \hbox (badness 2837) in paragraph at lines 6021--6024
[]\T1/ptm/m/n/10 The re-turned value is an ob-ject of class []\T1/pcr/m/n/10 "s
addle.distn"[]\T1/ptm/m/n/10 . See the help file for
[2645]
[2646]
[2647]
[2648]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6306--6306
[]\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and
Wright (1991).
[2649]
[2650]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6495--6495
[]\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6497--6497
[]\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t
ilting was used[]
[2651]
[2652]
[2653]
Underfull \hbox (badness 1596) in paragraph at lines 6742--6746
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m
ent ex-pected by
[2654]
[2655]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6902--6902
[] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
c(0.05, 0.95),[]
[2656]
[2657]
[2658]
[2659]
[2660]
[2661]
[2662]
[2663]) (./class-pkg.tex
[2664]
Chapter 19.
[2665]
[2666]
[2667]
[2668]
[2669]
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[2671]
[2672]
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[2674]
[2675]
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[2678]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1006--1006
[] \T1/pcr/m/n/9 alpha = list(seq(0.05, 0, length.out = 1e4), seq(0.02, 0,
length.out = 1e5)),[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1007--1007
[] \T1/pcr/m/n/9 radii = list(seq(8, 1, length.out = 1e4), seq(4, 1, length
.out = 1e5)))[]
[2679]
[2680]) (./cluster-pkg.tex
Chapter 20.
[2681]
[2682]
[2683]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 253--253
[] \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met
hod = 0.5)[iC]) ,[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 254--254
[] \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method=
c(.5,.5,0, -.5))[iC]),[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 255--255
[] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
c(.5,.5,0, +.5))[iC]))[]
[2684]
[2685]
[2686] [2687]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519
[] \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot
= axes,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 523--523
[] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
...)[]
[2688]
[2689]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 638--638
[] \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c
orrect.d = TRUE)[]
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[2691]
[2692]
Underfull \hbox (badness 2941) in paragraph at lines 792--795
[][][]\T1/pcr/m/n/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-en
ces; [][][]\T1/pcr/m/n/10 clara.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 pam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 partition.object[][][][]\
T1/ptm/m/n/10 ,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 833--833
[] \T1/pcr/m/n/9 cl[,i] <- clara(xclara, nCl, medoids.x = FALSE, rngR = TRUE
)$clustering[]
[2693]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 835--835
[]\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[]
Underfull \hbox (badness 10000) in paragraph at lines 882--884
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2694]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 947--947
[] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code
=3), ...)[]
[2695]
Underfull \hbox (badness 4872) in paragraph at lines 992--994
[]\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is
Underfull \hbox (badness 1342) in paragraph at lines 1006--1010
[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
2012,
[2696]
Underfull \hbox (badness 2503) in paragraph at lines 1092--1096
[]\T1/ptm/m/n/10 Per Broberg (2006). SAGx: Sta-tis-ti-cal Anal-y-sis of the Gen
eChip. R pack-age ver-
[2697]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1118--1118
[] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1135--1135
[]\T1/pcr/m/n/9 ## You can manually set it before running this : doExtras <
- TRUE # or FALSE[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1144--1144
[] \T1/pcr/m/n/9 gskmn <- clusGap(x, FUNcluster = kmeans, nstart = 20, K.max
= 8, B = 60)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1146--1146
[] \T1/pcr/m/n/9 plot(gskmn, main = "clusGap(., FUNcluster = kmeans, n.start=
20, B= 60)")[]
Underfull \vbox (badness 10000) has occurred while \output is active
[2698]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1173--1173
[]\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap(<iid_rnorm_p=3>) ==> k = 1 clust
er is optimal")[]
Underfull \hbox (badness 4144) in paragraph at lines 1205--1209
[]\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 does not have a []\T1
/pcr/m/n/10 diss []\T1/ptm/m/n/10 nor a []\T1/pcr/m/n/10 data []\T1/ptm/m/n/10
com-po-nent, e.g., for
[2699]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1281--1281
[] \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1,
cex.txt = cex,[]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 1287--1287
[] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[]
[2700]
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[2702]
Underfull \hbox (badness 10000) in paragraph at lines 1474--1477
Underfull \hbox (badness 10000) in paragraph at lines 1488--1492
[][][]\T1/pcr/m/n/10 princomp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cmds
cale[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pam[][][][]\T1/ptm/m/n/10 , [
][][]\T1/pcr/m/n/10 clara[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 daisy[][
][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 par[][][][]\T1/ptm/m/n/10 , [][][]\T
1/pcr/m/n/10 identify[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cov.mve[][][
][]\T1/ptm/m/n/10 ,
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1512--1512
[]\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a
nd label ellipses[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1522--1522
[] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[]
[2703]
Underfull \hbox (badness 5741) in paragraph at lines 1562--1565
[]\T1/pcr/m/n/10 coefHier() []\T1/ptm/m/n/10 di-rectly in-ter-faces to the un-d
er-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only
[2704]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1631--1631
[] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa
rnType,[]
[2705]
Underfull \hbox (badness 1552) in paragraph at lines 1680--1682
[]\T1/ptm/b/n/10 A\T1/ptm/m/n/10 symmetric bi-nary vari-able, aka []\T1/pcr/m/n
/10 "A" []\T1/ptm/m/n/10 in re-sult []\T1/pcr/m/n/10 Types[]\T1/ptm/m/n/10 , se
e
Underfull \hbox (badness 1629) in paragraph at lines 1694--1698
[]\T1/ptm/b/n/10 I\T1/ptm/m/n/10 nterval scaled -- the \T1/ptm/b/n/10 de-fault
\T1/ptm/m/n/10 for all nu-meric
Underfull \hbox (badness 3746) in paragraph at lines 1694--1698
\T1/ptm/m/n/10 (incl []\T1/pcr/m/n/10 integer[]\T1/ptm/m/n/10 ) columns of []\T
1/pcr/m/n/10 x[]\T1/ptm/m/n/10 , aka []\T1/pcr/m/n/10 "I" []\T1/ptm/m/n/10 in r
e-sult []\T1/pcr/m/n/10 Types[]\T1/ptm/m/n/10 , see
[2706]
Underfull \hbox (badness 1540) in paragraph at lines 1769--1777
\T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh
ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1
0 w[]^^N[]$\T1/ptm/m/n/10 , where $\OML/cmm/m/it/10 w[]$[]\T1/pcr/m/n/10 =
[2707]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1856--1856
[]\T1/pcr/m/n/9 ## Example 2 in reference, extended --- different ways of "m
ixed" / "gower":[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1860--1860
[]\T1/pcr/m/n/9 summary(d0 <- daisy(flower)) # -> the first 3 {0,1} treate
d as *N*ominal[]
Overfull \hbox (90.78033pt too wide) in paragraph at lines 1861--1861
[]\T1/pcr/m/n/9 summary(dS123 <- daisy(flower, type = list(symm = 1:3))) # fi
rst 3 treated as *S*ymmetric[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1862--1862
[]\T1/pcr/m/n/9 stopifnot(dS123 == d0) # i.e., *S*ymmetric <==> *N*ominal {fo
r 2-level factor}[]
Overfull \hbox (106.98032pt too wide) in paragraph at lines 1866--1866
[]\T1/pcr/m/n/9 summary(dA123 <- daisy(flowerN)) # .. all 3 logicals treated *
A*symmetric binary (w/ warning)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1868--1868
[]\T1/pcr/m/n/9 summary(dA13 <- daisy(flower, type = list(asymm = c(1, 3), ord
ratio = 7)))[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1875--1875
[]\T1/pcr/m/n/9 Nflow[,1:3] <- lapply(flower[,1:3], function(f) as.integer(as.
character(f)))[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1876--1876
[]\T1/pcr/m/n/9 summary(dN <- daisy(Nflow)) # w/ warning: treated binary .. 1:
3 as interval[]
Overfull \hbox (117.7803pt too wide) in paragraph at lines 1877--1877
[]\T1/pcr/m/n/9 ## Still, using Euclidean/Manhattan distance for {0-1} *is* id
entical to treating them as "N" :[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 1893--1893
[]\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE,
[2708]
[2709]
[2710]
[2711]
[2712]
Underfull \hbox (badness 10000) in paragraph at lines 2212--2215
Underfull \hbox (badness 3179) in paragraph at lines 2223--2229
[][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] []\T1/ptm/m/n/10 which is also the
[][][]\T1/pcr/m/n/10 predict[][][] []\T1/ptm/m/n/10 method for []\T1/pcr/m/n/1
0 ellipsoid []\T1/ptm/m/n/10 ob-jects.
[2713]
[2714]
Underfull \hbox (badness 10000) in paragraph at lines 2380--2383
[][][]\T1/pcr/m/n/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-en
ces; [][][]\T1/pcr/m/n/10 fanny.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 partition.object[][][][]\T1/ptm/m/n/10 ,
[2715]
Underfull \hbox (badness 1292) in paragraph at lines 2448--2451
[]\T1/ptm/m/n/10 named vec-tor with []\T1/pcr/m/n/10 iterations[]\T1/ptm/m/n/10
, the num-ber of it-er-a-tions needed and
[2716]
Underfull \hbox (badness 6675) in paragraph at lines 2457--2459
[]\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl
us-ter-ing, see
Underfull \hbox (badness 10000) in paragraph at lines 2480--2483
[][][]\T1/pcr/m/n/10 fanny[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.f
anny[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 dissimilarity.object[][][][]\
T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 partition.object[][][][]\T1/ptm/m/n/10 ,
[2717]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2555--2555
[] \T1/pcr/m/n/9 "4" = "red", "5" = "blue")[levels(f
lowerN$color)][]
Overfull \hbox (90.78033pt too wide) in paragraph at lines 2556--2556
[]\T1/pcr/m/n/9 levels(flowerN$soil) <- c("1" = "dry", "2" = "normal", "3" =
"wet")[levels(flowerN$soil)][]
[2718]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 2619--2619
[]\T1/pcr/m/n/10 medoids(x, clustering, diss = inherits(x, "dist"), USE.NAMES
= FALSE, ...)
[2719]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 2666--2666
[] \T1/pcr/m/n/9 stopifnot(length(cl.k) == nrow(votes.repub), 1 <= cl.k, cl.k
<= k, table(cl.k) >= 2)[]
[2720]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2771--2771
[]\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to
\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/
9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[]
[2721]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 2850--2850
[] \T1/pcr/m/n/10 variant = c("original", "o_1", "o_2", "f_3", "f_4", "f_5"
, "faster"),[]
[2722]
[2723]
[2724]
[2725]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 3078--3078
[]\T1/pcr/m/n/9 ## use obs. 1 & 16 as starting medoids -- same result (for see
d above, *and* typically) :[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3080--3080
[]\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 3083--3083
[]\T1/pcr/m/n/9 keep_nms <- setdiff(names(pamx), c("call", "objective"))# .$ob
jective["build"] differ[]
[2726]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3187--3187
[]\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[]
[2727]
[2728]
[2729]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3381--3381
[] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3382--3382
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2730]
Underfull \hbox (badness 10000) in paragraph at lines 3449--3452
[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via []\T1/pcr/m
/n/10 pltree() []\T1/ptm/m/n/10 is pro-vided by []\T1/pcr/m/n/10 dg <-
[2731]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3499--3499
[] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3500--3500
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2732]
[2733]
[2734]
Underfull \hbox (badness 10000) in paragraph at lines 3685--3688
[]\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 does not have a []\T1
/pcr/m/n/10 diss []\T1/ptm/m/n/10 com-po-nent as for [][][]\T1/pcr/m/n/10 pam[]
[][](*,
Underfull \hbox (badness 1448) in paragraph at lines 3685--3688
\T1/pcr/m/n/10 keep.diss=FALSE)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 dist []\T1/p
tm/m/n/10 must be the dis-sim-i-lar-ity if a clus-plot is
[2735]
Underfull \hbox (badness 10000) in paragraph at lines 3748--3753
[][][]\T1/pcr/m/n/10 partition.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n
/10 clusplot.partition[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 clusplot.de
fault[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pam[][][][]\T1/ptm/m/n/10 ,
[2736]
Underfull \hbox (badness 1748) in paragraph at lines 3810--3815
\T1/ptm/m/n/10 dis-patches to [][][]\T1/pcr/m/n/10 plot.hclust[][][](..)[]\T1/p
tm/m/n/10 . If more flex-i-ble plots are needed, con-sider []\T1/pcr/m/n/10 xx
<-
Underfull \hbox (badness 6268) in paragraph at lines 3822--3825
[][][]\T1/pcr/m/n/10 agnes[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 agnes.o
bject[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 diana[][][][]\T1/ptm/m/n/10
, [][][]\T1/pcr/m/n/10 diana.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/1
0 hclust[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 par[][][][]\T1/ptm/m/n/10
, [][][]\T1/pcr/m/n/10 plot.agnes[][][][]\T1/ptm/m/n/10 ,
[2737]
Underfull \hbox (badness 10000) in paragraph at lines 3883--3885
[]\T1/ptm/m/n/10 Available as `\T1/pcr/m/n/10 pluton.dat\T1/ptm/m/n/10 ' from t
he archive of the Uni-ver-sity of Antwer-pen,
[2738]
[2739]
Underfull \hbox (badness 10000) in paragraph at lines 4002--4005
[][][]\T1/pcr/m/n/10 summary.agnes[][][] []\T1/ptm/m/n/10 pro-duc-ing more out-
put; [][][]\T1/pcr/m/n/10 agnes[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 ag
nes.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/
n/10 ,
[2740]
Underfull \hbox (badness 10000) in paragraph at lines 4033--4036
[][][]\T1/pcr/m/n/10 summary.clara[][][] []\T1/ptm/m/n/10 pro-duc-ing more out-
put; [][][]\T1/pcr/m/n/10 clara[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cl
ara.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/
n/10 ,
[2741]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 4086--4086
[] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
TRUE, ...)[]
Underfull \hbox (badness 2035) in paragraph at lines 4097--4099
[]\T1/ptm/m/n/10 a []\T1/pcr/m/n/10 dissimilarity []\T1/ptm/m/n/10 ob-ject or a
[]\T1/pcr/m/n/10 summary.dissimilarity []\T1/ptm/m/n/10 one for
[2742]
[2743]
[2744]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4290--4290
[] \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w
idth "* s[i]),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 4292--4292
[] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
= TRUE, ...)[]
[2745]
[2746]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4434--4434
[]\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus
ter-wise coloring[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4443--4443
[] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
do.n.k=FALSE)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4445--4445
[] \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma
in")); frame()[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 4448--4448
[]\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol
denrod4", "gray20")[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4450--4450
[] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
do.n.k=FALSE,[]
[2747]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4457--4457
[]\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro
wnames == indices[]
[2748]
[2749]
[2750]
[2751]
[2752]
[2753]
Underfull \hbox (badness 10000) in paragraph at lines 4828--4834
[]\T1/ptm/m/n/10 Our ver-sion of the []\T1/pcr/m/n/10 xclara []\T1/ptm/m/n/10 i
s slightly more rounded than the one from
Underfull \hbox (badness 10000) in paragraph at lines 4844--4846
[]\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file
`\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side
Overfull \hbox (52.98038pt too wide) in paragraph at lines 4857--4857
[]\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10
01:2000}, {2001:3000}
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4859--4859
[]\T1/pcr/m/n/9 p.ID <- c(78, 1411, 2535) ## PAM\TS1/pcr/m/n/9 '\T1/pcr/m/n/9
s medoid indices == pam(xclara, 3)$id.med[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4869--4869
[] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o
bservations:[]
[2754]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4873--4873
[] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? -
- Robust range:[]
[2755]) (./codetools-pkg.tex
[2756]
Chapter 21.
Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16
[] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
= FALSE,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17
[] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun =
!all,[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18
[] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[]
[2757]
Underfull \hbox (badness 10000) in paragraph at lines 65--70
[]\T1/pcr/m/n/10 checkUsageEnv []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 checkUsage
Package []\T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply
[2758]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 118--118
[]\T1/pcr/m/n/10 makeConstantFolder(..., leaf, handler, call, exit, isLocal, f
oldable,[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 121--121
[]\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[]
[2759]
[2760]
[2761]) (./foreign-pkg.tex
[2762]
Chapter 22.
Underfull \hbox (badness 10000) in paragraph at lines 33--37
[]\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o
ut of a Data
Underfull \hbox (badness 10000) in paragraph at lines 33--37
\T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able as [][]$\T1/p
cr/m/n/10 https : / / support .
Underfull \hbox (badness 10000) in paragraph at lines 33--37
\T1/pcr/m/n/10 sas . com / content / dam / SAS / support / en / technical-[]pap
ers /
Overfull \hbox (74.28088pt too wide) in paragraph at lines 33--37
\T1/pcr/m/n/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[]s
et-[]in-[]sas-[]transport-[]xport-[]format .
[2763]
Underfull \hbox (badness 1231) in paragraph at lines 67--70
[]\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr
om, or a
[2764]
[2765]
Underfull \hbox (badness 3601) in paragraph at lines 234--242
[]\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude []\T1/pcr/m
/n/10 "datalabel"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "time.stamp"[]\T1/ptm/m/n/
10 ,
[2766]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 292--292
[]\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
FALSE,
[2767]
[2768]
[2769]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 458--458
[] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame,[]
[2770]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 459--459
[] \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen
d", "no"),[]
Underfull \hbox (badness 2846) in paragraph at lines 502--511
[]\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif-
fer-ent lev-
Underfull \hbox (badness 3746) in paragraph at lines 502--511
\T1/ptm/m/n/10 els. For []\T1/pcr/m/n/10 "append" []\T1/ptm/m/n/10 (the de-faul
t), the first orig-i-nal value la-bel is
Underfull \hbox (badness 2269) in paragraph at lines 502--511
\T1/ptm/m/n/10 kept while fur-ther du-pli-cated la-bels are re-named to []\T1/p
cr/m/n/10 paste0(label,
Underfull \hbox (badness 10000) in paragraph at lines 512--515
[]\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with
du-
Underfull \hbox (badness 10000) in paragraph at lines 512--515
\T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault []\T1/pcr/m/n/10 "_dup
licated_"[]\T1/ptm/m/n/10 ) if
[2771]
Underfull \hbox (badness 10000) in paragraph at lines 546--554
[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 https : / / learn . microsoft . com /
en-[]us / windows / win32 / intl /
Underfull \hbox (badness 7613) in paragraph at lines 564--570
[]\T1/ptm/m/n/10 There may be at-tributes []\T1/pcr/m/n/10 "label.table" []\T1/
ptm/m/n/10 and []\T1/pcr/m/n/10 "variable.labels"[]\T1/ptm/m/n/10 . At-tribute
[2772]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 619--619
[]\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg
ument settings.[]
Overfull \hbox (112.38031pt too wide) in paragraph at lines 620--620
[]\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to
R factor labels) are uncomplete,[]
[2773]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 653--653
[]\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ
ate variables[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 657--657
[]\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt
h=w), "\n"))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 664--664
[]\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste,
collapse="")[]
[2774]
[2775]
Underfull \hbox (badness 10000) in paragraph at lines 808--809
Overfull \hbox (4.38043pt too wide) in paragraph at lines 818--818
[]\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[]
[2776]
Underfull \hbox (badness 10000) in paragraph at lines 865--869
[]\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o
ut of a Data
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\T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able at [][]$\T1/p
cr/m/n/10 https : / / support .
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\T1/pcr/m/n/10 sas . com / content / dam / SAS / support / en / technical-[]pap
ers /
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\T1/pcr/m/n/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[]s
et-[]in-[]sas-[]transport-[]xport-[]format .
[2777]
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[] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv)
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[]\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x)))
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[2780]
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[][][]$\T1/pcr/m/n/10 https : / / www . clicketyclick . dk / databases / xbase
/ format / data _ types .
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[] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric",
"codes"))[]
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[2782]
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[]\T1/ptm/m/n/10 The work for this func-tion is done by []\T1/pcr/m/n/10 foreig
n:::writeForeignStata[]\T1/ptm/m/n/10 ,
[2783]
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[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 package="SPSS"[]\T1/ptm/m/n/10 , as a sid
e ef-fect, the dec-i-mal in-di-ca-tor is al-ways set by []\T1/pcr/m/n/10 SET
[2784]) (./lattice-pkg.tex
Chapter 23.
[2785]
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\T1/ptm/m/n/10 pro-vide a holis-tic in-tro-duc-tion to the Trel-lis paradigm: [
][]$\T1/pcr/m/n/10 http : / / web . archive . org /
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\T1/pcr/m/n/10 web / 20081020164041 / http : / / cm . bell-[]labs . com / cm /
ms / departments / sia /
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[2787]
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[] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.xyplot"),[]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul
t.dotplot"),[]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.barchart"),[]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.stripplot"),[]
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[] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[]
Underfull \vbox (badness 10000) has occurred while \output is active
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.bwplot"),[]
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[]\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as
ar-gu-ments to
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[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of
fac-tors will be
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\T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a
use-ful lay-out.
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[]\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 y []\T1/ptm/m/n/10 sho
uld be num-bers be-tween 0 and 1, giv-ing co-or-di-nates
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[]\T1/ptm/m/n/10 Logical flag, whether leg-end should have a
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[]\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to
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[]\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][][]\T1/pcr/m/
n/10 plot.trellis[][][][]\T1/ptm/m/n/10 ,
[2803]
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[][][]\T1/pcr/m/n/10 panel.dotplot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
panel.stripplot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.superpose[]
[][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.loess[][][][]\T1/ptm/m/n/10 ,
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[] \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar
dSprays$rowpos))),[]
[2806]
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[]\T1/ptm/m/n/10 additional ar-gu-ments passed to [][][]\T1/pcr/m/n/10 xyplot[]
[][][]\T1/ptm/m/n/10 , which may pass them on to
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[]\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p
assed to
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[]\T1/ptm/m/n/10 style set-tings be-yond the stan-dard []\T1/pcr/m/n/10 col[]\T
1/ptm/m/n/10 , []\T1/pcr/m/n/10 lty[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lwd[]\T1
/ptm/m/n/10 , etc; see
[2807]
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[]\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix
An-drews
[2808]
[2809]
[2810]
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[] \T1/pcr/m/n/10 auto.key = lattice.getOption("default.args")$auto
.key,[]
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[] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[]
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[]\T1/ptm/m/n/10 When []\T1/pcr/m/n/10 breaks []\T1/ptm/m/n/10 is un-spec-i-fie
d, the value of
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[]\T1/pcr/m/n/10 lattice.getOption("histogram.breaks") []\T1/ptm/m/n/10 is firs
t checked. If
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Overfull \hbox (12.78088pt too wide) in paragraph at lines 2342--2342
[] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.qqmath"),[]
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Overfull \hbox (60.78088pt too wide) in paragraph at lines 2702--2702
[] \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev
elplot.raster")[]
[2820]
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[] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl
ot"),[]
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[2821]
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[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when []\T1/
pcr/m/n/10 x []\T1/ptm/m/n/10 is a ma-trix.
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[]\T1/pcr/m/n/10 row.values []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 column.values
[]\T1/ptm/m/n/10 must have the same lengths as
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[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be
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\T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][][]\T1/pcr/m/n/10 grid.ra
ster[][][][]\T1/ptm/m/n/10 . See also
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[]\T1/ptm/m/n/10 Logical flag, passed to [][][]\T1/pcr/m/n/10 rasterGrob[][][]
[]\T1/ptm/m/n/10 when
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[]\T1/pcr/m/n/10 allow.multiple[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 outer[]\T1/p
tm/m/n/10 , []\T1/pcr/m/n/10 prepanel[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 scales
[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 strip[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 gr
oups[]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti
ons should be used,
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\T1/ptm/m/n/10 both for the false color im-age and the color key (if present).
Ef-
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\T1/ptm/m/n/10 fec-tively, set-ting this to []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n
/10 changes the de-fault panel func-tion from
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[]\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for
the de-fault panel func-tion
[2824]
[2825]
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[] \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite
= TRUE),[]
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[] \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite
= TRUE),[]
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[] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
= TRUE),[]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[]
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[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when []\T1/
pcr/m/n/10 x []\T1/ptm/m/n/10 is a ma-trix.
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[]\T1/pcr/m/n/10 row.values []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 column.values
[]\T1/ptm/m/n/10 must have the same lengths as
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[]\T1/pcr/m/n/10 allow.multiple[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 outer[]\T1/p
tm/m/n/10 , []\T1/pcr/m/n/10 auto.key[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 prepan
el[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 strip[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10
groups[]\T1/ptm/m/n/10 ,
[2828]
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pdfTeX warning (ext4): destination with the same identifier (name{Rfn.parallel}
) has been already used, duplicate ignored
<to be read again>
\relax
l.3506 \aliasA{parallel}{B\_08\_splom}{parallel}
[2831]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[]
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[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[]
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[]\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x)))
[2837]
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[]\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault
set-tings by
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\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
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[] \T1/pcr/m/n/10 symbol = palette.colors(palette = "Okabe-Ito")
[c(6, 2, 4, 7, 3, 5, 8)],[]
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[] \T1/pcr/m/n/10 region = hcl.colors(14, palette = "YlGnBu", re
v = TRUE),[]
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[] \T1/pcr/m/n/10 reference = "gray90", bg = "transparent", fg = "
black",[]
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[] \T1/pcr/m/n/10 strip.bg = rep("gray95", 7), strip.fg = rep("gra
y70", 7),[]
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[]\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict
= FALSE)
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[]\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un-
spec-i-fied in
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[]\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i
s-sued when
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[]\T1/pcr/m/n/10 theme[]\T1/ptm/m/n/10 ). These are used to mod-ify the cur-ren
t set-tings (ob-tained by
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[]\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in []\T1/pcr/m/n/10 trell
is.settings []\T1/ptm/m/n/10 has not been fi-nal-ized,
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\T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca
n be ob-tained by
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[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. []\T1/pcr/m/n/10 col []\T1/ptm/m/n/
10 is used for com-po-nents []\T1/pcr/m/n/10 "plot.symbol"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 "plot.line"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "plot.polygon"[
]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "superpose.symbol"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 "superpose.line"[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 "super
pose.polygon"[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 col.points
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[]\T1/ptm/m/n/10 over-rides []\T1/pcr/m/n/10 col[]\T1/ptm/m/n/10 , but is used
only for []\T1/pcr/m/n/10 "plot.symbol" []\T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/10 "superpose.symbol"[]\T1/ptm/m/n/10 . Sim-i-larly, []\T1/pcr/m/
n/10 col.line []\T1/ptm/m/n/10 over-rides []\T1/pcr/m/n/10 col []\T1/ptm/m/n/10
for
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[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents []\T1/pcr/m/n/10 pl
ot.symbol[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 plot.polygon[]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents []\T1/pcr/m/n/10
plot.polygon []\T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/10 auto.key[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 aspect[]\T1/ptm/m/
n/10 , []\T1/pcr/m/n/10 between[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 grid[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 skip[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 strip[]\T1/
ptm/m/n/10 , []\T1/pcr/m/n/10 xscale.components[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
= "Height")[]
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[]\T1/pcr/m/n/10 main[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 page[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 par.strip.text[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 prepanel[]\
T1/ptm/m/n/10 , []\T1/pcr/m/n/10 scales[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 skip
[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 strip[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 xscale.components[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 yscale.co
mponents[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 axis[]\T1/ptm/m/n/10 , []\T1/pcr/m/
n/10 par.settings[]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 trellis[]\T1/ptm/m/n/10 ,
by de-fault plot-ted by []\T1/pcr/m/n/10 print.trellis[]\T1/ptm/m/n/10 .
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[]\T1/pcr/m/n/10 plot.shingle []\T1/ptm/m/n/10 dis-plays the ranges of shin-gle
s via rect-an-gles. []\T1/pcr/m/n/10 print.shingle []\T1/ptm/m/n/10 and
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[][][]\T1/pcr/m/n/10 Lattice[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 draw.
key[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 trellis.par.get[][][][]\T1/ptm
/m/n/10 , and [][][]\T1/pcr/m/n/10 xyplot[][][][]\T1/ptm/m/n/10 , specif-i-call
y the en-try for
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[] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[]
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[] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[]
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[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.
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[]\T1/pcr/m/n/10 horizontal=FALSE []\T1/ptm/m/n/10 is use-ful for strips on the
left of pan-els us-ing
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[]\T1/pcr/m/n/10 strip.default []\T1/ptm/m/n/10 is called for its side-effect,
which is to draw a strip ap-pro-pri-ate for
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[2864]
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[]\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[]
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[]\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[]
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[]\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[]
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[]\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[]
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[] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[]
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[] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[]
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[] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[]
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[] \T1/pcr/m/n/10 prefix = pre
fix),[]
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[] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[]
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[] \T1/pcr/m/n/10 prefix = pre
fix),[]
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[] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[]
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[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of
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[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
De-faults to
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\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 trellis.focus[]\T1/ptm/m/n/10 , the de-faul
t is []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 in in-ter-ac-tive mode, and
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[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 panel.identify.qqmath[]\T1/ptm/m/n/10 , e
x-tra pa-ram-e-ters are passed on to
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[]\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 trellis.switchFocus[]\T1/ptm/m/n/10 , the
se are used (in com-bi-na-tion with
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[][][]\T1/pcr/m/n/10 identify[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Latt
ice[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.trellis[][][][]\T1/ptm/m
/n/10 , [][][]\T1/pcr/m/n/10 trellis.currentLayout[][][][]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
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[2873]
Underfull \hbox (badness 3601) in paragraph at lines 6472--6477
[]\T1/ptm/m/n/10 Creates Box and Whisker plot of []\T1/pcr/m/n/10 x []\T1/ptm/m
/n/10 for ev-ery level of []\T1/pcr/m/n/10 y []\T1/ptm/m/n/10 (or the other way
round
Underfull \hbox (badness 2486) in paragraph at lines 6472--6477
\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 horizontal=FALSE[]\T1/ptm/m/n/10 ). By de-fa
ult, the ac-tual box-plot statis-tics are cal-cu-lated us-ing
[2874]
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[] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[]
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[2876]
[2877]
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[]\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The
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[]\T1/ptm/m/n/10 numeric, be-tween 0 and 1, giv-ing a min-i-mum sat-u-ra-tion i
n
[2878]
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[] \T1/pcr/m/n/9 shade.colors.palette = makeShadePalette(hcl.colors(1
0, "Inferno"),[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6861--6861
[] \T1/pcr/m/n/9 shade.colors.palette = makeShadePalette(hcl.colors(1
0, "Dark Mint"),[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6864--6864
[] \T1/pcr/m/n/9 shade.colors.palette = makeShadePalette(hcl.colors(1
0, "Harmonic"),[]
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[2880]
[2881]
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[2883]
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[]\T1/pcr/m/n/10 panel.levelplot.raster []\T1/ptm/m/n/10 is an al-ter-na-tive p
anel func-tion that uses the raster draw-
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\T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more
ef-fi-cient. When us-ing
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[2885]
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[] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels =
NULL,[]
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[]\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments
to
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[]\T1/pcr/m/n/10 diag.panel.splom []\T1/ptm/m/n/10 to know what ar-gu-ments thi
s func-tion is passed
[2886]
[2887]
Underfull \hbox (badness 10000) in paragraph at lines 7435--7438
\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 diag.panel []\T1/ptm/m/n/10 from []\T1/pcr/
m/n/10 panel.pairs[]\T1/ptm/m/n/10 . Cur-rently ig-nored by
Overfull \hbox (101.58032pt too wide) in paragraph at lines 7460--7460
[] \T1/pcr/m/n/9 function(i,j) hcl.colors(11)[i+j-1]) ## rainbow(
11, start=.12, end=.5)[i+j-1])[]
[2888]
[2889]
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[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2890]
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[] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[]
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[2892]
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[]\T1/pcr/m/n/10 "lm" []\T1/ptm/m/n/10 adds a lin-ear re-gres-sion line (same a
s [][][]\T1/pcr/m/n/10 panel.lmline[][][][]\T1/ptm/m/n/10 , ex-cept
Underfull \hbox (badness 1163) in paragraph at lines 7836--7844
\T1/ptm/m/n/10 for de-fault graph-i-cal pa-ram-e-ters). []\T1/pcr/m/n/10 "loess
" []\T1/ptm/m/n/10 adds a loess fit (same as
[2893]
Underfull \hbox (badness 2772) in paragraph at lines 7859--7862
[]\T1/ptm/m/n/10 Most gen-er-ally, []\T1/pcr/m/n/10 grid []\T1/ptm/m/n/10 can b
e a list of ar-gu-ments to be sup-plied to
[2894]
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[] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
= c(1/6, 4/6)),[]
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[] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[]
[2895]
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[] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[]
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[] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ide
ntifier, name.type)[]
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[2896]
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[]\T1/pcr/m/n/10 col[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 alpha[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 lty[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lwd[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 fill[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pch[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 cex[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lineheight[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 font[]\T1/ptm/m/n/10 ,
[2897]
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[]\T1/pcr/m/n/9 xyplot(y ~ x, d, panel = panel.rect, col = 4, alpha = 0.5, wid
th = 0.1, height = 0.1)[]
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[]\T1/pcr/m/n/9 xyplot(y ~ x, d, panel = panel.polygon, col = 4, alpha = 0.5,
rule = "evenodd")[]
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[]\T1/pcr/m/n/9 ## Example adapted from https://journal.r-project.org/articles
/RJ-2012-017/[]
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[]\T1/pcr/m/n/9 xyplot(y ~ x, data = d, panel = panel.polygon, rule = "none",
col = "grey")[]
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[]\T1/pcr/m/n/9 xyplot(y ~ x, data = d, panel = panel.polypath, rule = "windin
g", col = "grey")[]
[2898]
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[]\T1/pcr/m/n/9 xyplot(y ~ x, data = d, panel = panel.polypath, rule = "evenod
d", col = "grey")[]
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[]\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[]
[2899]
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[]\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c
al pa-ram-e-ters for
[2900]
[2901]
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[] \T1/pcr/m/n/9 panel.superpose(x, y, ..., panel.groups = panel.ave
rage, grid = FALSE,[]
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[] \T1/pcr/m/n/9 args = list(mean = mean(x), sd
= sd(x)), ...)[]
[2902]
[2903]
[2904]
[2905]
[2906]
[2907]
Underfull \hbox (badness 10000) in paragraph at lines 8878--8881
[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to []\T1/pcr/m/n/10 panel.super
pose
Underfull \hbox (badness 10000) in paragraph at lines 8878--8881
[]\T1/ptm/m/n/10 from []\T1/pcr/m/n/10 panel.superpose.2[]\T1/ptm/m/n/10 , and
to []\T1/pcr/m/n/10 panel.groups []\T1/ptm/m/n/10 from
[2908]
[2909]
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[]\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[]
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[]\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[]
[2910]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 9066--9066
[]\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[]
Underfull \hbox (badness 3118) in paragraph at lines 9085--9088
[]\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. []\T1/pcr/m/n/10 type [
]\T1/ptm/m/n/10 has a dif-fer-ent mean-ing in
[2911]
Underfull \hbox (badness 1515) in paragraph at lines 9160--9164
[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2912]
[2913]
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[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2914]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 9376--9376
[] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[]
[2915]
[2916]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9515--9515
[]\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[]
[2917]
Underfull \hbox (badness 1028) in paragraph at lines 9574--9578
\T1/pcr/m/n/10 condition []\T1/ptm/m/n/10 for 2-D, and []\T1/pcr/m/n/10 left, r
ight.x, right.y, left.name, right.x.name,
[2918]
[2919]
[2920]
[2921]
[2922]
[2923]
[2924]
Underfull \hbox (badness 7238) in paragraph at lines 10018--10022
[]\T1/ptm/m/n/10 Factor with lev-els []\T1/pcr/m/n/10 "Svansota"[]\T1/ptm/m/n/1
0 , []\T1/pcr/m/n/10 "No. 462"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Manchuria"[]
\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "No. 475"[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 10018--10022
[]\T1/pcr/m/n/10 "Velvet"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Peatland"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "Glabron"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "No. 4
57"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Wisconsin No. 38"[]\T1/ptm/m/n/10 ,
[2925]
[2926]
[2927]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma}
) has been already used, duplicate ignored
<to be read again>
\relax
l.10249 \aliasA{melanoma}{H\_melanoma}{melanoma}
[2928]
[2929]
[2930]
Underfull \hbox (badness 10000) in paragraph at lines 10411--10416
\T1/pcr/m/n/10 diseases[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Diabetes[]\T1/ptm/m/
n/10 , []\T1/pcr/m/n/10 Flu and pneumonia[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 He
art disease[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Lower
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[] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list(
columns = 2),[]
[2931]
[2932]) (./mgcv-pkg.tex
Chapter 24.
[2933]
[2934]
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[]\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,
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[] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret
e=FALSE,[]
[2935]
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[] \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in
tercept=NULL,[]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known
scale.
[2936]
[2937]
[2938]
[2939]
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[][][]\T1/pcr/m/n/10 mgcv.parallel[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gamObject[][][][]\T1
/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/ptm/m/n/10 , [][][]\T1
/pcr/m/n/10 smooth.terms[][][][]\T1/ptm/m/n/10 ,
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[][][]\T1/pcr/m/n/10 linear.functional.terms[][][][]\T1/ptm/m/n/10 , [][][]\T1/
pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][] [][]predict.
gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10
,
Underfull \hbox (badness 10000) in paragraph at lines 382--389
[][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 g
am.side[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.selection[][][][]\T1/p
tm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][][]\T1/ptm
/m/n/10 ,
[2940]
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[]\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2
,bs=bs,k=k)+[]
[2941]
[2942]
[2943]
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[]\T1/ptm/m/n/10 The link func-tion: one of []\T1/pcr/m/n/10 "logit"[]\T1/ptm/m
/n/10 , []\T1/pcr/m/n/10 "probit"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cloglog"
[]\T1/ptm/m/n/10 and
[2944]
[2945]
Underfull \hbox (badness 1406) in paragraph at lines 707--708
[]\T1/ptm/m/n/10 The MKL BLAS is mut-lithreaded by de-fault. Un-der linux set-t
ing en-vi-ron-ment vari-able
[2946]
[2947]
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[]\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe
n us-ing pe-nal-ized re-gres-sion
[2948]
Underfull \hbox (badness 1259) in paragraph at lines 880--881
[]\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro
-duc-tion with R (2nd edi-tion).
[2949]
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[2950]
[2951]
[2952]
[2953]
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[2955]
[2956]
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[2958]
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[]\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$
q^.5),col=2)[]
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[]\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[]
[2959]
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[] \T1/pcr/m/n/9 plot(b$y[oy],rs[oy,ii[1]],ylim=c(-3,3),type="l",ylab="scor
e residuals",[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1453--1453
[]\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor
+rx+obstruct[]
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[]\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in
d]),type="l",[]
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[] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind])
,lwd=2,col=i)[]
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[]\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights=
d,data=surv)[]
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[] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid),
initial = 0,[]
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[] \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][
nrow(um)] <- 1[]
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[]\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter
polate to te[]
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[]\T1/pcr/m/n/9 bd <- bam(y~s(x0)+ s(x1) + s(x1,fac,bs="sz",k=5)+s(x2,k=20),di
screte=TRUE)[]
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[]\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE)
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[]\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,[]
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[]\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][][]\T1/pcr/m/n
/10 formula.gam[][][] []\T1/ptm/m/n/10 and also
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known
scale.
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[]\T1/ptm/m/n/10 A list spec-i-fy-ing the neigh-bour-hood struc-ture for [][][]
\T1/pcr/m/n/10 NCV[][][][]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 a []\T1/ptm/m/n/10
is the vec-tor
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[]\T1/ptm/m/n/10 gives the points dropped for the neigh-bour-hood []\T1/pcr/m/n
/10 j[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 d []\T1/ptm/m/n/10 is the vec-tor
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\T1/ptm/m/n/10 of in-dices of points to pre-dict, with cor-re-spond-ing end-poi
nts []\T1/pcr/m/n/10 md[]\T1/ptm/m/n/10 . So
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\T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v
en-tion mech-a-nism de-scribed in
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[][][]\T1/pcr/m/n/10 mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
gamObject[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/pt
m/m/n/10 , [][][]\T1/pcr/m/n/10 smooth.terms[][][][]\T1/ptm/m/n/10 ,
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[][][]\T1/pcr/m/n/10 linear.functional.terms[][][][]\T1/ptm/m/n/10 , [][][]\T1/
pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][] [][]predict.
gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10
,
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[][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 g
am.side[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.selection[][][][]\T1/p
tm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][][]\T1/ptm
/m/n/10 ,
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[]\T1/pcr/m/n/10 gam.control(nthreads=1,ncv.threads=1,irls.reg=0.0,epsilon = 1
e-07,
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[] \T1/pcr/m/n/10 maxit = 200,mgcv.tol=1e-7,mgcv.half=15, trace = F
ALSE,[]
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[] \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco
l(x)),[]
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[] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol
(x)),[]
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[] \T1/pcr/m/n/10 pearson.extra=0,dev.extra=0,n.true=-1,Sl=NULL,nei=NU
LL,...)[]
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[]\T1/ptm/m/n/10 Random ef-fects can be added to []\T1/pcr/m/n/10 gam []\T1/ptm
/m/n/10 mod-els us-ing []\T1/pcr/m/n/10 s(...,bs="re") []\T1/ptm/m/n/10 terms (
see
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[]\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[]
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[]\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix
ed penalty, if
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[] \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i
d=1)+s(x1,id=1)+[]
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[]\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0,
d1b = 0,
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[3023]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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[]\T1/ptm/m/n/10 In the event of []\T1/pcr/m/n/10 lme []\T1/ptm/m/n/10 con-ver-
gence fail-ures, con-sider mod-i-fy-ing
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[][][]\T1/pcr/m/n/10 magic[][][] []\T1/ptm/m/n/10 for an al-ter-na-tive for cor
-re-lated data, [][][]\T1/pcr/m/n/10 te[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m
/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.gam[][][][]\T1/ptm
/m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10 ,
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[][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 n
egbin[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 vis.gam[][][][]\T1/ptm/m/n/1
0 ,[][][]\T1/pcr/m/n/10 pdTens[][][][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 gamm4 [
]\T1/ptm/m/n/10 ( [][]$\T1/pcr/m/n/10 https : / / cran . r-[]project .
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[]\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see []
[][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 ar-gu-ment
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[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
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[]\T1/pcr/m/n/10 ginla(G,A=NULL,nk=16,nb=100,J=1,interactive=FALSE,integ=0,app
rox=0)
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[]\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by []\T1/pcr/m/n/10 gam(..
.,fit=FALSE) []\T1/ptm/m/n/10 or
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[] \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d
ata. A simple[]
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[] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j]
,lty=lty[j])[]
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[] \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo
r comparison[]
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[] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r
norm(100)*.4[]
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[]\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n
a.action,
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[]\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona
lize=FALSE)[]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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[]\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999,
all.derivs=FALSE)
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[]\T1/pcr/m/n/10 lp(c,A,b,C=NULL,d=NULL,Bi=NULL,maxit=max(1000, nrow(A) * 10),
phase1 = FALSE)
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[]\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
to rule the world.",[]
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[] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[]
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[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
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[]\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt
ion with bam...[]
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[]\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate
d covariates[]
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[] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]]
,na.rm=TRUE)[]
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[]\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: []\T1/pcr/m/n/10 Dim
.pdIndot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 coef.pdIdnot[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 corMatrix.pdIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 logDet.pd
Idnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdConstruct.pdIdnot[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 pdFactor.pdIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdMatrix.p
dIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 solve.pdIdnot[]\T1/ptm/m/n/10 , []\T1
/pcr/m/n/10 summary.pdIdnot[]\T1/ptm/m/n/10 .
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[]\T1/ptm/m/n/10 These func-tions ([]\T1/pcr/m/n/10 pdTens[]\T1/ptm/m/n/10 , []
\T1/pcr/m/n/10 pdConstruct.pdTens[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdFactor.p
dTens[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 pdMatrix.pdTens[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 coef.pdTens
[]\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 summary.pdTens[]\T1/ptm/m/n/10 ) would n
ot nor-mally be
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[]\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s
cale=-1,[]
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[] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi
ds=FALSE,[]
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[]\T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion
is some-times to clone the
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[] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,gc.level=0,...)[]
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[]\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 type=="terms" []\T1/ptm/m/n/10 or []\T1/pc
r/m/n/10 type="iterms" []\T1/ptm/m/n/10 then terms (smooth or para-
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[] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL
L,...)[]
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[]\T1/pcr/m/n/9 x1 <- seq(.2,.8,length=m1);x2 <- seq(.2,.8,length=m2) ## margi
nal grid points[]
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[]\T1/pcr/m/n/9 df <- data.frame(x0=rep(.5,n),x1=rep(x1,m2),x2=rep(x2,each=m1)
,x3=rep(0,n))[]
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[] \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s
mooth deriv i[]
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are
as for
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[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are
as for
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[]\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from
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[][][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][][]\T1/ptm/m/n/10 , al
-though el-e-ments []\T1/pcr/m/n/10 X []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 S [
]\T1/ptm/m/n/10 are not needed,
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[]\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion
cri-te-rion re-ported is one of GCV,
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[]\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef-
fects in a GAM in the same
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\T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre
s-sion terms. This method
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\T1/ptm/m/n/10 can be used with [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10
by mak-ing use of []\T1/pcr/m/n/10 s(...,bs="re") []\T1/ptm/m/n/10 terms in a
model: see
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[]\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the []\T1/pcr/m/n
/10 paraPen []\T1/ptm/m/n/10 ar-gu-ment to [][][]\T1/pcr/m/n/10 gam[][][] []\T1
/ptm/m/n/10 can be used:
Underfull \hbox (badness 5862) in paragraph at lines 11584--11587
\T1/ptm/m/n/10 see [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/ptm/m/n/10 . If s
mooth-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g.
[3134]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11650--11650
[]\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11660--11660
[]\T1/pcr/m/n/9 ## The effect of the new factor levels (or any interaction inv
olving them)[]
[3135]
Underfull \hbox (badness 10000) in paragraph at lines 11691--11694
[]\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of []\T1/pcr/m/n/
10 "deviance"[]\T1/ptm/m/n/10 ,
[3136]
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[3138]
[3139]
[3140]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 11993--11993
[]\T1/pcr/m/n/10 s(..., k=-1,fx=FALSE,bs="tp",m=NA,by=NA,xt=NULL,id=NULL,sp=NU
LL,pc=NULL)
[3141]
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Overfull \hbox (9.78043pt too wide) in paragraph at lines 12366--12366
[] \T1/pcr/m/n/9 true <- mu + (del * sigma) * sinh((1/del) * asinh(qnorm(qq))
+ (eps/del))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12380--12380
[]\T1/pcr/m/n/9 b <- gam(list(accel~s(times, k=20, bs = "ad"), ~s(times, k = 1
0), ~1, ~1),[]
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[]\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to
model ma-trix X, or, if
Overfull \hbox (36.78088pt too wide) in paragraph at lines 12491--12491
[]\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE,
cov = TRUE,[]
[3149]
Underfull \hbox (badness 10000) in paragraph at lines 12508--12512
[]\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 inverse==TRUE []\T1/ptm/m/n/10 and []\T1/p
cr/m/n/10 both.sides==FALSE []\T1/ptm/m/n/10 then the re-
Underfull \hbox (badness 10000) in paragraph at lines 12548--12552
[]\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 inverse==TRUE []\T1/ptm/m/n/10 and []\T1/p
cr/m/n/10 both.sides==FALSE []\T1/ptm/m/n/10 then the re-
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[]\T1/pcr/m/n/10 Sl.setup(G,cholesky=FALSE,no.repara=FALSE,sparse=FALSE,keepS=
FALSE)
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[3152]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 12695--12695
[] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$
vectors[,ind]))[]
Underfull \hbox (badness 1975) in paragraph at lines 12706--12711
[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[3153]
Underfull \hbox (badness 1803) in paragraph at lines 12783--12787
\T1/ptm/m/n/10 The last en-try will be the []\T1/pcr/m/n/10 by []\T1/ptm/m/n/10
vari-able, if []\T1/pcr/m/n/10 object$by []\T1/ptm/m/n/10 is not []\T1/pcr/m/n
/10 "NA"[]\T1/ptm/m/n/10 .
Underfull \hbox (badness 1502) in paragraph at lines 12795--12807
[]\T1/pcr/m/n/10 cs.smooth.spec []\T1/ptm/m/n/10 (cu-bic re-gres-sion splines w
ith shrinkage-to-zero); []\T1/pcr/m/n/10 cc.smooth.spec
[3154]
Underfull \hbox (badness 2401) in paragraph at lines 12812--12816
[]\T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able
. Plot meth-ods can be
Underfull \hbox (badness 2970) in paragraph at lines 12812--12816
\T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for []\T1/pc
r/m/n/10 mgcv:::plot.sos.smooth[]\T1/ptm/m/n/10 ,
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Underfull \hbox (badness 6876) in paragraph at lines 13007--13013
[][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use adap-tive smooths of on
e or two vari-ables, spec-i-fied via terms like
[3158]
Underfull \hbox (badness 10000) in paragraph at lines 13048--13049
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
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[3160]
Underfull \hbox (badness 10000) in paragraph at lines 13166--13167
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 13220--13220
[] \T1/pcr/m/n/9 b <- gam(y~s(x0,bs=bs,m=c(4,2))+s(x1,bs=bs)+s(x2,k=15,bs=bs,
m=c(4,3,0))+[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13232--13232
[] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5,
1.5) (black)[]
[3162]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13244--13244
[] \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions
and intervals[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13249--13249
[] \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i
ntervals away[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13255--13255
[] \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w
ild and wide[]
Overfull \hbox (3.70428pt too wide) in paragraph at lines 13256--13256
[] \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/cmtt/m/n/9 `\T1
/pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[]
[3163]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
Underfull \hbox (badness 10000) in paragraph at lines 13325--13327
\T1/ptm/m/n/10 term []\T1/pcr/m/n/10 s(...,bs="cr",...)[]\T1/ptm/m/n/10 , []\T1
/pcr/m/n/10 s(...,bs="cs",...) []\T1/ptm/m/n/10 or
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[3165]
Underfull \hbox (badness 10000) in paragraph at lines 13455--13456
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
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[3167]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13536--13536
[]\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data) ## first
deriv penalty[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13537--13537
[]\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi
ed 2nd deriv[]
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[3169]
Underfull \hbox (badness 10000) in paragraph at lines 13690--13691
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
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[3174]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13940--13940
[]\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[]
[3175]
Underfull \hbox (badness 10000) in paragraph at lines 14001--14003
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
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[3177]
Underfull \hbox (badness 10000) in paragraph at lines 14160--14163
[]\T1/ptm/m/n/10 For the []\T1/pcr/m/n/10 smooth.construct []\T1/ptm/m/n/10 met
hod a smooth spec-i-fi-ca-tion ob-
Underfull \hbox (badness 3312) in paragraph at lines 14160--14163
\T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term []\T1/pcr/m/n/10 s(x,...,bs
="re",)[]\T1/ptm/m/n/10 . For the
Underfull \hbox (badness 7099) in paragraph at lines 14160--14163
[]\T1/pcr/m/n/10 predict.Matrix []\T1/ptm/m/n/10 method an ob-ject of class []\
T1/pcr/m/n/10 "random.effect"
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[3179]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 14246--14246
[]\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with
2 variances[]
[3180]
Underfull \hbox (badness 10000) in paragraph at lines 14291--14297
[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a
Underfull \hbox (badness 7832) in paragraph at lines 14291--14297
[]\T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) []\T1/ptm/m/n/10 term in a
[]\T1/pcr/m/n/10 gam []\T1/ptm/m/n/10 for-
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[3182]
[3183]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 14506--14506
[]\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[]
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[3185]
Underfull \hbox (badness 10000) in paragraph at lines 14609--14617
[][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths on th
e sphere, via terms like
Underfull \hbox (badness 10000) in paragraph at lines 14635--14636
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
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[3188]
Underfull \hbox (badness 7613) in paragraph at lines 14780--14783
[]\T1/ptm/m/n/10 method an ob-ject of class []\T1/pcr/m/n/10 "sz.interaction" [
]\T1/ptm/m/n/10 pro-duced by the
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[]\T1/ptm/m/n/10 The terms can have a smooth-ing pa-ram-e-ter per smooth, or a
sin-gle smooth-ing pa-ram-e-
Overfull \hbox (128.58029pt too wide) in paragraph at lines 14847--14847
[]\T1/pcr/m/n/9 b <- gam(y ~ s(x)+s(f1,x,bs="sz")+s(f2,x,bs="sz")+s(f1,f2,x,bs
="sz",id=1),data=dat,method="REML")[]
[3190]
[3191]
[3192]
Underfull \hbox (badness 3396) in paragraph at lines 14993--14996
[][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths of an
y num-ber of vari-ables, spec-i-fied via terms like
Underfull \hbox (badness 10000) in paragraph at lines 15038--15040
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
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[3198]
Underfull \hbox (badness 10000) in paragraph at lines 15329--15331
[]\T1/pcr/m/n/10 bs="fs" []\T1/ptm/m/n/10 A spe-cial smoother class (see
[3199]
Underfull \hbox (badness 10000) in paragraph at lines 15363--15367
[][][]\T1/pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][][]\
T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 t2[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m
/n/10 tprs[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Duchon.spline[][][][]\T
1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cubic.regression.spline[][][][]\T1/ptm/m/n/
10 ,
Underfull \hbox (badness 10000) in paragraph at lines 15363--15367
[][][]\T1/pcr/m/n/10 p.spline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 d.sp
line[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 mrf[][][][]\T1/ptm/m/n/10 , [
][][]\T1/pcr/m/n/10 soap[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Spherical
.Spline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 adaptive.smooth[][][][]\T1
/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 15363--15367
[][][]\T1/pcr/m/n/10 user.defined.smooth[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/
m/n/10 smooth.construct.re.smooth.spec[][][][]\T1/ptm/m/n/10 ,
[3200]
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[3204]
Underfull \hbox (badness 2158) in paragraph at lines 15652--15652
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[3205]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 15731--15731
[]\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[]
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[3207]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 15865--15865
[] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[]
[3208]
[3209]
Underfull \hbox (badness 4846) in paragraph at lines 15996--15999
[]\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or
es-ti-ma-tors if
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[3211]
[3212]
[3213]
[3214]
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[]\T1/pcr/m/n/10 vcov(object, sandwich=FALSE, freq = FALSE, dispersion = NULL,
unconditional=FALSE, ...)[]
[3230]
Underfull \hbox (badness 1715) in paragraph at lines 17242--17243
[]\T1/ptm/m/n/10 Basically, just ex-tracts []\T1/pcr/m/n/10 object$Ve[]\T1/ptm/
m/n/10 , []\T1/pcr/m/n/10 object$Vp []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 object
$Vc []\T1/ptm/m/n/10 (if avail-able) from a
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[3232]
[3233]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 17433--17433
[]\T1/pcr/m/n/10 XWXd(X,w,k,ks,ts,dt,v,qc,nthreads=1,drop=NULL,ar.stop=-1,ar.r
ow=-1,ar.w=-1,
Overfull \hbox (48.78088pt too wide) in paragraph at lines 17435--17435
[]\T1/pcr/m/n/10 XWyd(X,w,y,k,ks,ts,dt,v,qc,drop=NULL,ar.stop=-1,ar.row=-1,ar.
w=-1,lt=NULL)[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17437--17437
[]\T1/pcr/m/n/10 diagXVXd(X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,rt=
NULL)[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 17438--17438
[]\T1/pcr/m/n/10 ijXVXd(i,j,X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,r
t=NULL)[]
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[]\T1/ptm/m/n/10 Negative to ig-nore. Oth-er-wise sum rows
Underfull \hbox (badness 1668) in paragraph at lines 17458--17459
[]\T1/pcr/m/n/10 (ar.stop[i-1]+1):ar.stop[i] []\T1/ptm/m/n/10 of the rows se-le
cted by []\T1/pcr/m/n/10 ar.row
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[3237]
[3238]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 17656--17656
[]\T1/pcr/m/n/9 ## 1. If the zero inflation rate becomes decoupled from the li
near predictor,[]
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[]\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun
ded in regions[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17669--17669
[]\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[]
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[3241]) (./nlme-pkg.tex
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Chapter 25.
[3243]
Underfull \hbox (badness 1009) in paragraph at lines 78--87
[]\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served
- fit-ted) are used; else, if
[3244]
Underfull \hbox (badness 1009) in paragraph at lines 168--177
[]\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served
- fit-ted) are used; else, if
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[3246]
[3247]
[3248]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 448--448
[] \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[]
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[3250]
[3251]
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[]\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 251-254 ---------------------------
---------------[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 605--605
[]\T1/pcr/m/n/9 # Compare an "lme" object with a "gls" object (test would be n
on-sensical!)[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 608--608
[]\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 222-225 ---------------------------
---------------[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 615--615
[]\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 352-365 ---------------------------
---------------[]
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[3257]
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[] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil
lary fissure"),[]
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[3260]
Underfull \hbox (badness 5446) in paragraph at lines 1140--1142
[]\T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel
.htm[]\T1/ptm/m/n/10 ', the first edi-tion of
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[3267]
Underfull \hbox (badness 10000) in paragraph at lines 1617--1620
[][][]\T1/pcr/m/n/10 lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fixed.
effects.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 ranef.lmList[][][][
]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.ranef.lmList[][][][]\T1/ptm/m/n/10
,
Underfull \hbox (badness 3780) in paragraph at lines 1634--1636
[]\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a
ted with each com-po-nent of the
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[3272]
Underfull \hbox (badness 2042) in paragraph at lines 1975--1981
\T1/ptm/m/n/10 is in-ner to the []\T1/pcr/m/n/10 displayLevel []\T1/ptm/m/n/10
group-ing fac-tor. If equal to []\T1/pcr/m/n/10 TRUE[]\T1/ptm/m/n/10 ,
[3273]
[3274]
Underfull \hbox (badness 1132) in paragraph at lines 2127--2129
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
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[3276]
Underfull \hbox (badness 4168) in paragraph at lines 2238--2244
[][][]\T1/pcr/m/n/10 ACF.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corAR
MA[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/1
0 , [][][]\T1/pcr/m/n/10 Dim.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m
/n/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 ,
[3277]
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[] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[]
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[3283]
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Underfull \hbox (badness 10000) in paragraph at lines 2816--2820
[][][]\T1/pcr/m/n/10 corFactor[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cor
Matrix.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 recalc.corStruct[
][][][]\T1/ptm/m/n/10 ,
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Underfull \hbox (badness 6493) in paragraph at lines 3548--3556
[][][]\T1/pcr/m/n/10 corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corGau
s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corLin[][][][]\T1/ptm/m/n/10 , [
][][]\T1/pcr/m/n/10 corRatio[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corSp
her[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][][]\T
1/ptm/m/n/10 ,
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[][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/p
cr/m/n/10 getCovariate.data.frame[][][][]\T1/ptm/m/n/10 ,
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Underfull \hbox (badness 10000) in paragraph at lines 5540--5543
[][][]\T1/pcr/m/n/10 getGroups.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/
m/n/10 getGroups.data.frame[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 getGro
ups.gls[][][][]\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 covariance ma-trix, ei-ther []\T1/pcr/m/n/10 "random.effects" []
\T1/ptm/m/n/10 for the random-effects
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[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in [
]\T1/pcr/m/n/10 model[]\T1/ptm/m/n/10 ,
[3338]
Underfull \hbox (badness 2057) in paragraph at lines 6194--6205
[][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gl
sControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 glsObject[][][][]\T1/ptm/
m/n/10 , [][][]\T1/pcr/m/n/10 glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m
/n/10 plot.gls[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.gls[][][][]
\T1/ptm/m/n/10 ,
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Underfull \hbox (badness 10000) in paragraph at lines 6258--6260
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
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[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in [
]\T1/pcr/m/n/10 model[]\T1/ptm/m/n/10 ,
[3344]
Underfull \hbox (badness 10000) in paragraph at lines 6602--6608
[][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gn
lsControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gnlsObject[][][][]\T1/pt
m/m/n/10 , [][][]\T1/pcr/m/n/10 gnlsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc
r/m/n/10 predict.gnls[][][][]\T1/ptm/m/n/10 ,
Overfull \hbox (54.78088pt too wide) in paragraph at lines 6629--6629
[]\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min
Scale = 0.001,
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Underfull \hbox (badness 10000) in paragraph at lines 6667--6669
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
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Underfull \hbox (badness 10000) in paragraph at lines 6936--6943
[][][]\T1/pcr/m/n/10 formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gappl
y[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gsummary[][][][]\T1/ptm/m/n/10 ,
[][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.nff
GroupedData[][][][]\T1/ptm/m/n/10 ,
[3350]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6954--6954
[] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6959--6959
[]\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted
from object[]
Underfull \hbox (badness 2875) in paragraph at lines 6981--6983
[]\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a []\T1/pcr/m/n/10 gr
oupedData []\T1/ptm/m/n/10 ob-ject or a
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Underfull \hbox (badness 10000) in paragraph at lines 7196--7202
[][][]\T1/pcr/m/n/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr
/m/n/10 Initialize.glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initi
alize.lmeStruct[][][][]\T1/ptm/m/n/10 ,
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Underfull \hbox (badness 1997) in paragraph at lines 7341--7349
[]\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial
-iza-tion and op-ti-
Underfull \hbox (badness 2205) in paragraph at lines 7341--7349
\T1/ptm/m/n/10 miza-tion al-go-rithms used in []\T1/pcr/m/n/10 lme[]\T1/ptm/m/n
/10 . De-faults to []\T1/pcr/m/n/10 list(niterEM=20,
Underfull \hbox (badness 3118) in paragraph at lines 7364--7367
[][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initializ
e.reStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.corStruct[][
][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.varFunc[][][][]\T1/ptm/m/
n/10 ,
[3357]
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[3359]
Underfull \hbox (badness 3354) in paragraph at lines 7574--7576
[]\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when []\T1/pcr/m/n/
10 which []\T1/ptm/m/n/10 is not equal to
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Underfull \hbox (badness 10000) in paragraph at lines 8101--8118
[][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lm
e.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lme.groupedData[][][][]\T
1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lmeControl[][][][]\T1/ptm/m/n/10 , [][][]\T
1/pcr/m/n/10 lmeObject[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8101--8118
[][][]\T1/pcr/m/n/10 lmeStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lmL
ist[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/1
0 , [][][]\T1/pcr/m/n/10 plot.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
predict.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 qqnorm.lme[][][][]\T1/
ptm/m/n/10 ,
[3368]
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[] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data
= TRUE)[]
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[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
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Overfull \hbox (36.78088pt too wide) in paragraph at lines 8418--8418
[]\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni
terEM = 25,
Underfull \hbox (badness 1189) in paragraph at lines 8443--8445
[]\T1/ptm/m/n/10 maximum num-ber of eval-u-a-tions of the ob-jec-tive func-tion
per-mit-ted for
[3373]
Underfull \hbox (badness 10000) in paragraph at lines 8466--8468
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
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[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
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Underfull \hbox (badness 10000) in paragraph at lines 9266--9273
[][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 ,[][][]\T1/pcr/m/n/10 gls[][][][
]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logLik.corStruct[][][][]\T1/ptm/m/n/10 ,
[][][]\T1/pcr/m/n/10 logLik.glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 logLik.lmeStruct[][][][]\T1/ptm/m/n/10 ,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9277--9277
[]\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML")
[3386]
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[3389]
[3390]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Matrix})
has been already used, duplicate ignored
<to be read again>
\relax
l.9628 ...rA{Matrix}{Assign Matrix Values}{Matrix}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Matrix.1}
) has been already used, duplicate ignored
<to be read again>
\relax
l.9628 ...rA{Matrix}{Assign Matrix Values}{Matrix}
[3391]
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[]\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a
s
Underfull \hbox (badness 3108) in paragraph at lines 9692--9695
[]\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive
-definite
Underfull \hbox (badness 2521) in paragraph at lines 9692--9695
\T1/ptm/m/n/10 ma-trix rep-re-sented by []\T1/pcr/m/n/10 object[]\T1/ptm/m/n/10
. Must have the same di-men-sions as
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Overfull \hbox (18.78088pt too wide) in paragraph at lines 10362--10362
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,
[3403]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10366--10366
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,[]
Underfull \hbox (badness 1596) in paragraph at lines 10395--10421
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
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[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,[]
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Overfull \hbox (36.78088pt too wide) in paragraph at lines 10700--10700
[] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
NULL, ...)[]
Underfull \hbox (badness 2213) in paragraph at lines 10711--10716
[]\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][][]\T1/pcr/m/n/10 nlmi
nb[][][] []\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 iter.max[]\T1/ptm/m/n/10 ) or the [
][][]\T1/pcr/m/n/10 nlm[][][]
Underfull \hbox (badness 6961) in paragraph at lines 10733--10737
[]\T1/ptm/m/n/10 a log-i-cal value passed as the []\T1/pcr/m/n/10 trace []\T1/p
tm/m/n/10 to [][][]\T1/pcr/m/n/10 nlminb[][][](.., control=
[3409]
Underfull \hbox (badness 10000) in paragraph at lines 10752--10754
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
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[3413]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 11048--11048
[]\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one*
message instead of one *each*[]
Overfull \hbox (90.78033pt too wide) in paragraph at lines 11049--11049
[]\T1/pcr/m/n/9 mat.class <- class(matrix(1)) # ("matrix", "array") for R >= 4
.0.0; ("matrix" in older R)[]
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[3418]
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Overfull \hbox (25.98041pt too wide) in paragraph at lines 11439--11439
[]\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*))
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Underfull \hbox (badness 6268) in paragraph at lines 11826--11836
[][][]\T1/pcr/m/n/10 pdBlocked[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdC
ompSymm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdDiag[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 pdFactor[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
pdIdent[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 pdMatrix[][][][]\T1/ptm/m/n/10 ,
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Underfull \hbox (badness 10000) in paragraph at lines 12087--12093
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 coef.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdBlocked[][][][]\T1
/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/
pcr/m/n/10 pdConstruct[][][][]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 value []\T1/ptm/m/n/10 is an \T1/ptm/m/it/
10 ini-tial-ized []\T1/pcr/m/n/10 pdMat []\T1/ptm/m/n/10 ob-ject, []\T1/pcr/m/n
/10 object []\T1/ptm/m/n/10 will be con-structed from
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Underfull \hbox (badness 2452) in paragraph at lines 12565--12572
[][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdC
ompSymm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdDiag[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 pdIdent[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
pdNatural[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdSymm[][][][]\T1/ptm/m/
n/10 , [][][]\T1/pcr/m/n/10 reStruct[][][][]\T1/ptm/m/n/10 ,
[3437]
Underfull \hbox (badness 10000) in paragraph at lines 12631--12637
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdFactor[][][][]\T1/p
tm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 pdMatrix.reStruct[][][][]\T1/ptm/m/n/10 ,
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Overfull \hbox (25.98041pt too wide) in paragraph at lines 13220--13220
[]\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*))
[3447]
[3448]
[3449]
[3450]
[3451]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13585--13585
[]\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline =
0, id = 0.05)[]
[3452]
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[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nffGroupe
dData[]\T1/ptm/m/n/10 , rep-re-sent-ing a
[3453]
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[]\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If []\T1/pcr/m/
n/10 TRUE []\T1/ptm/m/n/10 and ei-ther []\T1/pcr/m/n/10 inner
Underfull \hbox (badness 3713) in paragraph at lines 13655--13662
[]\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 innerGroups []\T1/ptm/m/n/10 are non-[]\T1
/pcr/m/n/10 NULL[]\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent []\T1/pcr/m/n/
10 inner
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13712--13712
[]\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
panel,[]
[3454]
Underfull \hbox (badness 10000) in paragraph at lines 13719--13722
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nfnGroupe
dData[]\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 2469) in paragraph at lines 13719--13722
[]\T1/pcr/m/n/10 groupedData []\T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary
co-vari-ate and a sin-gle
[3455]
Underfull \hbox (badness 10000) in paragraph at lines 13827--13830
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nmGrouped
Data[]\T1/ptm/m/n/10 , rep-re-sent-ing a
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Underfull \hbox (badness 10000) in paragraph at lines 13921--13923
[][][]\T1/pcr/m/n/10 groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 c
ollapse.groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.nfnGroupe
dData[][][][]\T1/ptm/m/n/10 ,
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[3463]
[3464]
[3465]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14445--14445
[]\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[]
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fects}) has been already used, duplicate ignored
<to be read again>
\relax
l.15098 ...Extract Random Effects}{random.effects}
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l.15098 ...Extract Random Effects}{random.effects}
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Overfull \hbox (25.98041pt too wide) in paragraph at lines 15734--15734
[]\T1/pcr/m/n/9 plot(Remifentanil, type = "l", lwd = 2) # shows the 65 patient
s\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 remi profiles
[3486]
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[]\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served
- fit-ted) are used; else, if
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[3488]
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[] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[]
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[3490]
[3491]
[3492]
[3493]
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[][][]\T1/pcr/m/n/10 groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 l
me[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/10 , [
][][]\T1/pcr/m/n/10 solve.reStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
summary.reStruct[][][][]\T1/ptm/m/n/10 ,
[3494]
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[] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[]
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[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3502]
[3503]
[3504]
[3505]
[3506]
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\T1/pcr/m/n/10 of an Identity" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pdIdent[]\
T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "General Positive-Definite,
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\T1/pcr/m/n/10 Natural Parametrization" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 p
dNatural[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "General
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\T1/pcr/m/n/10 Positive-Definite" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pdSymm[
]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 data.class(object)
[3507]
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[]\T1/pcr/m/n/10 "Constant plus power of variance
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[]\T1/pcr/m/n/10 "Constant plus proportion of variance
[3508]
[3509]
[3510]
[3511]
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[][][]\T1/pcr/m/n/10 varComb[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varCo
nstPower[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varConstProp[][][][]\T1/p
tm/m/n/10 , [][][]\T1/pcr/m/n/10 varExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m
/n/10 varFixed[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varIdent[][][][]\T1
/ptm/m/n/10 ,
[3512]
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[3514]
[3515]
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[]\T1/pcr/m/n/9 # Generate some synthetic data using the two-component error m
odel and use
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[]\T1/pcr/m/n/9 # overparameterisation in the case of a constant term in the v
ariance function[]
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[3517]
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[3519]
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[3521]
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[][][]\T1/pcr/m/n/10 Variogram.corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n
/10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.co
rLin[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 18153--18163
[][][]\T1/pcr/m/n/10 Variogram.corRatio[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m
/n/10 Variogram.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogr
am.corSpher[][][][]\T1/ptm/m/n/10 ,
[3522]
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
[3523]
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
[3524]
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
[3525]
Underfull \hbox (badness 1577) in paragraph at lines 18373--18375
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 "[][]corR
atio[][][]"[]\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
[3526]
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
Underfull \hbox (badness 10000) in paragraph at lines 18471--18480
[][][]\T1/pcr/m/n/10 corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Va
riogram[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.default[][][][]\
T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.corExp[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 18471--18480
[][][]\T1/pcr/m/n/10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 Variogram.corLin[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.co
rRatio[][][][]\T1/ptm/m/n/10 ,
[3527]
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
[3528]
[3529]
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[]\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served
- fit-ted) are used; else, if
[3530]
[3531]
Underfull \hbox (badness 1009) in paragraph at lines 18788--18797
[]\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served
- fit-ted) are used; else, if
[3532]
[3533]
[3534]
[3535]
[3536]
[3537]
[3538]
[3539]
[3540]) (./nnet-pkg.tex
Chapter 26.
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom}
) has been already used, duplicate ignored
<to be read again>
\relax
l.47 ...t Multinomial Log-linear Models}{multinom}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom.
1}) has been already used, duplicate ignored
<to be read again>
\relax
l.47 ...t Multinomial Log-linear Models}{multinom}
[3541]
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[] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
FALSE,[]
[3542]
[3543]
[3544]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 371--371
[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3545]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 428--428
[]\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c(
0,0,1),50)),[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 431--431
[]\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[]
[3546]
[3547]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 511--511
[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3548]) (./rpart-pkg.tex
Chapter 27.
[3549]
[3550]
[3551]
[3552]
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[]\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse =
TRUE, ...)[]
[3553]
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\T1/ptm/m/n/10 age: []\T1/pcr/m/n/10 pretty = 0 []\T1/ptm/m/n/10 im-plies []\T1
/pcr/m/n/10 minlength = 0L[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pretty = NULL []\
T1/ptm/m/n/10 im-plies
[3554]
[3555]
[3556]
Underfull \hbox (badness 1442) in paragraph at lines 592--598
[]\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 FALSE[]\T1/ptm/m/n/10 , the leaf nodes wil
l be at the hor-i-zon-tal plot co-or-di-nates of
[3557]
[3558]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 738--738
[] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
""),[]
Underfull \hbox (badness 10000) in paragraph at lines 771--775
[]\T1/ptm/m/n/10 Logical. If []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 (de-fault),
adds to the la-bel
Underfull \hbox (badness 1142) in paragraph at lines 771--775
\T1/pcr/m/n/10 #events level1/ #events level2/ \T1/ptm/m/n/10 etc. for method [
]\T1/pcr/m/n/10 class[]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 n
[3559]
[3560]
[3561]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 915--915
[]\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 934--934
[]\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"),[]
[3562]
[3563]
[3564]
[3565]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1180--1180
[]\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m
ethod,
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1181--1181
[] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[]
Underfull \hbox (badness 2846) in paragraph at lines 1243--1245
[]\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the []\T1/pcr/m/n
/10 rpart []\T1/ptm/m/n/10 al-go-rithm. See
[3566]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1287--1287
[]\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the
text is clipped[]
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[]\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c
p = 0.01,
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[] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate
= 2, xval = 10,[]
[3567]
[3568]
[3569]
[3570]
[3571]
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[3573]
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[]\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val-
ues are `[]\T1/pcr/m/n/10 diploid[]\T1/ptm/m/n/10 ',
[3574]
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[] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
FALSE,[]
[3575]
[3576]
[3577]) (./spatial-pkg.tex
[3578]
Chapter 28.
[3579]
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[3581]
[3582]
[3583]
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[3585]
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[3593]
[3594]
[3595]
[3596]
[3597]) (./survival-pkg.tex
[3598]
Chapter 29.
[3599]
[3600]
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[]\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data
= lung, nmin = 1[]
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[]\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2) # Nearly the same, until t
he last point[]
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[]\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a
nd Grambsch.[]
[3601]
[3602]
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[]\T1/ptm/m/n/10 an op-tional list or vec-tor of group-ing el-e-ments, each as
long as
[3603]
[3604]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has
been already used, duplicate ignored
<to be read again>
\relax
l.384 ... Myelogenous Leukemia survival data}{aml}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml.1}) h
as been already used, duplicate ignored
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\relax
l.384 ... Myelogenous Leukemia survival data}{aml}
[3605]
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[]\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da
ta = ovarian)
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[]\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[]
[3606]
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[] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
lung)[]
[3607]
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[]\T1/ptm/m/n/10 If H(t; z) is the pre-dicted cu-mu-la-tive haz-ard for an ob-s
er-va-tion with co-vari-ate vec-tor z,
[3608]
[3609]
[3610]
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[]\T1/pcr/m/n/9 py <- pseudo(survfit(Surv(time, status) ~1, lung), time=730) #
2 year survival
Overfull \hbox (30.78088pt too wide) in paragraph at lines 808--808
[]\T1/pcr/m/n/10 brier(fit, times, newdata, ties = TRUE, detail = FALSE, timef
ix = TRUE,
[3611]
[3612]
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[] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[]
[3613]
[3614]
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[] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[]
[3615]
[3616]
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[]\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi
al and negative-binomial data.
[3617]
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[]\T1/pcr/m/n/9 ppois(4, 10.24153) #chance of seeing 4 or fewer events wit
h large rate[]
[3618]
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[]\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert)
[3619]
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[]\T1/pcr/m/n/9 marginal.model <- coxph(Surv(time, status) ~ rx, data= rats, c
luster=litter,
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colon}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.1407 ...erapy for Stage B/C colon cancer}{colon}
[3620]
[3621]
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[] \T1/pcr/m/n/10 influence=0, ranks = FALSE, reverse=FALSE, timefix=TRUE, ke
epstrata=10, ...)[]
[3622]
[3623]
[3624]
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[]\T1/pcr/m/n/9 options(na.action = na.exclude) # predict all 1384 obs, incl
uding missing[]
[3625]
[3626]
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[]\T1/pcr/m/n/10 cox.zph(fit, transform="km", terms=TRUE, singledf=FALSE, glob
al=TRUE)
[3627]
[3628]
[3629]
[3630]
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[]\T1/ptm/m/n/10 One user mis-take that has re-cently arisen is to slav-ishly f
ol-low the ad-vice of
Underfull \hbox (badness 7486) in paragraph at lines 2145--2150
\T1/ptm/m/n/10 some cod-ing guides and prepend []\T1/pcr/m/n/10 survival:: []\T
1/ptm/m/n/10 onto ev-er-thing, in-clud-ing the spe-
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\T1/ptm/m/n/10 cial terms, e.g., []\T1/pcr/m/n/10 survival::coxph(survival:Surv
(time, status) ~ age +
[3631]
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[][][]\T1/pcr/m/n/10 coxph.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
coxphms.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 coxph.control[][][]
[]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cluster[][][][]\T1/ptm/m/n/10 , [][][]\
T1/pcr/m/n/10 strata[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Surv[][][][]\
T1/ptm/m/n/10 ,
[3632]
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[]\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix
=TRUE)[]
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[3634]
[3635]
[3636]
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[3638]
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[3640]
[3641]
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[] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" "
exponential"[]
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[]\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass,
etype,
[3642]
[3643]
[3644]
[3645]
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[]\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[]
[3646]
[3647]
[3648]
[3649]
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[]\T1/ptm/m/n/10 outcome: []\T1/pcr/m/n/10 censor[]\T1/ptm/m/n/10 , []\T1/pcr/m
/n/10 thymic lymphoma[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 reticulum cell sarcoma
other
[3650]
[3651]
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[]\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney)
[3652]
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[] \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre
ssion", "death")))[]
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[]\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan
-Meier plot gen-er-ated with
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[] \T1/pcr/m/n/10 conf.type = c("log", "log-log", "plain", "logit", "ar
csin"),[]
[3653]
[3654]
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[] \T1/pcr/m/n/9 rmap=list(sex=sex, age=age*365.35, year=as.Da
te(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/01/01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[]
[3655]
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[] []
[3657]
[3658]
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[]\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[]
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[3660]
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[3663]
[3664]
[3665]
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[] \T1/pcr/m/n/9 entry.dt = as.Date(paste("2011", 1:10, "5"
, sep=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 -\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[]
[3666]
[3667]
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[]\T1/pcr/m/n/9 tdata <- data.frame(x= lung$age, y = 10*log(lung$age-35) + rno
rm(228, 0, 2))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4704--4704
[]\T1/pcr/m/n/9 knots <- unlist(attributes(fit1$model[[2]])[c(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 Boundary.knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , \TS1/pcr/m/n/9 '\T1
/pcr/m/n/9 knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )])[]
[3668]
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[]\T1/pcr/m/n/9 unname(coef(fit1)[-1] - coef(fit1)[1]) # differences: yhat[2:
4] - yhat[1][]
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[] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca
le=1,[]
[3675]
[3676]
[3677]
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[]\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign),
collapse,[]
[3678]
[3679]
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[]\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5530--5530
[] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means
, na.rm=TRUE)[]
[3680]
[3681]
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[]\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival
is at +infinity[]
[3682]
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[] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars"), expand=FALSE
, ...)[]
[3683]
Underfull \hbox (badness 1852) in paragraph at lines 5766--5768
[]\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.survfit"[]\T1/pt
m/m/n/10 , which is the re-sult of the
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[3686]
[3687]
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[]\T1/pcr/m/n/9 rhat <- predict(rfit, newdata=expand.grid(ph.ecog=0:3, sex=1:2
), se.fit=TRUE)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6032--6032
[]\T1/pcr/m/n/9 # the estimate for ph.ecog=3 is very unstable (n=1), pseudoval
ues smooth it.[]
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[]\T1/pcr/m/n/9 # In all the above we should be using the robust variance, e.g
., svyglm, but[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6058--6058
[]\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me
thod,
Overfull \hbox (36.78088pt too wide) in paragraph at lines 6059--6059
[] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co
mbine, ...)[]
[3688]
[3689]
[3690]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 6222--6222
[] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[]
[3691]
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[]\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age
+ sex, mgus,[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6345--6345
[]\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50
,60,70,100)) +[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6347--6347
[]\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[]
[3692]
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[3698]
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[]\T1/pcr/m/n/9 gfit <- survfit(Surv(day1, day2, status) ~ batch, braking, id=
locomotive)[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 6803--6803
[] \T1/pcr/m/n/9 xlab="Locomotive Age in Months", ylab="Mean cumulative nu
mber replacements")[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6806--6806
[]\T1/pcr/m/n/9 # natural target, an estimate of the number of replacements b
y a given time[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6808--6808
[]\T1/pcr/m/n/9 # When two valve seats failed at the same inspection, we need
to jitter one[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6810--6810
[]\T1/pcr/m/n/9 ties <- which(with(valveSeat, diff(id)==0 & diff(time)==0)) #
first of a tie[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6814--6814
[]\T1/pcr/m/n/9 vdata$time1 <- ifelse(!duplicated(vdata$id), 0, c(0, temp[-len
gth(temp)]))[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 6841--6841
[] \T1/pcr/m/n/10 collapse=FALSE, weighted= (type %in% c("dfbeta", "dfbe
tas")), ...)[]
[3699]
[3700]
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[] \T1/pcr/m/n/10 type="pstate", collapse=FALSE, weighted= collapse, data.f
rame=FALSE,[]
[3701]
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[]\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[]
Underfull \hbox (badness 1043) in paragraph at lines 7046--7049
[]\T1/pcr/m/n/10 "dfbetas"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "working"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "ldcase"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lsresp
"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ldshape"[]\T1/ptm/m/n/10 , and
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[3704]
[3705]
[3706]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7353--7353
[]\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), lung)[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 7354--7354
[]\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), lung)[]
[3707]
[3708]
[3709]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 7544--7544
[]\T1/pcr/m/n/10 rttright(formula, data, weights, subset, na.action, times, id
, timefix = TRUE,
[3710]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 7627--7627
[]\T1/pcr/m/n/9 cdf <- cdf[!duplicated(aml$time[index], fromLast=TRUE)] # rem
ove duplicate times[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7631--7631
[]\T1/pcr/m/n/9 wt2 <- rttright(Surv(dtime, death) ~ hormon, rotterdam, times=
365*c(3, 5))[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder})
has been already used, duplicate ignored
<to be read again>
\relax
l.7635 ...ata from a soldering experiment}{solder}
[3711]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7690--7690
[]\T1/pcr/m/n/9 dummy <- expand.grid(Opening= c("S", "M", "L"), Solder=c("Thin
", "Thick"))[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 7692--7692
[] \T1/pcr/m/n/9 dimnames=list(Opening= c("S", "M", "L"), Solder=c(
"Thin", "Thick")))[]
[3712]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 7752--7752
[]\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1,
col = 1,
[3713]
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[3717]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8118--8118
[]\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r
r =expected,[]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8119--8119
[]\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli
ne = FALSE,[]
[3718]
[3719]
[3720]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 8277--8277
[] \T1/pcr/m/n/10 extend=FALSE, rmean=getOption(\TS1/pcr/m/n/10 '\T1/pcr/m/n/
10 survfit.rmean\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ), data.frame=FALSE, dosum, ...
)[]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8280--8280
[] \T1/pcr/m/n/10 extend=FALSE, rmean=getOption(\TS1/pcr/m/n/10 '\T1/pcr/m/n/
10 survfit.rmean\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ), data.frame=FALSE, ...)[]
[3721]
[3722]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 8471--8471
[] \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/
10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p
cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/
n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10
, \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T
S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[]
[3723]
[3724]
[3725]
Underfull \hbox (badness 1253) in paragraph at lines 8750--8753
[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 median[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10
quantile []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 plot []\T1/ptm/m/n/10 meth-ods
first con-struct a sur-vival curve us-ing
[3726]
[3727]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8889--8889
[]\T1/pcr/m/n/10 survcheck(formula, data, subset, na.action, id, istate, istat
e0="(s0)",
[3728]
[3729]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9021--9021
[]\T1/pcr/m/n/10 survcondense(formula, data, subset, weights, na.action= na.pa
ss, id,
[3730]
[3731]
[3732]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9221--9221
[]\T1/pcr/m/n/9 check <- coxph(Surv(time, status) ~ factor(pat.karno) + strata
(inst), lung)[]
[3733]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 9227--9227
[] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1
, year=accept.dt),[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 9252--9252
[] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[]
Underfull \hbox (badness 1038) in paragraph at lines 9294--9300
[]\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre
-dicted sur-vival
[3734]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 9346--9346
[] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[]
[3735]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9432--9432
[]\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival
by 1/2 years[]
[3736]
[3737]
[3738]
Underfull \hbox (badness 10000) in paragraph at lines 9652--9657
[][][]\T1/pcr/m/n/10 survfit.formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 survfit.coxph[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 survfit.object[][
][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.survfit[][][][]\T1/ptm/m/n/10
,
[3739]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9672--9672
[] \T1/pcr/m/n/10 se.fit=TRUE, conf.int=.95, individual=FALSE, stype=2,
ctype,[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 9673--9673
[] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit",
"arcsin"),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 9678--9678
[] \T1/pcr/m/n/10 se.fit=FALSE, conf.int=.95, individual=FALSE, stype=2
, ctype,[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 9679--9679
[] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit",
"arcsin"),[]
[3740]
[3741]
[3742]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9901--9901
[] \T1/pcr/m/n/10 stype=1, ctype=1, id, cluster, robust, istate, timefi
x=TRUE,[]
[3743]
Underfull \hbox (badness 4441) in paragraph at lines 10042--10052
[]\T1/ptm/m/n/10 by de-fault, the surv-fit rou-tines only re-turn in-for-ma-tio
n at the
[3744]
Underfull \hbox (badness 2653) in paragraph at lines 10054--10059
\T1/pcr/m/n/10 ctype=1[]\T1/ptm/m/n/10 , "fleming-harrington" which is equiv-a-
lent to []\T1/pcr/m/n/10 stype=2,
[3745]
[3746]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10242--10242
[]\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored
(status=3),[]
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[3748]
[3749]
[3750]
[3751]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 10674--10674
[]\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
survtype,
[3752]
Underfull \hbox (badness 1354) in paragraph at lines 10715--10719
[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
e time range
[3753]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 10761--10761
[]\T1/pcr/m/n/10 survConcordance(formula, data, weights, subset, na.action) #
use concordance
[3754]
[3755]
Underfull \hbox (badness 2035) in paragraph at lines 10925--10932
\T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][][]\T1/pcr/m/n/10 su
rvreg.distributions[][][][]\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 10925--10932
\T1/ptm/m/n/10 These in-clude []\T1/pcr/m/n/10 "weibull"[]\T1/ptm/m/n/10 , []\T
1/pcr/m/n/10 "exponential"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "gaussian"[]\T1/p
tm/m/n/10 ,
Underfull \hbox (badness 1297) in paragraph at lines 10925--10932
[]\T1/pcr/m/n/10 "logistic"[]\T1/ptm/m/n/10 ,[]\T1/pcr/m/n/10 "lognormal" []\T1
/ptm/m/n/10 and []\T1/pcr/m/n/10 "loglogistic"[]\T1/ptm/m/n/10 . Oth-er-wise, i
t is
[3756]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11015--11015
[]\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[]
[3757]
[3758]
[3759]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 11172--11172
[] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[]
[3760]
[3761]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11304--11304
[] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x
^2*temp -1))[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 11307--11307
[] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[]
[3762]
[3763]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11483--11483
[]\T1/pcr/m/n/9 pfit2 <- pyears(Surv(years, death) ~ fgrp + agegrp, scale =100
0, data=test)[]
[3764]
[3765]
[3766]
[3767]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11712--11712
[]\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic
al trial plus[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11713--11713
[]\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data
set has data[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11719--11719
[] \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day
, alk.phos))[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 11721--11721
[]\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil
i), data=pbc2)[]
[3768]
[3769]
[3770]
[3771]
[3772]
[3773]
[3774]
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[]\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l
inear",[]
[3775]
[3776]
[3777])
[3778] (./fullrefman.ind
[3779]
[3780]
[3781]
[3782]
[3783]
[3784]
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[3802]
[3803]
[3804]
[3805]
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2878--2880
[]| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.bs.smooth.spec\T1/ptm/m/n/10 ,
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2882--2884
[]| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 ,
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2884--2886
[]| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 ,
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2886--2888
[]| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 ,
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2888--2890
[]| \T1/pcr/m/n/10 smooth.construct.gp.smooth.spec\T1/ptm/m/n/10 ,
Overfull \hbox (25.3567pt too wide) in paragraph at lines 2890--2892
[]| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 ,
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2892--2894
[]| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 ,
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2894--2896
[]| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 ,
[3806]
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[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 ,
Overfull \hbox (25.3567pt too wide) in paragraph at lines 2898--2900
[]| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.sz.smooth.spec\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 %&%,diagonalMatrix,matrix-method
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[]\T1/pcr/m/n/10 %&%,diagonalMatrix,vector-method
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[]\T1/pcr/m/n/10 %&%,matrix,diagonalMatrix-method
[3829]
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[]\T1/pcr/m/n/10 %&%,sparseVector,sparseVector-method
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[]\T1/pcr/m/n/10 %&%,vector,diagonalMatrix-method
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[]\T1/pcr/m/n/10 all.equal,sparseVector,vector-method
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[]\T1/pcr/m/n/10 all.equal,vector,sparseVector-method
[3832]
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[]\T1/pcr/m/n/10 Arith,CsparseMatrix,CsparseMatrix-method
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[]\T1/pcr/m/n/10 Arith,CsparseMatrix,numeric-method
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[]\T1/pcr/m/n/10 Arith,ddenseMatrix,logical-method
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[]\T1/pcr/m/n/10 Arith,ddenseMatrix,numeric-method
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[]\T1/pcr/m/n/10 Arith,ddenseMatrix,sparseVector-method
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[]\T1/pcr/m/n/10 Arith,dgCMatrix,dgCMatrix-method
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[]\T1/pcr/m/n/10 Arith,dgeMatrix,dgeMatrix-method
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[]\T1/pcr/m/n/10 Arith,dgeMatrix,sparseVector-method
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[]\T1/pcr/m/n/10 Arith,dsCMatrix,dsCMatrix-method
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[]\T1/pcr/m/n/10 Arith,dsparseMatrix,logical-method
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[]\T1/pcr/m/n/10 Arith,dsparseMatrix,nsparseMatrix-method
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[]\T1/pcr/m/n/10 Arith,dsparseMatrix,numeric-method
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[]\T1/pcr/m/n/10 Arith,dsparseVector,dsparseVector-method
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[]\T1/pcr/m/n/10 Arith,dtCMatrix,dtCMatrix-method
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[]\T1/pcr/m/n/10 Arith,lgCMatrix,lgCMatrix-method
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[]\T1/pcr/m/n/10 Arith,lgeMatrix,lgeMatrix-method
[3833]
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[]\T1/pcr/m/n/10 Arith,lgTMatrix,lgTMatrix-method
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[]\T1/pcr/m/n/10 Arith,logical,ddenseMatrix-method
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[]\T1/pcr/m/n/10 Arith,lsparseMatrix,Matrix-method
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[]\T1/pcr/m/n/10 Arith,lsparseMatrix,nsparseMatrix-method
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[]\T1/pcr/m/n/10 Arith,Matrix,lsparseMatrix-method
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[]\T1/pcr/m/n/10 Arith,Matrix,nsparseMatrix-method
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[]\T1/pcr/m/n/10 Arith,ngeMatrix,ngeMatrix-method
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[]\T1/pcr/m/n/10 Arith,nsparseMatrix,Matrix-method
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[]\T1/pcr/m/n/10 Arith,numeric,CsparseMatrix-method
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[]\T1/pcr/m/n/10 Arith,numeric,ddenseMatrix-method
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[]\T1/pcr/m/n/10 Arith,numeric,dsparseMatrix-method
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[]\T1/pcr/m/n/10 Arith,sparseVector,ddenseMatrix-method
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[]\T1/pcr/m/n/10 Arith,triangularMatrix,diagonalMatrix-method
[3834]
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[]\T1/pcr/m/n/10 aspell_write_personal_dictionary_file
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ptm/m/n/10 ,
[3840]
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[]\T1/pcr/m/n/10 chol2inv,triangularMatrix-method
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[]\T1/pcr/m/n/10 Cholesky,triangularMatrix-method
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[]\T1/pcr/m/n/10 coerce,BunchKaufman,dtrMatrix-method
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[]\T1/pcr/m/n/10 coerce,CHMsimpl,dtCMatrix-method
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[]\T1/pcr/m/n/10 coerce,CHMsuper,dgCMatrix-method
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[]\T1/pcr/m/n/10 coerce,Cholesky,dtrMatrix-method
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[]\T1/pcr/m/n/10 coerce,copMatrix,corMatrix-method
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[]\T1/pcr/m/n/10 coerce,corMatrix,copMatrix-method
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[]\T1/pcr/m/n/10 coerce,dgCMatrix,matrix.csc-method
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[]\T1/pcr/m/n/10 coerce,dgRMatrix,matrix.csr-method
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[]\T1/pcr/m/n/10 coerce,dgTMatrix,matrix.coo-method
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[]\T1/pcr/m/n/10 coerce,diagonalMatrix,symmetricMatrix-method
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[]\T1/pcr/m/n/10 coerce,factor,sparseMatrix-method
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[]\T1/pcr/m/n/10 coerce,generalMatrix,packedMatrix-method
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[]\T1/pcr/m/n/10 coerce,Matrix,CsparseMatrix-method
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[3846]
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[]\T1/pcr/m/n/10 coerce,Matrix,generalMatrix-method
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[]\T1/pcr/m/n/10 coerce,Matrix,triangularMatrix-method
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[]\T1/pcr/m/n/10 coerce,Matrix,unpackedMatrix-method
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[3847]
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[]\T1/pcr/m/n/10 Compare,CsparseMatrix,CsparseMatrix-method
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[2] (./base-pkg.tex
Chapter 1.
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[]\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber []\T1/pcr/m/n/
10 x []\T1/ptm/m/n/10 such that []\T1/pcr/m/n/10 1 + x != 1[]\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 It equals []\T1/pcr/m/n/10 double.base ^ ulp.digits []\T1/ptm/m/
n/10 if ei-ther []\T1/pcr/m/n/10 double.base []\T1/ptm/m/n/10 is
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\T1/ptm/m/n/10 2 or []\T1/pcr/m/n/10 double.rounding []\T1/ptm/m/n/10 is 0; oth
-er-wise, it is []\T1/pcr/m/n/10 (double.base ^
Underfull \hbox (badness 4454) in paragraph at lines 149--157
[]\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber []\T1/pcr/m/n/10 x [
]\T1/ptm/m/n/10 such that []\T1/pcr/m/n/10 1 - x != 1[]\T1/ptm/m/n/10 . It
Underfull \hbox (badness 1028) in paragraph at lines 149--157
\T1/ptm/m/n/10 equals []\T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits []\T
1/ptm/m/n/10 if []\T1/pcr/m/n/10 double.base
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[]\T1/ptm/m/n/10 is 2 or []\T1/pcr/m/n/10 double.rounding []\T1/ptm/m/n/10 is 0
; oth-er-wise, it is []\T1/pcr/m/n/10 (double.base
Underfull \hbox (badness 1394) in paragraph at lines 149--157
\T1/pcr/m/n/10 ^ double.neg.ulp.digits) / 2[]\T1/ptm/m/n/10 . Nor-mally []\T1/p
cr/m/n/10 1.110223e-16[]\T1/ptm/m/n/10 . As
[5]
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[]\T1/ptm/m/n/10 the num-ber of \T1/ptm/m/it/10 bytes \T1/ptm/m/n/10 in the C [
]\T1/pcr/m/n/10 time_t []\T1/ptm/m/n/10 type: a 64-bit []\T1/pcr/m/n/10 time_t
[]\T1/ptm/m/n/10 (value
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[]\T1/pcr/m/n/10 8[]\T1/ptm/m/n/10 ) is much pre-ferred these days. Note that t
his is the type used by
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[]\T1/ptm/m/n/10 introduced in \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.0.0. When [][]
[]\T1/pcr/m/n/10 capabilities[][][]("long.double") []\T1/ptm/m/n/10 is
Underfull \hbox (badness 3009) in paragraph at lines 235--247
[]\T1/pcr/m/n/10 *.exponent[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 *.min.exp[]\T1/p
tm/m/n/10 , and []\T1/pcr/m/n/10 *.max.exp[]\T1/ptm/m/n/10 , com-puted en-tirel
y anal-o-gously to their
[6]
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[]\T1/ptm/m/n/10 Note that it is le-gal for a plat-form to have a `[]\T1/pcr/m/
n/10 long double[]\T1/ptm/m/n/10 ' C type which is
Underfull \hbox (badness 6691) in paragraph at lines 255--260
\T1/ptm/m/n/10 iden-ti-cal to the `[]\T1/pcr/m/n/10 double[]\T1/ptm/m/n/10 ' ty
pe --- this hap-pens on ARM CPUs. In that case
Underfull \hbox (badness 1521) in paragraph at lines 255--260
[][][]\T1/pcr/m/n/10 capabilities[][][]("long.double") []\T1/ptm/m/n/10 will be
false but on ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 prior to 4.0.4,
[7]
Underfull \hbox (badness 10000) in paragraph at lines 375--379
[][][]\T1/pcr/m/n/10 R.version[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10
Sys.info[][][] []\T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-l
ar,
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[]
\T1/pcr/m/n/10 insertions[]\T1/ptm/m/n/10 ',
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[]\T1/pcr/m/n/9 agrep("laysy", c("1 lazy", "1", "1 LAZY"), max.distance = 2, v
alue = TRUE)[]
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[]\T1/pcr/m/n/9 agrep("laysy", c("1 lazy", "1", "1 LAZY"), max.distance = 2, i
gnore.case = TRUE)[]
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[] \T1/pcr/m/n/10 ..., check.attributes = TRUE, check.class = TRUE, g
iveErr = FALSE)[]
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[]\T1/pcr/m/n/9 all.equal(tan(d45), one, tolerance = 0, scale = 1+(-2:2)/1e9)
# "absolute"[]
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[]\T1/pcr/m/n/9 mtext(paste("mean(all.equal(x1, x2*(1 + eps_k))) {100 x} Mean
rel.diff.=",[]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 976--976
[]\T1/pcr/m/n/9 all.equal(two^20, 2^20, check.attributes = FALSE)# "target is
bar, current is numeric"[]
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[]\T1/pcr/m/n/9 all.equal(two^20, 2^20, check.attributes = FALSE, check.class
= FALSE) # TRUE[]
Underfull \vbox (badness 10000) has occurred while \output is active
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[]\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F
ALSE)
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Underfull \hbox (badness 1221) in paragraph at lines 1535--1541
[]\T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion, where \T1/phv/m/n/10 R \T1/p
tm/m/n/10 uses ``floored'' in-te-ger di-vi-sion, i.e., []\T1/pcr/m/n/10 q <- x
%/% y :=
[26]
Underfull \hbox (badness 10000) in paragraph at lines 1623--1631
\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . oracle
. com / cd / E19957-[]01 / 806-[]3568 / ncg _
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Underfull \vbox (badness 10000) has occurred while \output is active
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[] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em
pty.names = TRUE,[]
Underfull \hbox (badness 1303) in paragraph at lines 1998--2001
[]\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more
than 256 (or
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[]\T1/pcr/m/n/9 names(dL <- as.data.frame(L))
# "NA."[]
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[]\T1/pcr/m/n/9 names(dL1 <- as.data.frame(L, col.names = names(L)))
# "NA."[]
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[]\T1/pcr/m/n/9 names(dL1.<- as.data.frame(L, check.name
s=FALSE)) # "NA"[]
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[]\T1/pcr/m/n/9 names(dL2 <- as.data.frame(L, col.names = names(L), check.name
s=FALSE)) # NA[]
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[]\T1/pcr/m/n/9 names(dLn <- as.data.frame(L, new.names = TRUE, check.name
s=FALSE)) # NA[]
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[]\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[]
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[]\T1/ptm/m/n/10 If [][][]\T1/pcr/m/n/10 is.object[][][](x) []\T1/ptm/m/n/10 is
true and it has a [][][]\T1/pcr/m/n/10 class[][][] []\T1/ptm/m/n/10 for which
an
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[]\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla
ss "POSIXlt"[]
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[]\T1/pcr/m/n/9 if(file.exists(tab)) { # typically on Windows; on Linux when
\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 configure --with-internal-tzcode\TS1/cmtt/m/n/9
`[]
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[]\T1/ptm/m/n/10 There are no re-stric-tions on the name given as []\T1/pcr/m/n
/10 x[]\T1/ptm/m/n/10 : it can be a non-syntactic name (see
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[]\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse1(substitute(what), back
tick=FALSE),
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[]\T1/pcr/m/n/10 unCfillPOSIXlt(x) []\T1/ptm/m/n/10 is a fast [][]prim-i-tive[]
[][] ver-sion of []\T1/pcr/m/n/10 balancePOSIXlt(x,
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[]\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2,
lwd = 1, bty="n")[]
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[]\T1/pcr/m/n/9 plot(range(x0), c(1e-40, 1), log = "xy", xlab = "x", ylab = ""
, type = "n",[]
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[] \T1/pcr/m/n/9 main = "Bessel Functions J_nu(x) near 0\n log - log sc
ale") ; axis(2, at=1)[]
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[]\T1/pcr/m/n/9 plot(range(x0), 10^c(-100, 80), log = "xy", xlab = "x", ylab =
"", type = "n",[]
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[] \T1/pcr/m/n/9 main = "Bessel Functions K_nu(x) near 0\n log - log sc
ale") ; axis(2, at=1)[]
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[]\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5,
sep = ", ")),[]
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[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
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[]\T1/pcr/m/n/9 L <- as.list(E <- setNames( , c("if", "for", "while", "repeat"
, "function",[]
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[] \T1/pcr/m/n/9 "(", "{", "[", "<-", "<<-",
"->", "=")))[]
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[]\T1/pcr/m/n/9 for(i in seq_along(L)) L[[i]] <- call(E[[i]]) # instead of lap
ply(E, call) ..[]
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[]\T1/pcr/m/n/9 list_ <- function (...) \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 names<-
\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 (list(...), vapply(sys.call()[-1L], as.character
, ""))[]
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[]\T1/pcr/m/n/9 (Tab <- noquote(sapply(list_(is.call, typeof, class, mode), \(
F) sapply(L, F))))[]
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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an
ob-ject
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\T1/ptm/m/n/10 of class []\T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"[]\T1/ptm/
m/n/10 , []\T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" []\T1/ptm/m/n/10 o
r
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[] \T1/pcr/m/n/10 Xchk = any(nas %in% c("X11", "jpeg", "png", "tif
f")))[]
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[]\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par
-i-son[][][] and
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[]\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[]
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[]\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na
med ar-gu-
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[]\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu
e and valid
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[]\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[]
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[]\T1/pcr/m/n/9 as.character(list(A = "Abc", xy = c("x", "y"))) # "Abc" "c(\"
x\", \"y\")"[]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c
har-ac-ter by
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[]\T1/ptm/m/n/10 When a generic func-tion []\T1/pcr/m/n/10 fun []\T1/ptm/m/n/10
is ap-plied to an ob-ject with class at-tribute []\T1/pcr/m/n/10 c("first",
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[]\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i
n-tro-duc-tion see [][]$\T1/pcr/m/n/10 https : / /
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[]\T1/pcr/m/n/9 stopifnot(identical(as.complex(NA_real_), NA_real_ + 0i)) # ha
s always been true[]
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[]\T1/pcr/m/n/9 NAs <- vapply(list(NA, NA_integer_, NA_real_, NA_character_, N
A_complex_),[]
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[]\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile
r, math-library:[]
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[]\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[]
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[]\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class []\T1/pcr/m/n
/10 interrupt []\T1/ptm/m/n/10 that in-her-its di-rectly from class
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[]\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols.
They can be es-tab-lished us-ing
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[]\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i
s []\T1/pcr/m/n/10 interactive[]\T1/ptm/m/n/10 . This should
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[]\T1/pcr/m/n/10 zstdfile(description, open = "", encoding = getOption("encodi
ng"),[]
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[]\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[]
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[]\T1/ptm/m/n/10 character string, par-tially matched to []\T1/pcr/m/n/10 c("de
fault", "internal",
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[]\T1/pcr/m/n/10 file[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pipe[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 fifo[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 url[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 gzfile[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 bzfile[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 xzfile[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 zstdfile[]\T1/
ptm/m/n/10 , []\T1/pcr/m/n/10 unz[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 socketConnection[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 socketAcce
pt []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 serverSocket []\T1/ptm/m/n/10 re-turn
a con-nec-tion ob-ject
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[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
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[]\T1/pcr/m/n/10 file []\T1/ptm/m/n/10 can be used with []\T1/pcr/m/n/10 descri
ption = "clipboard" []\T1/ptm/m/n/10 in mode []\T1/pcr/m/n/10 "r" []\T1/ptm/m/n
/10 only. This
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[]\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[]
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[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
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[]\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect
s to https://[]
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[]\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[]
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[]\T1/pcr/m/n/10 data.frame []\T1/ptm/m/n/10 con-verts each of its ar-gu-ments
to a data frame by call-ing
Underfull \hbox (badness 1975) in paragraph at lines 8897--8907
[][][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)[]\T1/ptm/m/n/10 . As
that is a generic func-tion, meth-ods can be
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[] \T1/pcr/m/n/9 c = seq(as.Date("2004-01-01"), by = "week", l
ength.out = 3),[]
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\T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") []\T1/ptm/m
/n/10 may give []\T1/pcr/m/n/10 NA[]\T1/ptm/m/n/10 , and
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[]\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: --------
-------------[]
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[]\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO
!\n"); pi+2})[]
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[] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "(
", "function"),[]
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[] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh
owAttributes"),[]
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[]\T1/pcr/m/n/10 ..deparseOpts []\T1/ptm/m/n/10 is the [][][]\T1/pcr/m/n/10 cha
racter[][][] []\T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used b
y
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[]\T1/ptm/m/n/10 Surround un-eval-u-ated ex-pres-sions, but not [][][]\T1/pcr/m
/n/10 formula[][][][]\T1/ptm/m/n/10 s, with
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[]\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t
er-mi-nant if
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[] \T1/pcr/m/n/10 z <- as.POSIXct(c("2016-12-31 23:59:59", "2017-01-01 00:0
0:01"))[]
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[]\T1/pcr/m/n/10 provideDimnames(x) []\T1/ptm/m/n/10 pro-vides []\T1/pcr/m/n/10
dimnames []\T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has
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[]\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE
RS)))) # recycling[]
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[]\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
on both levels[]
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[]\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of []\
T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . Cur-rently this is only used by
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[]\T1/pcr/m/n/9 ## From R 4.1.0 to 4.1.2, ...names() sometimes did not match n
ames(list(...));[]
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[]\T1/pcr/m/n/9 chk.n2 <- function(...) stopifnot(identical(print(...names()),
names(list(...))))[]
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19
85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .
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\T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr
/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _
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\T1/pcr/m/n/10 754-[]2019$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / /
en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/
pcr/m/n/10 https :
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[] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA
ttributes"))[]
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[]\T1/pcr/m/n/9 ## Write an ASCII version of the \TS1/pcr/m/n/9 '\T1/pcr/m/n/9
base\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 function mean() to our temp file, ..[]
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[]\T1/pcr/m/n/9 drop(1:3 %*% 2:4) # scalar product - w/o drop(.), would retur
n 1x1 matrix[]
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[]\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9]))
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[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for
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[]\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) []\T1/ptm/m/n/10 is equiv-a-len
t to but faster than
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[]\T1/ptm/m/n/10 Do not use []\T1/pcr/m/n/10 dyn.unload []\T1/ptm/m/n/10 on a D
LL loaded by [][][]\T1/pcr/m/n/10 library.dynam[][][][]\T1/ptm/m/n/10 : use
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[]\T1/ptm/m/n/10 Changing the cur-rent en-cod-ing from a run-ning R ses-sion ma
y lead to con-fu-sion (see
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[]\T1/pcr/m/n/9 Encoding(x.) # "unknown" (UTF-8 loc.) | "latin1" (8859-1/CP-12
52 loc.) | ....[]
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[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of
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[]\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][][]\T1/pcr/m/n/1
0 dev2bitmap[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 bitmap[][][] []\T1/pt
m/m/n/10 and
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[]\T1/ptm/m/n/10 The path to HTML []\T1/pcr/m/n/10 tidy[]\T1/ptm/m/n/10 . Used
by []\T1/pcr/m/n/10 R CMD check []\T1/ptm/m/n/10 if
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[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
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[]\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing []\T1/pc
r/m/n/10 where []\T1/ptm/m/n/10 as
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[]\T1/pcr/m/n/10 get0(): []\T1/ptm/m/n/10 The object---as from [][][]\T1/pcr/m/
n/10 get[][][](x, *)[]\T1/ptm/m/n/10 --- if []\T1/pcr/m/n/10 exists(x, *) []\T1
/ptm/m/n/10 is true, oth-er-wise
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[]\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide
a constructor[]
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[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
done: see
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[]\T1/ptm/m/n/10 Junction points and sym-bolic links are fol-lowed, so in-for-m
a-tion is given about the
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[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as []\T1/pcr
/m/n/10 PATH []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 R_LIBS []\T1/ptm/m/n/10 with
[]\T1/pcr/m/n/10 fsep =
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[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See
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[][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil
e.access[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.path[][][][]\T1/ptm/
m/n/10 , [][][]\T1/pcr/m/n/10 file.show[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m
/n/10 list.files[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 unlink[][][][]\T1
/ptm/m/n/10 ,
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .
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[] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B
as it exists already[]
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[]\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
= "0777")[]
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Underfull \hbox (badness 10000) in paragraph at lines 15429--15432
[][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil
e.exists[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.path[][][][]\T1/ptm/
m/n/10 , [][][]\T1/pcr/m/n/10 list.files[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/
m/n/10 unlink[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 basename[][][][]\T1/
ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive = TRUE)[]
[222]
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[]\T1/pcr/m/n/10 packageNotFoundError []\T1/ptm/m/n/10 cre-ates an er-ror con-d
i-tion ob-ject of class
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[]\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio
ns it is found:[]
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[]\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE,
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[] \T1/pcr/m/n/10 left.open = FALSE, checkSorted = TRUE, checkNA =
TRUE)[]
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[]\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr
i-bu-tion func-tion, and in-deed,
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[]\T1/pcr/m/n/9 stopifnot(identical(it, ## suppressing the checks is faster *B
UT* dangerous, unless[]
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[] \T1/pcr/m/n/9 ## you *know* that X is sorted and
tt contains no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[]
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[] \T1/pcr/m/n/9 findInterval(tt, X, checkSorted=FALSE, che
ckNA=FALSE)))[]
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[] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)
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[] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[]
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[]\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have
type symbol (aka name).[]
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[]\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co
mbination with[]
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[]\T1/ptm/m/n/10 either a log-i-cal spec-i-fy-ing whether el-e-ments of a real
or com-plex vec-
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\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger
penalty (see
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[]\T1/pcr/m/n/10 big.mark[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 big.interval[]\T1/
ptm/m/n/10 , []\T1/pcr/m/n/10 small.mark[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sma
ll.interval[]\T1/ptm/m/n/10 ,
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[][][]\T1/pcr/m/n/10 formatC[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 paste
[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 as.character[][][][]\T1/ptm/m/n/1
0 , [][][]\T1/pcr/m/n/10 sprintf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 p
rint[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 prettyNum[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 toString[][][][]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[]
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[]\T1/pcr/m/n/10 prettyNum() []\T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (p
os-si-bly for-mat-ted) num-bers, also in
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[] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark =
decimal.mark,[]
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[]\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric
(x)),[]
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[]\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][]
[]\T1/pcr/m/n/10 complex[][][] []\T1/ptm/m/n/10 only for
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[]\T1/pcr/m/n/10 "f" []\T1/ptm/m/n/10 gives num-bers in the usual []\T1/pcr/m/n
/10 xxx.xxx []\T1/ptm/m/n/10 for-mat; []\T1/pcr/m/n/10 "e" []\T1/ptm/m/n/10 and
[]\T1/pcr/m/n/10 "E" []\T1/ptm/m/n/10 give
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[]\T1/ptm/m/n/10 This works via []\T1/pcr/m/n/10 prettyNum()[]\T1/ptm/m/n/10 ,
which calls []\T1/pcr/m/n/10 .format.zeros(*,
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[]\T1/ptm/m/n/10 For num-bers, []\T1/pcr/m/n/10 formatC() []\T1/ptm/m/n/10 call
s []\T1/pcr/m/n/10 prettyNum() []\T1/ptm/m/n/10 when needed which it-self calls
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[]\T1/ptm/m/n/10 If you set []\T1/pcr/m/n/10 format []\T1/ptm/m/n/10 it over-ri
des the set-ting of []\T1/pcr/m/n/10 mode[]\T1/ptm/m/n/10 , so []\T1/pcr/m/n/10
formatC(123.45, mode =
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[]\T1/pcr/m/n/10 prettyNum []\T1/ptm/m/n/10 is the util-ity func-tion for pret-
ti-fy-ing []\T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 x []\T1/ptm/m/n
/10 can be com-plex (or
[239]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 16642--16642
[]\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big
.mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[]
Underfull \vbox (badness 10000) has occurred while \output is active
[240]
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[]\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you
want see the effect[]
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[]\T1/pcr/m/n/10 Reduce(f, x, init, right = FALSE, accumulate = FALSE, simplif
y = TRUE)
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 17335--17335
[]\T1/pcr/m/n/9 ## very low-level: get()ing the "missing argument", e.g., insi
de browser()[]
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[] \T1/pcr/m/n/9 is.symbol(E$m) # => valid argument to get(), and *also* ge
ts \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 missing arg\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[]
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[]\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil
l a DLLInfoList[]
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Underfull \hbox (badness 2418) in paragraph at lines 17637--17641
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing [
]\T1/pcr/m/n/10 CRoutine[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 CallRoutine[]\T1/pt
m/m/n/10 ,
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Underfull \hbox (badness 6510) in paragraph at lines 17644--17647
[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 name []\T1/ptm/m/n/10 con-tains only one s
ym-bol name and []\T1/pcr/m/n/10 unlist []\T1/ptm/m/n/10 is []\T1/pcr/m/n/10 TR
UE[]\T1/ptm/m/n/10 , then the sin-gle
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[][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][][]\T1/ptm/m/n/10 , [][][]\T1
/pcr/m/n/10 is.loaded[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .C[][][][]\T
1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .Fortran[][][][]\T1/ptm/m/n/10 , [][][]\T1/
pcr/m/n/10 .External[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .Call[][][][]
\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 ## Not run: ## for translation, those strings should appear in
R-pkg.pot as[]
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[]\T1/pcr/m/n/9 if(is.na(thisLang) || !nzchar(thisLang)) thisLang <- "en" # "f
actory" default[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 17863--17863
[]\T1/pcr/m/n/9 gettext(enT, domain="R-stats")# "leeres Modell angegeben" (if
translation works)[]
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[]\T1/pcr/m/n/9 ## Here, we reset to the *original* setting before the full ex
ample started:[]
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[]\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE,
Overfull \hbox (0.78088pt too wide) in paragraph at lines 18034--18034
[]\T1/pcr/m/n/10 grepv(pattern, x, ignore.case = FALSE, perl = FALSE, value =
TRUE,[]
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[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
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Overfull \hbox (20.58041pt too wide) in paragraph at lines 18391--18391
[] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around
"checking hack"[]
Underfull \vbox (badness 10000) has occurred while \output is active
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Overfull \hbox (36.7804pt too wide) in paragraph at lines 18420--18420
[]\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[]
Underfull \vbox (badness 10000) has occurred while \output is active
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Overfull \hbox (0.78088pt too wide) in paragraph at lines 18476--18476
[] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[]
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Overfull \hbox (9.78043pt too wide) in paragraph at lines 18858--18858
[]\T1/pcr/m/n/9 (ii <- grouping(x <- c(1, 1, 3:1, 1:4, 3), y <- c(9, 9:1), z <
- c(2, 1:9)))
[271]
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[]\T1/pcr/m/n/9 z <- gzcon(url("https://www.stats.ox.ac.uk/pub/datasets/csb/ch
12.dat.gz"))[]
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[]\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE)
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[]\T1/ptm/m/n/10 The most portable name for the ISO 8859-15 en-cod-ing, com-mon
ly known as `Latin 9',
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\T1/ptm/m/n/10 is []\T1/pcr/m/n/10 "iso885915"[]\T1/ptm/m/n/10 : most plat-form
s sup-port both []\T1/pcr/m/n/10 "latin-9" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/1
0 "latin9" []\T1/ptm/m/n/10 but GNU
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Underfull \hbox (badness 1163) in paragraph at lines 19517--19519
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 https : / / unicode-[]org . github . io / icu /
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19525--19525
[]\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s
ettings, we can only reset to the default.[]
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[]\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE,
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[] \T1/pcr/m/n/10 num.eq = FALSE, single.NA = FALSE, attrib.as.se
t = FALSE,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19650--19650
[] \T1/pcr/m/n/10 ignore.bytecode = FALSE, ignore.environment = F
ALSE,[]
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[]\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------
----------------[]
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[]\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is
ignored by default[]
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[]\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share
an environment:[]
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[]\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi
ng "srcref" :[]
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[]\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u
se ifelse(),[]
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[]\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[]
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Underfull \hbox (badness 10000) in paragraph at lines 20058--20060
[]\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][][]\T
1/pcr/m/n/10 stop[][][] []\T1/ptm/m/n/10 and
[289]
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[][][]\T1/pcr/m/n/10 as.character[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
as.complex[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 as.double[][][][]\T1/pt
m/m/n/10 , [][][]\T1/pcr/m/n/10 as.integer[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc
r/m/n/10 as.logical[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 as.raw[][][][]
\T1/ptm/m/n/10 ,
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Underfull \hbox (badness 10000) in paragraph at lines 20359--20367
\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . oracle
. com / cd / E19957-[]01 / 806-[]3568 / ncg _
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[]\T1/pcr/m/n/10 is.atomic []\T1/ptm/m/n/10 is true for the [][]atomic[][][] ty
pes ([]\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "integer"[]\
T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "numeric"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[]
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[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
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[]\T1/pcr/m/n/9 isSymmetric(D3) # FALSE (as row and co
lumn names differ)[]
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[]\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE (as names are
not checked)[]
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[]\T1/pcr/m/n/10 .kappa_tri(z, exact = FALSE, LINPACK = TRUE, norm = NULL, upl
o = "U", ...)[]
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Overfull \hbox (12.78088pt too wide) in paragraph at lines 21001--21001
[]\T1/pcr/m/n/10 rcond(x, norm = c("O","I","1"), triangular = FALSE, uplo = "U
", ...)[]
[303]
Underfull \hbox (badness 2961) in paragraph at lines 21085--21088
[]\T1/ptm/m/n/10 LAPACK and LIN-PACK are from [][]$\T1/pcr/m/n/10 https : / / n
etlib . org / lapack/$[][] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / /
[304]
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[]\T1/pcr/m/n/9 ## Moore-Penrose inverse { ~= MASS::ginv(); differing tol (val
ue & meaning)}:[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 21163--21163
[]\T1/pcr/m/n/9 try( kappa(m76, exact=TRUE, norm="1") )# error in solve().. m
ust be square[]
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[]\T1/pcr/m/n/9 ## ==> use pseudo-inverse instead of solve() for rectangular {
and norm != "2"}:[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 21185--21185
[] \T1/pcr/m/n/9 inv_z = solve(A, tol = 1e-19))) # 5.22057e16 on x86_
64 Linux with GCC[]
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[]\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p
hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to
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[]\T1/ptm/m/n/10 In late 2017 a []\T1/pcr/m/n/10 libcurl []\T1/ptm/m/n/10 in-st
al-la-tion was seen di-vided into two li-braries, []\T1/pcr/m/n/10 libcurl []\T
1/ptm/m/n/10 and
Underfull \hbox (badness 10000) in paragraph at lines 22017--22024
[][][]$\T1/pcr/m/n/10 https : / / curl . se / docs / sslcerts . html$[][] \T1/p
tm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / curl . se / docs /
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[]\T1/ptm/m/n/10 At startup, the li-brary search path is ini-tial-ized from the
en-vi-ron-ment vari-ables []\T1/pcr/m/n/10 R_LIBS[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2970) in paragraph at lines 22148--22151
[]\T1/pcr/m/n/10 LOCALAPPDATA []\T1/ptm/m/n/10 (usu-ally []\T1/pcr/m/n/10 C:\Us
ers\username\AppData\Local[]\T1/ptm/m/n/10 ) on Win-dows is a
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\T1/ptm/m/n/10 hid-den di-rec-tory and may not be viewed by some soft-ware. It
may be opened by
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[]\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use
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[][][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][][]\T1/ptm/m/n/10 : thi
s will sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 library []\T1/ptm/m/n/10 is called with no
[]\T1/pcr/m/n/10 package []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 help []\T1/ptm/m
/n/10 ar-gu-ment, it lists all avail-able pack-
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[][][]\T1/pcr/m/n/10 attach[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 detach
[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 search[][][][]\T1/ptm/m/n/10 , []
[][]\T1/pcr/m/n/10 objects[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 autoloa
d[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 requireNamespace[][][][]\T1/ptm/
m/n/10 ,
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[]\T1/ptm/m/n/10 Do not use [][][]\T1/pcr/m/n/10 dyn.unload[][][] []\T1/ptm/m/n
/10 on a DLL loaded by []\T1/pcr/m/n/10 library.dynam[]\T1/ptm/m/n/10 : use
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[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
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[] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. =
FALSE)[]
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[][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil
e.access[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 files[][][] []\T1/ptm/
m/n/10 for many more file han-dling func-tions and
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[] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments
as for lists[]
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[] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
prob = 0.2))),[]
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[]\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the
same names ![]
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[]\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w
/ same name in .GlobalEnv[]
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[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways
be sup-
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[]\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/
ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of
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[]\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other
Unix-alikes[]
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[]\T1/pcr/m/n/9 c(m = months(then), wd = weekdays(then)) # in C_TIME locale \T
S1/pcr/m/n/9 '\T1/pcr/m/n/9 cT\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 ; typically German
[]
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[]\T1/pcr/m/n/9 c(m = months(then), wd = weekdays(then)) # "standard" (still p
latform specific ?)[]
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[]\T1/pcr/m/n/9 ## Not run: Sys.setlocale("LC_COLLATE", "C") # turn off loca
le-specific sorting,[]
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[]\T1/pcr/m/n/9 Sys.setenv("LANGUAGE" = "es") # set the language for error/war
ning messages[]
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[][][]\T1/pcr/m/n/10 raw[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logical[]
[][] []\T1/ptm/m/n/10 or `number-like' vec-tors (i.e., of types [][][]\T1/pcr/m
/n/10 double[][][] []\T1/ptm/m/n/10 (class
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[]\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary = r ), complex(real =
r , imaginary = NA ),[]
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[] \T1/pcr/m/n/9 complex(real = r , imaginary = NaN), complex(real = N
aN, imaginary = r ))[]
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[]\T1/pcr/m/n/9 zM ##--> many "NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s" (= 1) and th
e four non-NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s (3 different ones, at 7,9,10)[]
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[]\T1/pcr/m/n/9 match.arg(c("a", ""), c("", NA, "bb", "abc"), several.ok=TRUE
) # |--> "abc"[]
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[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion
(also known as a `clo-sure'):
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[]\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross \T1/ptm/m/n/10 prod-ucts, []
[][]\T1/pcr/m/n/10 crossprod[][][]() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 tcro
ssprod() []\T1/ptm/m/n/10 are typ-i-cally prefer-able.
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[]\T1/pcr/m/n/10 memCompress(from, type = c("gzip", "bzip2", "xz", "zstd", "no
ne"))
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\T1/ptm/m/n/10 al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 https : / / lea
rn . microsoft . com / en-[]gb / windows /
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\T1/pcr/m/n/10 desktop / Memory / physical-[]address-[]extension$[][] \T1/ptm/m
/n/10 and [][]$\T1/pcr/m/n/10 https : / / learn .
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[] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
all,[]
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[]\T1/pcr/m/n/10 anyNA(recursive = FALSE) []\T1/ptm/m/n/10 works the same way a
s []\T1/pcr/m/n/10 is.na[]\T1/ptm/m/n/10 ; []\T1/pcr/m/n/10 anyNA(recursive =
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[]\T1/pcr/m/n/10 as.name []\T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-
nally to a char-ac-ter vec-tor (so meth-ods for
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[]\T1/ptm/m/n/10 For an [][][]\T1/pcr/m/n/10 environment[][][] env[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 names(env) []\T1/ptm/m/n/10 gives the names of the cor-r
e-spond-ing list,
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\T1/ptm/m/n/10 i.e., []\T1/pcr/m/n/10 names(as.list(env, all.names = TRUE)) []\
T1/ptm/m/n/10 which are also given by [][][]\T1/pcr/m/n/10 ls[][][](env,
Underfull \hbox (badness 3148) in paragraph at lines 26148--26154
\T1/pcr/m/n/10 all.names = TRUE, sorted = FALSE)[]\T1/ptm/m/n/10 . If the en-vi
-ron-ment is used as a hash ta-ble,
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[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of []\T1/pcr/m/n/1
0 c("bytes", "chars",
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[]\T1/ptm/m/n/10 optional [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 e
ven-tu-ally to be passed to []\T1/pcr/m/n/10 print()[]\T1/ptm/m/n/10 , used by
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\T1/ptm/m/n/10 tion []\T1/pcr/m/n/10 GetFinalPathNameByHandle []\T1/ptm/m/n/10
and in case of an er-ror (such as in-suf-fi-cient per-
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[]\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s
tartup mes-sages given by
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[]\T1/pcr/m/n/10 .onAttach[]\T1/ptm/m/n/10 . These mes-sages (and any es-sen-ti
al ones from []\T1/pcr/m/n/10 .onLoad[]\T1/ptm/m/n/10 ) should use
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[]\T1/ptm/m/n/10 Uses of []\T1/pcr/m/n/10 library []\T1/ptm/m/n/10 with ar-gu-m
ent []\T1/pcr/m/n/10 help []\T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion ab
out the pack-
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\T1/ptm/m/n/10 age should use []\T1/pcr/m/n/10 format []\T1/ptm/m/n/10 on the c
om-puted pack-age in-for-ma-tion ob-ject and pass this to
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[]\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ
e.only)
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[] \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk
gs"))[]
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[]\T1/pcr/m/n/10 loadNamespace []\T1/ptm/m/n/10 does not at-tach the name space
it loads to the search path.
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[]\T1/pcr/m/n/10 attachNamespace []\T1/ptm/m/n/10 can be used to at-tach a fram
e con-tain-ing the ex-ported val-ues of a
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[]\T1/pcr/m/n/10 isNamespaceLoaded(pkg) []\T1/ptm/m/n/10 is equiv-a-lent to but
more ef-fi-cient than []\T1/pcr/m/n/10 pkg %in%
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[] \T1/pcr/m/n/9 ## The string "foo" and the symbol \TS1/pcr/m/n/9 '\T1/pcr/m/
n/9 foo\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 can be used interchangeably here:[]
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[]\T1/ptm/m/n/10 The de-fault method for []\T1/pcr/m/n/10 is.numeric []\T1/ptm/
m/n/10 re-turns []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 if its ar-gu-ment is of
[][]mode[][][]
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\T1/ptm/m/n/10 ject as ob-tained by [][][]\T1/pcr/m/n/10 R.version[][][][]\T1/p
tm/m/n/10 . For []\T1/pcr/m/n/10 as.numeric_version []\T1/ptm/m/n/10 and
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[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
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[]\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/
10 R \T1/ptm/m/n/10 starts up. Ini-
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[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
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Underfull \hbox (badness 3138) in paragraph at lines 28609--28615
[]\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][][]\T1/pcr/
m/n/10 setRepositories[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 28609--28615
\T1/ptm/m/n/10 e.g. the de-fault `[]\T1/pcr/m/n/10 "https://bioconductor.org"[]
\T1/ptm/m/n/10 ' or the Eu-ro-pean mir-ror
Underfull \hbox (badness 2088) in paragraph at lines 28609--28615
\T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de
"[]\T1/ptm/m/n/10 '. Can be set by
Underfull \hbox (badness 1389) in paragraph at lines 28648--28650
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
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[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by
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[]\T1/ptm/m/n/10 Used by [][][]\T1/pcr/m/n/10 install.packages[][][] []\T1/ptm/
m/n/10 (and in-di-rectly
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[]\T1/ptm/m/n/10 default email-ing method used by [][][]\T1/pcr/m/n/10 create.p
ost[][][] []\T1/ptm/m/n/10 and hence [][][]\T1/pcr/m/n/10 bug.report[][][] []\T
1/ptm/m/n/10 and
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[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see
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[]\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec,
300X faster[]
Underfull \vbox (badness 10000) has occurred while \output is active
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[]\T1/ptm/m/n/10 where el-e-ment []\T1/pcr/m/n/10 A[c(arrayindex.x, arrayindex.
y)] = FUN(X[arrayindex.x],
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[]\T1/pcr/m/n/10 str2expression(s) []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 str2la
ng(s) []\T1/ptm/m/n/10 re-turn spe-cial ver-sions of []\T1/pcr/m/n/10 parse(tex
t=s,
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[]\T1/pcr/m/n/9 tryCatch(parse(text = txt, srcfile = sf), error = function(e)
"Syntax error.")[]
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\T1/ptm/m/n/10 zero-length [][][]\T1/pcr/m/n/10 character[][][](0)[]\T1/ptm/m/n
/10 . Note that when []\T1/pcr/m/n/10 collapse []\T1/ptm/m/n/10 is a string,
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[][][]\T1/pcr/m/n/10 toString[][][] []\T1/ptm/m/n/10 typ-i-cally calls []\T1/pc
r/m/n/10 paste(*, collapse=", ")[]\T1/ptm/m/n/10 . String ma-nip-u-la-tion with
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[]\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as
the longest input.[]
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[]\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha
t you wanted[]
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[]\T1/pcr/m/n/9 ## zero length arguments recycled as \TS1/cmtt/m/n/9 `\T1/pcr/
m/n/9 ""\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 -- NB: \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 {
}\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 <==> character(0) here[]
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[]\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 recycle0 = TRUE\TS1/pcr/m/n/9
' \T1/pcr/m/n/9 allows standard vectorized behaviour, i.e., zero-length[]
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[]\T1/pcr/m/n/9 ## recycling resulting in zero-length result
character(0):[]
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[]\T1/pcr/m/n/9 paste("The value is", val[valid], "-- not so good!") # -> "..
value is -- not .."[]
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[]\T1/pcr/m/n/9 paste("The value is", val[valid], "-- good: empty!", recycle0=
TRUE) # -> character(0)[]
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[]\T1/pcr/m/n/9 paste("foo", {}, "bar", collapse = "|") # |--
> "foo bar"[]
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[]\T1/pcr/m/n/9 ## If all arguments are empty (and collapse a string), "" r
esults always[]
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[]\T1/pcr/m/n/9 mtcars |> subset(cyl == 4) |> nrow() # same as nrow(subset(mt
cars, cyl == 4))[]
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[]\T1/pcr/m/n/9 stop() |> (function(...) {})() # stop() is not used on RHS so
is not evaluated[]
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[]\T1/ptm/m/n/10 All other []\T1/pcr/m/n/10 type[]\T1/ptm/m/n/10 s give a warn-
ing or an er-ror; us-ing, e.g., []\T1/pcr/m/n/10 type =
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\T1/ptm/m/n/10 i.e., strictly in-clude the bounds of []\T1/pcr/m/n/10 x[]\T1/pt
m/m/n/10 . New from \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0, al-low-ing
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[]\T1/ptm/m/n/10 This func-tion is al-most never used: []\TS1/cmtt/m/n/10 `\T1/
pcr/m/n/10 name\TS1/cmtt/m/n/10 ` []\T1/ptm/m/n/10 or, more care-fully, [][][]\
T1/pcr/m/n/10 get[][][](name, envir =
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[]\T1/pcr/m/n/9 try(structure(mysqrt, comment = "primitive function")) # depre
cation warning; soon an error[]
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[]\T1/ptm/m/n/10 character string (or []\T1/pcr/m/n/10 NULL[]\T1/ptm/m/n/10 ) i
n-di-cat-ing [][][]\T1/pcr/m/n/10 NA[][][] []\T1/ptm/m/n/10 val-ues in printed
out-put, see
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[]\T1/ptm/m/n/10 Option []\T1/pcr/m/n/10 width []\T1/ptm/m/n/10 con-trols the p
rint-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion
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[]\T1/pcr/m/n/9 (x <- 2^seq(-8, 30, by=1/4)) # auto-prints; by default all in
"exponential" format[]
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[]\T1/ptm/m/n/10 LAPACK and LIN-PACK are from [][]$\T1/pcr/m/n/10 https : / / n
etlib . org / lapack/$[][] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / /
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[] \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 =
rep(c(0,0,1),2))[]
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[]\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3
\u147b\u203c")[]
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[]\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\
U147b\U203c"[]
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[]\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm
l#Literal-constants[]
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[]\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[]
Underfull \vbox (badness 10000) has occurred while \output is active
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[]\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use []\T1/pcr/m/n/10 R.v
ersion$os []\T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use
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[]\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[]
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[]\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind =
NULL)[]
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Underfull \hbox (badness 3713) in paragraph at lines 31921--31932
[]\T1/pcr/m/n/10 normal.kind []\T1/ptm/m/n/10 can be []\T1/pcr/m/n/10 "Kinderma
n-Ramage"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Buggy Kinderman-Ramage" []\T1/ptm
/m/n/10 (not
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Underfull \hbox (badness 2932) in paragraph at lines 32073--32080
\T1/ptm/m/n/10 Now see [][]$\T1/pcr/m/n/10 https : / / www . math . sci . hiros
hima-[]u . ac . jp / ~m-[]mat / MT / VERSIONS /
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[]\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca
n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the
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[] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m
ax", "min"))[]
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[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no []\T1/pcr/m/n/10 N
A[]\T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
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Overfull \hbox (15.18042pt too wide) in paragraph at lines 32506--32506
[]\T1/pcr/m/n/9 rapply(X, function(x) x, how = "replace") -> X.; stopifnot(ide
ntical(X, X.))[]
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[]\T1/pcr/m/n/9 rapply(X, deparse, control = "all") # passing extras. argument
of deparse()[]
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[]\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "list")[]
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[]\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[]
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[]\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", h
ow = "unlist")[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 32518--32518
[]\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[]
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Overfull \hbox (25.98041pt too wide) in paragraph at lines 32828--32828
[]\T1/pcr/m/n/9 ## Bit representation [ sign | exponent | mantissa ] of doubl
e prec numbers :[]
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[]\T1/pcr/m/n/9 bitC <- function(x) noquote(vapply(as.double(x), function(x) {
# split one double[]
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[]\T1/pcr/m/n/9 d2bI <- function(x) vapply(as.double(x), function(x) intToBits
(numToInts(x)), raw(64L))[]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 32841--32841
[]\T1/pcr/m/n/9 d2b <- function(x) vapply(as.double(x), function(x)
numToBits(x) , raw(64L))[]
Underfull \vbox (badness 10000) has occurred while \output is active
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[]\T1/ptm/m/n/10 The sec-tion `Pro-cess-ing doc-u-men-ta-tion files' in the `Wr
it-ing R Ex-ten-sions' man-ual:
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[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
to
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\T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the
mode:
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\T1/ptm/m/n/10 one of []\T1/pcr/m/n/10 "numeric"[]\T1/ptm/m/n/10 , []\T1/pcr/m/
n/10 "double"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "integer"[]\T1/ptm/m/n/10 , []
\T1/pcr/m/n/10 "int"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/
10 ,
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Underfull \hbox (badness 2080) in paragraph at lines 33477--33487
[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 infoRDS[]\T1/ptm/m/n/10 , an \T1/phv/m/n/
10 R \T1/ptm/m/n/10 list with el-e-ments []\T1/pcr/m/n/10 version []\T1/ptm/m/n
/10 (ver-sion num-ber, cur-rently 2 or 3),
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[]\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[]
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Underfull \hbox (badness 7558) in paragraph at lines 34039--34043
[]\T1/pcr/m/n/10 regexpr []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 gregexpr []\T1/p
tm/m/n/10 sup-port `named cap-ture'. If groups are named, e.g.,
Underfull \hbox (badness 1968) in paragraph at lines 34049--34051
[]\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P
OSIX stan-dard, and the
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Underfull \hbox (badness 10000) in paragraph at lines 34060--34062
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 https : / /
pubs . opengroup . org / onlinepubs /
Underfull \hbox (badness 1975) in paragraph at lines 34063--34067
[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 pcre2pattern []\T1/ptm/m/n/10 or []\T1/pc
r/m/n/10 pcrepattern man []\T1/ptm/m/n/10 page (found as part of [][]$\T1/pcr/m
/n/10 https : / / www .
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 34435--34435
[]\T1/pcr/m/n/9 rep(1:4, each = 2, times = 3) # length 24, 3 complete
replications[]
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[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
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Underfull \hbox (badness 2302) in paragraph at lines 34739--34742
[]\T1/pcr/m/n/10 signif []\T1/ptm/m/n/10 rounds the val-ues in its first ar-gu-
ment to the spec-i-fied num-ber of \T1/ptm/m/it/10 sig-nif-i-cant
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\T1/ptm/m/n/10 dig-its. Hence, for []\T1/pcr/m/n/10 numeric x[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 signif(x, dig) []\T1/ptm/m/n/10 is the same as []\T1/pcr/m/n/
10 round(x, dig -
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Overfull \hbox (12.78088pt too wide) in paragraph at lines 34869--34869
[] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"))[]
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[] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[]
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[] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[]
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Overfull \hbox (66.78088pt too wide) in paragraph at lines 35327--35327
[] \T1/pcr/m/n/10 useHash = (n > 1e+07 && !replace && is.null(prob)
&& size <= n/2))[]
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Overfull \hbox (12.78088pt too wide) in paragraph at lines 35768--35768
[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
FALSE)[]
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 strip.white []\T1/ptm/m/n/10 is of length
1, it ap-plies to all fields; oth-er-wise, if
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Overfull \hbox (15.18042pt too wide) in paragraph at lines 36058--36058
[]\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n")
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Underfull \hbox (badness 4752) in paragraph at lines 36317--36320
[]\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence []\T1/pcr/
m/n/10 1, 2, ..., length(along.with)[]\T1/ptm/m/n/10 .
Underfull \hbox (badness 5563) in paragraph at lines 36321--36327
[]\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence []\T1/pcr/m/n/10 1, 2
, ..., length(from) []\T1/ptm/m/n/10 (as if ar-gu-ment
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[]\T1/ptm/m/n/10 A vec-tor of class []\T1/pcr/m/n/10 "Date"[]\T1/ptm/m/n/10 . T
ype []\T1/pcr/m/n/10 "[][]integer[][][]" []\T1/ptm/m/n/10 is of-ten pre-served
on pur-pose, sav-ing
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[]\T1/pcr/m/n/9 ## find all 7th of the month _strictly_ inside two dates, the
last being a 7th.[]
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Underfull \hbox (badness 6094) in paragraph at lines 36948--36952
[]\T1/pcr/m/n/10 getAllConnections []\T1/ptm/m/n/10 re-turns a se-quence of in-
te-ger con-nec-tion de-scrip-tors for use
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\T1/ptm/m/n/10 with []\T1/pcr/m/n/10 getConnection[]\T1/ptm/m/n/10 , cor-re-spo
nd-ing to the row names of the ta-ble re-turned by
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[]\T1/ptm/m/n/10 In Win-dows, com-mand line in-ter-pre-ta-tion is done by the a
p-pli-ca-tion as well as the
Underfull \hbox (badness 3492) in paragraph at lines 37039--37050
\T1/ptm/m/n/10 shell. It may de-pend on the com-piler used: Mi-crosoft's rules
for the C run-time
Underfull \hbox (badness 10000) in paragraph at lines 37039--37050
\T1/ptm/m/n/10 are given at [][]$\T1/pcr/m/n/10 https : / / learn . microsoft .
com / en-[]us / cpp / c-[]language /
Underfull \hbox (badness 1635) in paragraph at lines 37039--37050
\T1/pcr/m/n/10 parsing-[]c-[]command-[]line-[]arguments ? view = msvc-[]160$[][
]\T1/ptm/m/n/10 . It may de-pend on the
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Overfull \hbox (66.78088pt too wide) in paragraph at lines 37591--37591
[] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index
.return = FALSE)[]
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[]\T1/pcr/m/n/9 sort_by.data.frame(mtcars, ~ list(am, -mpg)) |> subset(select
= c(am, mpg))[]
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[] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length
= Inf,[]
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[] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes"
, "keepNA"),[]
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[][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 vec-tor, passed as []\T1/
pcr/m/n/10 control []\T1/ptm/m/n/10 to [][][]\T1/pcr/m/n/10 deparse[][][]()[]\T
1/ptm/m/n/10 , see also
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[][][]\T1/pcr/m/n/10 .deparseOpts[][][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \
T1/ptm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to
[548]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 38074--38074
[]\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments
should print:)[]
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[]\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m
/n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[]
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[]\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
being added[]
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[][][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919
799 / functions /
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[]\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known")
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[]\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
FALSE)[]
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[]\T1/ptm/m/n/10 Stack over-flow er-rors can be caught and han-dled by ex-it-in
g han-dlers es-tab-lished with
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[]\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three
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Underfull \hbox (badness 6110) in paragraph at lines 39331--39341
[]\T1/ptm/m/n/10 A func-tion []\T1/pcr/m/n/10 .First []\T1/ptm/m/n/10 (and [][]
[]\T1/pcr/m/n/10 .Last[][][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-at
e `\T1/pcr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or
Underfull \hbox (badness 2635) in paragraph at lines 39331--39341
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have been
saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want a dif-fer-ent
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\T1/ptm/m/n/10 set of pack-ages than the de-fault ones when you start, in-sert
a call to [][][]\T1/pcr/m/n/10 options[][][] []\T1/ptm/m/n/10 in the
Underfull \hbox (badness 1231) in paragraph at lines 39331--39341
\T1/pcr/m/n/10 = character()) []\T1/ptm/m/n/10 will at-tach no ex-tra pack-ages
on startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (or
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\T1/ptm/m/n/10 set []\T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL []\T1/ptm/m/n/10 as
an en-vi-ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/10 ).
Us-ing
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[]\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file
s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 '
Underfull \hbox (badness 10000) in paragraph at lines 39387--39393
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for
first in architecture-specific di-rec-to-ries,
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\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be
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[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is
also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/pt
m/m/n/10 ' which is read
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\T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron-
ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the
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\T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i
n site or user en-vi-ron-ment
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[]\T1/pcr/m/n/9 # Variable expansion in double quotes, string literals with ba
ckslashes in[]
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[]\T1/ptm/m/n/10 The de-fault han-dler stores the er-ror mes-sage in a buffer;
it can be re-trieved by
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[]\T1/pcr/m/n/10 geterrmessage()[]\T1/ptm/m/n/10 . It also stores a trace of th
e call stack that can be re-trieved by
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[]\T1/ptm/m/n/10 alternative to []\T1/pcr/m/n/10 exprs []\T1/ptm/m/n/10 or []\T
1/pcr/m/n/10 ...[]\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an
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[] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e
xprs = exprs)))
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[]\T1/pcr/m/n/9 stopifnot(all.equal(pi, 3.141593), 2 < 2, (1:10 < 12), "a" <
"b") |> try()[]
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[]\T1/pcr/m/n/9 stopifnot(all.equal(rep(list(pi),4), list(3.1, 3.14, 3.141, 3.
1415))) |> try()[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 39747--39747
[]\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 {Yes, learn how to use do.c
all(substitute, ...) in a powerful manner !!}[]
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[]\T1/pcr/m/n/9 bdy <- do.call(substitute, list(bdy, list(stopifnot =
quote(warnifnot))))[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 39750--39750
[]\T1/pcr/m/n/9 bdy[[N-1]] <- do.call(substitute, list(bdy[[N-1]], list(stop =
quote(warning))))[]
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Underfull \hbox (badness 1436) in paragraph at lines 39814--39818
[]\T1/ptm/m/n/10 integer de-ter-min-ing the []\T1/pcr/m/n/10 format()[]\T1/ptm/
m/n/10 ing of sec-onds when needed. Note
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[]\T1/pcr/m/n/9 ## time with fractional seconds (setting \TS1/cmtt/m/n/9 `\T1/
pcr/m/n/9 tz = ..\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 for reproducible output)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 40222--40222
[]\T1/pcr/m/n/9 z3 # prints without fractional seconds by default, digits.sec
= NULL ("= 0")[]
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[]\T1/pcr/m/n/9 format(s1 <- seq.Date(as.Date(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 19
78-01-01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ), by = \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 day
\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , len = 7), "%a")[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 40256--40256
[]\T1/pcr/m/n/9 format(s2 <- seq.Date(as.Date(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 20
00-01-01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ), by = \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 mon
th\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , len = 12), "%b")[]
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[] \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[]
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Overfull \hbox (6.78088pt too wide) in paragraph at lines 40646--40646
[] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[]
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[]\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[]
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Overfull \hbox (52.98038pt too wide) in paragraph at lines 41140--41140
[]\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e
verything gets added.[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 41143--41143
[]\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also
missing, ....[]
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Overfull \hbox (36.78088pt too wide) in paragraph at lines 41182--41182
[]\T1/pcr/m/n/10 format(x, digits = max(3L, getOption("digits") - 3L), zdigits
= 4L, ...)[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 41184--41184
[]\T1/pcr/m/n/10 print(x, digits = max(3L, getOption("digits") - 3L), zdigits
= 4L, ...)[]
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[]\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision
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Overfull \hbox (31.3804pt too wide) in paragraph at lines 41574--41574
[] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[]
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Overfull \hbox (20.58041pt too wide) in paragraph at lines 41784--41784
[]\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux,
macOS, FreeBSD:[]
Underfull \hbox (badness 2293) in paragraph at lines 41814--41820
[]\T1/ptm/m/n/10 This ex-pands tilde (see [][]tilde ex-pan-sion[][][]) and wild
-cards in file paths. For pre-cise de-
Underfull \hbox (badness 1237) in paragraph at lines 41814--41820
\T1/ptm/m/n/10 tails of wild-cards ex-pan-sion, see your sys-tem's doc-u-men-ta
-tion on the []\T1/pcr/m/n/10 glob []\T1/ptm/m/n/10 sys-tem call.
[603]
Underfull \hbox (badness 4792) in paragraph at lines 41832--41837
[]\T1/ptm/m/n/10 If a file-name starts with []\T1/pcr/m/n/10 . []\T1/ptm/m/n/10
this may need to be matched ex-plic-itly: for ex-am-ple
Underfull \hbox (badness 1107) in paragraph at lines 41832--41837
[]\T1/pcr/m/n/10 Sys.glob("*.RData") []\T1/ptm/m/n/10 may or may not match `\T1
/pcr/m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match
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Underfull \hbox (badness 10000) in paragraph at lines 42124--42128
[]\T1/pcr/m/n/10 sys.status() []\T1/ptm/m/n/10 re-turns a list with com-po-nent
s []\T1/pcr/m/n/10 sys.calls[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sys.parents []\
T1/ptm/m/n/10 and
Underfull \hbox (badness 1584) in paragraph at lines 42139--42142
[]\T1/pcr/m/n/10 sys.call []\T1/ptm/m/n/10 re-turns a call, []\T1/pcr/m/n/10 sy
s.function []\T1/ptm/m/n/10 a func-tion def-i-ni-tion, and []\T1/pcr/m/n/10 sys
.frame []\T1/ptm/m/n/10 and
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Overfull \hbox (25.98041pt too wide) in paragraph at lines 42277--42277
[]\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths
), keepNA=TRUE))[]
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Overfull \hbox (19.22812pt too wide) in paragraph at lines 42357--42357
[]\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/cmtt
/m/n/9 `\T1/pcr/m/n/9 A+C\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 could also be used
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Underfull \hbox (badness 1082) in paragraph at lines 42502--42505
[]\T1/ptm/m/n/10 logical. If []\T1/pcr/m/n/10 TRUE[]\T1/ptm/m/n/10 , func-tions
keep their source in-clud-ing com-ments, see
Underfull \hbox (badness 10000) in paragraph at lines 42529--42531
[][][]\T1/pcr/m/n/10 source[][][][]\T1/ptm/m/n/10 , and [][][]\T1/pcr/m/n/10 lo
adNamespace[][][] []\T1/ptm/m/n/10 which is called from [][][]\T1/pcr/m/n/10 li
brary[][][](.) []\T1/ptm/m/n/10 and uses
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Underfull \hbox (badness 1038) in paragraph at lines 42696--42699
[]\T1/ptm/m/n/10 a log-i-cal (not []\T1/pcr/m/n/10 NA[]\T1/ptm/m/n/10 ) in-di-c
at-ing whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or
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Underfull \hbox (badness 1442) in paragraph at lines 43080--43084
\T1/ptm/m/n/10 con-sider it to be piped or redi-rected: []\T1/pcr/m/n/10 stdout
= TRUE []\T1/ptm/m/n/10 uses a pipe whereas []\T1/pcr/m/n/10 stdout =
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Underfull \hbox (badness 4096) in paragraph at lines 43338--43341
[]\T1/ptm/m/n/10 Use [][][]\T1/pcr/m/n/10 ftable[][][] []\T1/ptm/m/n/10 for pri
nt-ing (and more) of mul-ti-di-men-sional ta-bles. [][][]\T1/pcr/m/n/10 margin.
table[][][][]\T1/ptm/m/n/10 ,
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Underfull \hbox (badness 7888) in paragraph at lines 43453--43457
[]\T1/ptm/m/n/10 On 64-bit plat-forms []\T1/pcr/m/n/10 bin []\T1/ptm/m/n/10 can
have $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., []\T1/pcr/
m/n/10 length(bin) >
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Overfull \hbox (63.78036pt too wide) in paragraph at lines 43715--43715
[] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1"
, "2"), c("A", "B")))),[]
Overfull \hbox (30.0281pt too wide) in paragraph at lines 43717--43717
[] \T1/pcr/m/n/9 array(list(\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 2\TS1/cm
tt/m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), names = nq),[]
Overfull \hbox (55.67578pt too wide) in paragraph at lines 43719--43719
[] \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 4\TS1/cmtt/m/n/9 ` \T1/pcr/m
/n/9 = NULL, \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 5\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 =
NULL), dim=4, dimnames=list(as.character(2:5)))))[]
Underfull \hbox (badness 10000) in paragraph at lines 43732--43734
[]\T1/pcr/m/n/10 removeTaskCallback []\T1/ptm/m/n/10 un-registers a func-tion t
hat was reg-is-tered ear-lier via
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Underfull \hbox (badness 3872) in paragraph at lines 43931--43934
[]\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call
-backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer .
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Underfull \hbox (badness 1655) in paragraph at lines 44420--44427
\T1/ptm/m/n/10 may also be known as `[]\T1/pcr/m/n/10 GB[]\T1/ptm/m/n/10 ', `[]
\T1/pcr/m/n/10 GB-Eire[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 Europe/Belfast[]\T1
/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 Europe/Guernsey[]\T1/ptm/m/n/10 ',
Underfull \hbox (badness 2253) in paragraph at lines 44428--44433
[]\T1/pcr/m/n/10 OlsonNames []\T1/ptm/m/n/10 re-turns a char-ac-ter vec-tor, se
e the ex-am-ples for typ-i-cal cases. It may
Underfull \hbox (badness 1655) in paragraph at lines 44428--44433
\T1/ptm/m/n/10 have an at-tribute []\T1/pcr/m/n/10 "Version"[]\T1/ptm/m/n/10 ,
some-thing like `[]\T1/pcr/m/n/10 "2023a"[]\T1/ptm/m/n/10 '. (It does on sys-te
ms us-ing
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Underfull \hbox (badness 4467) in paragraph at lines 44482--44491
[]\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 OlsonNames []\T1/ptm/m/n/10 re-
turns the time-zone names known to the cur-rently se-
Underfull \hbox (badness 3954) in paragraph at lines 44482--44491
\T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t
he file sys-tem varies,
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Underfull \hbox (badness 1337) in paragraph at lines 44579--44587
\T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de
r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 /
usr/local/etc\T1/ptm/m/n/10 ' or
Underfull \hbox (badness 10000) in paragraph at lines 44588--44591
[]\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym
-link tar-get name of
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Underfull \hbox (badness 3460) in paragraph at lines 44647--44650
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / data . iana . org /
Underfull \hbox (badness 4429) in paragraph at lines 44651--44653
[][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h
tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol-
Overfull \hbox (31.3804pt too wide) in paragraph at lines 44660--44660
[]\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET",
"Eire", ..., but[]
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Overfull \hbox (15.18042pt too wide) in paragraph at lines 45001--45001
[]\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15
g)\n", ncp))),[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 45003--45003
[]\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp
root finding:[]
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Overfull \hbox (84.78088pt too wide) in paragraph at lines 45100--45100
[] \T1/pcr/m/n/10 getOption("deparse
.max.lines", -1L)))[]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 45102--45102
[] \T1/pcr/m/n/10 getOption("deparse
.max.lines", -1L)))[]
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Underfull \hbox (badness 6542) in paragraph at lines 45376--45378
[]\T1/pcr/m/n/10 cospi(x)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sinpi(x)[]\T1/ptm/
m/n/10 , and []\T1/pcr/m/n/10 tanpi(x)[]\T1/ptm/m/n/10 , com-pute []\T1/pcr/m/n
/10 cos(pi*x)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sin(pi*x)[]\T1/ptm/m/n/10 , an
d
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[]\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[
\t\r\n]")
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Underfull \hbox (badness 1708) in paragraph at lines 45563--45571
[]\T1/pcr/m/n/10 try []\T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any
er-rors that oc-cur dur-ing the eval-u-a-tion. If
Underfull \hbox (badness 3713) in paragraph at lines 45563--45571
\T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][
][]\T1/pcr/m/n/10 stderr[][][] []\T1/ptm/m/n/10 con-nec-tion un-less
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Underfull \hbox (badness 4859) in paragraph at lines 45603--45608
[][][]\T1/pcr/m/n/10 options[][][] []\T1/ptm/m/n/10 for set-ting er-ror han-dle
rs and sup-press-ing the print-ing of er-ror mes-sages;
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Underfull \hbox (badness 3895) in paragraph at lines 45665--45678
[]\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the
struc-ture []\T1/pcr/m/n/10 TypeTable []\T1/ptm/m/n/10 in
Underfull \hbox (badness 1303) in paragraph at lines 45665--45678
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue
s are the vec-tor types []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/
m/n/10 "integer"[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2452) in paragraph at lines 45665--45678
[]\T1/pcr/m/n/10 "promise"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "object"[]\T1/ptm
/m/n/10 , []\T1/pcr/m/n/10 "language"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "char"
[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "..."[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "a
ny"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "expression"[]\T1/ptm/m/n/10 ,
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Overfull \hbox (9.78043pt too wide) in paragraph at lines 46018--46018
[]\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[]
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[]\T1/ptm/m/n/10 When a func-tion call-ing []\T1/pcr/m/n/10 UseMethod("fun") []
\T1/ptm/m/n/10 is ap-plied to an ob-ject with class vec-tor
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 46536--46536
[]\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local
es and fonts[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 46545--46545
[]\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little-
endian platforms[]
[673]
Underfull \hbox (badness 1721) in paragraph at lines 46607--46624
[][][]\T1/pcr/m/n/10 file.rename[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 f
ile.symlink[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 dir.create[][][][]\
T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 dir.exists[][][][]\T1/ptm/m/n/10 , [][][]\
T1/pcr/m/n/10 normalizePath[][][][]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 try( substr(x, 1,1) ) # gives \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 in
valid multibyte string\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 error in a UTF-8 locale[]
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[]\T1/ptm/m/n/10 The atomic modes are []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/1
0 , []\T1/pcr/m/n/10 "integer"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "numeric" []\
T1/ptm/m/n/10 (syn-onym []\T1/pcr/m/n/10 "double"[]\T1/ptm/m/n/10 ),
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 mode = "any"[]\T1/ptm/m/n/10 , []\T1/pcr/m
/n/10 is.vector []\T1/ptm/m/n/10 may re-turn []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/
n/10 for the atomic modes, [][][]\T1/pcr/m/n/10 list[][][] []\T1/ptm/m/n/10 and
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Underfull \hbox (badness 1014) in paragraph at lines 47004--47007
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the warn-ing should be out-put im-me
-di-ately, even if
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Overfull \hbox (36.78088pt too wide) in paragraph at lines 47113--47113
[] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes
sages:\n"),[]
[681]
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[]\T1/pcr/m/n/9 ## at the end prints all three warnings, from the \TS1/pcr/m/n
/9 '\T1/pcr/m/n/9 option(warn = 0)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 above[]
Overfull \hbox (90.78033pt too wide) in paragraph at lines 47198--47198
[]\T1/pcr/m/n/9 x <- 1:36; for(n in 1:13) for(m in 1:12) A <- matrix(x, n,m) #
There were 105 warnings ...[]
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[]\T1/pcr/m/n/10 weekdays []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 months []\T1/pt
m/m/n/10 re-turn a char-ac-ter vec-tor of names in the lo-cale in use, i.e.,
[683]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 47293--47293
[]\T1/pcr/m/n/9 ## Show how easily you get month, day, year, day (of {month, w
eek, yr}), ... :[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 47305--47305
[]\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Even simpler: Date -> Matrix
- dropping time info {sec,min,hour, isdst}[]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 47308--47308
[]\T1/pcr/m/n/9 d2mat(seq(as.Date("2000-02-02"), by=1, length.out=30)) # has R
1.0.0\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s release date[]
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Underfull \hbox (badness 10000) in paragraph at lines 47370--47375
[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 arr.ind == TRUE []\T1/ptm/m/n/10 and []\T1
/pcr/m/n/10 x []\T1/ptm/m/n/10 is an [][][]\T1/pcr/m/n/10 array[][][] []\T1/ptm
/m/n/10 (has a [][][]\T1/pcr/m/n/10 dim[][][] []\T1/ptm/m/n/10 at-tribute), the
re-sult is
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[]\T1/pcr/m/n/10 arrayInd(which(x), dim(x), dimnames(x))[]\T1/ptm/m/n/10 , name
ly a ma-trix whose rows each
[685]
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[]\T1/ptm/m/n/10 For a [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 vec-
tor []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 with both []\T1/pcr/m/n/10 FALSE []\T1/
ptm/m/n/10 and []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 val-ues, []\T1/pcr/m/n/10
which.min(x) []\T1/ptm/m/n/10 and
[686]
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[]\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is
at least one:[]
[687]
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[689]
[690]
[691]
[692]
[693]
Underfull \hbox (badness 2846) in paragraph at lines 47999--48003
[]\T1/pcr/m/n/10 .packages() []\T1/ptm/m/n/10 re-turns the names of the cur-ren
tly at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[694]
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[]\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[]
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[]\T1/pcr/m/n/10 .standard_regexps []\T1/ptm/m/n/10 re-turns a list of `stan-da
rd' reg-exps, in-clud-ing el-e-ments named
[695]) (./compiler-pkg.tex
[696]
Chapter 2.
[697]
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[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 options []\T1/ptm/m/n/10 ar-gu-ment can b
e used to con-trol com-piler op-er-a-tion. There are cur-
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\T1/ptm/m/n/10 rently four op-tions: []\T1/pcr/m/n/10 optimize[]\T1/ptm/m/n/10
, []\T1/pcr/m/n/10 suppressAll[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 suppressUndef
ined[]\T1/ptm/m/n/10 , and
[698]
[699]
[700]) (./datasets-pkg.tex
Chapter 3.
[701]
[702]
[703]
[704]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 297--297
[] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[]
[705]
[706]
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[]\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi
ven = FALSE)[]
[707]
[708]
[709]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 613--613
[] \T1/pcr/m/n/9 start = c(lrc = log(.35)), algorithm = "plinear", t
race = TRUE)[]
[710]
[711]
Underfull \hbox (badness 4779) in paragraph at lines 700--703
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[712]
[713]
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[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[714]
[715]
Underfull \hbox (badness 1097) in paragraph at lines 1034--1038
[]\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th
e iden-ti-fi-ca-tion of crim-i-nals.
[716]
[717]
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[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[718]
[719]
[720]
[721]
[722]
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[]\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
time (sec)")[]
[723]
[724]
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[]\T1/ptm/m/n/10 Finally, []\T1/pcr/m/n/10 freeny []\T1/ptm/m/n/10 is a data fr
ame with vari-ables []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lag.q
uarterly.revenue[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 price.index[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 income.level[]\
T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 market.potential []\T1/ptm/m/n/10 ob-taine
d from the above
[725]
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[] \T1/pcr/m/n/9 xlab = "Hip Angle", ylab = "Knee Angle", main = "\TS1/pcr
/m/n/9 '\T1/pcr/m/n/9 gait\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 data : Boy 1")[]
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[]\T1/pcr/m/n/9 matlines(gait[, -1, 1], gait[, -1, 2], type = "l", lty = 1, co
l = adjustcolor("thistle", 1/3))[]
[726]
[727]
[728]
Underfull \hbox (badness 4779) in paragraph at lines 1809--1812
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[729]
[730]
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[]\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil
y = binomial())[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1915--1915
[] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
data = infert)[]
[731]
[732]
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[]\T1/pcr/m/n/9 ## Iris versicolor "differs twice as much from I. setosa as fr
om I. virginica"[]
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[]\T1/pcr/m/n/9 ## equivalence of legacy array (iris3) and data.frame (iris) r
epresentation[]
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[] \T1/pcr/m/n/9 sub(" W.",".Width", dn
i3[[2]])))),[]
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[] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d
ni3[[3]]))))[]
[733]
[734]
[735]
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[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[736]
[737]
[738]
[739]
[740]
[741]
[742]
[743]
[744]
Underfull \hbox (badness 4779) in paragraph at lines 2810--2813
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[745]
[746]
[747]
[748]
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[]\T1/pcr/m/n/9 plot(bill_dep ~ bill_len, data = penguins, pch = sym[sex], col
= pal[species])[]
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[]\T1/pcr/m/n/9 m <- glm(sex ~ bill_len + bill_dep + body_mass, data = adelie,
family = binomial)[]
[749]
[750]
[751]
[752]
[753]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3420--3420
[]\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main =
1.2, pch = ".")[]
[754]
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[]\T1/pcr/m/n/9 myrandu <- matrix(NA_real_, 400, 3, dimnames = list(NULL, c("x
","y","z")))[]
[755]
[756]
[757]
[758]
[759]
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[]\T1/pcr/m/n/9 ## Alaska and Hawaii are placed just off the West Coast (for c
ompact map drawing):[]
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[]\T1/pcr/m/n/9 ## state.center2 := version of state.center with "correct" coo
rdinates for AK & HI:[]
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[]\T1/pcr/m/n/9 ## From https://pubs.usgs.gov/gip/Elevations-Distances/elvadis
t.html#Geographic%20Centers[]
[760]
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\T1/ptm/m/n/10 Av. Cir-cu-laire, 3, B-1180 BRUS-SELS Cur-rently at [][]$\T1/pcr
/m/n/10 https : / / www . sidc . be / SILSO /
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[]\T1/pcr/m/n/9 ## How to recreate the "old" sunspot.month (R <= 3.0.3) =: sun
spot.month.0[]
[761]
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[]\T1/pcr/m/n/9 (t2 <- c(min( end(sm)[1],end(sy)[1]), 12)) # Dec 1983 (will n
ot be updated!)[]
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[] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[]
[762] [763]
[764]
Underfull \hbox (badness 4779) in paragraph at lines 4088--4091
[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr
oupedData", "groupedData",
[765]
[766]
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[] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
supplement")[]
[767]
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[]\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/pcr/m/n/10 h
ttps : / / web . archive . org / web /
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\T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma
n / sitephotos /
[768]
[769]
[770]
[771]
[772]
[773] [774]
[775]
[776]
[777]
[778]
[779]
[780]
[781]) (./grDevices-pkg.tex
[782]
Chapter 4.
[783]
[784]
[785]
[786]
Underfull \hbox (badness 4752) in paragraph at lines 299--304
[]\T1/ptm/m/n/10 Apart from that, []\T1/pcr/m/n/10 axisTicks() []\T1/ptm/m/n/10
just calls the C func-tion []\T1/pcr/m/n/10 CreateAtVector() []\T1/ptm/m/n/10
in
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\T1/ptm/m/n/10 `\T1/ptm/m/sl/10 R\T1/pcr/m/n/10 /src/main/plot.c\T1/ptm/m/n/10
' which is also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack
-age func-tion
[787]
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[]\T1/pcr/m/n/9 aX(2, print(ya <- axisTicks(pu[3:4], log = TRUE))) # 10 20 50
100 (y axis)[]
[788]
[789]
[790]
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[]\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[]
[791]
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[793]
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[796]
Underfull \hbox (badness 2245) in paragraph at lines 919--924
[]\T1/ptm/m/n/10 Hexadecimal string col-ors can be in the long hex-adec-i-mal f
orm (e.g., []\T1/pcr/m/n/10 "#rrggbb" []\T1/ptm/m/n/10 or
[797]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 983--983
[]\T1/pcr/m/n/9 names(clmult) <- sapply(clmult, function(x) paste(crgb[,x[1]],
collapse = ","))[]
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[] \T1/pcr/m/n/9 lattice::cloud(blue ~ red + green, data = as.data.frame(tc
), col = cNms)[]
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[]\T1/pcr/m/n/9 cNms[isC] # "white" "black" "blue" "cyan" "green" "magenta" "r
ed" "yellow"[]
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[] \T1/pcr/m/n/9 plot3d (tc, col = cNms, size = 11) # --> rotate w/ mouse; e
nlarged corners:[]
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[798]
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[800]
[801]
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[]\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm
. The source code is in
[802]
[803]
[804]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1410--1410
[]\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab",
scale.in = 255))[]
[805]
[806]
[807]
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[]\T1/ptm/m/n/10 character: Does the de-vice sup-port pat-tern fills? One or mo
re of
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[]\T1/pcr/m/n/10 c("LinearGradient", "RadialGradient", "TilingPattern")
[808]
[809]
[810]
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[812]
Underfull \hbox (badness 1565) in paragraph at lines 1962--1967
[]\T1/ptm/m/n/10 The de-fault for []\T1/pcr/m/n/10 dev.print []\T1/ptm/m/n/10 i
s to pro-duce and print a postscript copy. This will not
Underfull \hbox (badness 1354) in paragraph at lines 1962--1967
\T1/ptm/m/n/10 sys-tem: see [][][]\T1/pcr/m/n/10 postscript[][][] []\T1/ptm/m/n
/10 for how to set this up. Win-dows users may pre-fer to use
[813]
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[]\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res
= 72,[]
[814]
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[]\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of []\T1/pcr
/m/n/10 ghostscript[]\T1/ptm/m/n/10 , but are likely to in-
Underfull \hbox (badness 2057) in paragraph at lines 2086--2096
[]\T1/pcr/m/n/10 "tiffg4"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiffgray"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "tifflzw"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiffp
ack"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiff12nc"[]\T1/ptm/m/n/10 , []\T1/pcr/
m/n/10 "tiff24nc"[]\T1/ptm/m/n/10 ,
[815]
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[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the
set-ting of
[816]
[817]
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[]\T1/pcr/m/n/10 embedGlyphs(file, glyphInfo, outfile = file, options = charac
ter())[]
[818]
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[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
doc-u-men-ta-tion) are
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[]\T1/pcr/m/n/10 embedGlyphs() []\T1/ptm/m/n/10 is rec-om-mended for []\T1/pcr/
m/n/10 pdf() []\T1/ptm/m/n/10 files that con-tain type-set glyphs (see
[819]
[820]
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[]\T1/ptm/m/n/10 are given, then it uses those in a call to []\T1/pcr/m/n/10 se
tGraphicsEventHandlers []\T1/ptm/m/n/10 to re-place
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\T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co
m-pat-i-bil-ity with pre-2.12.0
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\T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e
vent han-dlers is to set them us-ing
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[]\T1/pcr/m/n/10 setGraphicsEventHandlers []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10
setGraphicsEventEnv []\T1/ptm/m/n/10 on one or more graph-ics
[821]
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[]\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[]
[822]
[823]
[824]
[825]
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[]\T1/pcr/m/n/10 gray.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re
v = FALSE)
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[]\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re
v = FALSE)[]
[826]
[827]
[828]
[829]
Underfull \hbox (badness 10000) in paragraph at lines 3143--3144
[830]
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[833]
[834]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3472--3472
[]\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized
= FALSE)[]
[835]
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[]\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv",
scale.in = 255))[]
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[]\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale.
out = NULL))[]
[836]
[837]
[838]
Underfull \hbox (badness 10000) in paragraph at lines 3716--3722
[]\T1/pcr/m/n/10 nclass.FD []\T1/ptm/m/n/10 uses the Freedman-Diaconis choice b
ased on the inter-quartile range
[839]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 3791--3791
[]\T1/pcr/m/n/10 palette.colors(n = NULL, palette = "Okabe-Ito", alpha, recycl
e = FALSE,[]
[840]
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[]\T1/pcr/m/n/9 (palette(gray(seq(0,.9,length.out = 25)))) # gray scales; prin
t old palette[]
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[]\T1/pcr/m/n/9 ## Demonstrate the colors 1:8 in different palettes using a cu
stom matplot()[]
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[] \T1/pcr/m/n/9 matplot(x, type = "l", lwd = 4, lty = 1, col = 1:n, ylab =
"", main=main)[]
[841]
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[]\T1/pcr/m/n/9 palROB <- colorRampPalette(c("red", "darkorange2", "blue"), sp
ace = "Lab")[]
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[]\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE,
fixup = TRUE)
[842]
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[]\T1/ptm/m/n/10 the type of palettes to list: []\T1/pcr/m/n/10 "qualitative"[]
\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sequential"[]\T1/ptm/m/n/10 ,
[843]
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[]\T1/ptm/m/n/10 For ex-am-ple, []\T1/pcr/m/n/10 "Dark 3" []\T1/ptm/m/n/10 work
s well for shad-ing points or lines in up to five groups,
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\T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space
& oldid = 883465135$[][]\T1/ptm/m/n/10 .
[844]
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[845]
[846]
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[]\T1/ptm/m/n/10 as `\T1/pcr/m/n/10 "CP1250.enc"\T1/ptm/m/n/10 ' (Cen-tral Eu-r
o-pean), []\T1/pcr/m/n/10 "CP1251.enc"
[847]
[848]
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\T1/ptm/m/n/10 PostScript fonts fam-i-lies of those names which are in-cluded (
or cloned) in all com-mon
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\T1/ptm/m/n/10 cod-ings (ex-cept []\T1/pcr/m/n/10 "TeXtext"[]\T1/ptm/m/n/10 ) a
gree over that range. Some en-cod-ings are su-per-sets of
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\T1/ptm/m/n/10 ISO-Latin1. How-ever, if ac-cented and spe-cial char-ac-ters do
not come out as you ex-
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[]\T1/ptm/m/n/10 arguments []\T1/pcr/m/n/10 width[]\T1/ptm/m/n/10 , []\T1/pcr/m
/n/10 height[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 onefile[]\T1/ptm/m/n/10 , []\T1
/pcr/m/n/10 family[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 title[]\T1/ptm/m/n/10 , [
]\T1/pcr/m/n/10 fonts[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 version[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 paper[]\T1/ptm/m/n/
10 , []\T1/pcr/m/n/10 encoding[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 bg[]\T1/ptm/m
/n/10 , []\T1/pcr/m/n/10 fg[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pointsize[]\T1/p
tm/m/n/10 , []\T1/pcr/m/n/10 pagecentre[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 colormodel[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 useDingbats[]\T1
/ptm/m/n/10 , []\T1/pcr/m/n/10 useKerning[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 fi
llOddEven[]\T1/ptm/m/n/10 ,
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pdfTeX warning (ext4): destination with the same identifier (name{Rfn.symbol})
has been already used, duplicate ignored
<to be read again>
\relax
l.4896 \aliasA{symbol}{plotmath}{symbol}
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[]\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, [][]$\T1/pcr/m/n/10 https : / / ww
w . iso . org / standard / 34342 . html$[][]\T1/ptm/m/n/10 . See also
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[]\T1/pcr/m/n/9 ## Not run: dev.print(png, filename = "myplot.png", width = 10
24, height = 768)[]
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[]\T1/ptm/m/n/10 For use with []\T1/pcr/m/n/10 onefile = FALSE[]\T1/ptm/m/n/10
, give a C in-te-ger for-mat such as
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[]\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t
ion by Brian D'Urso
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[][][]\T1/pcr/m/n/10 postscriptFonts[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 Devices[][][][]\T1/ptm/m/n/10 , and [][][]\T1/pcr/m/n/10 check.options[][][]
[]\T1/ptm/m/n/10 which is called from both
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[]\T1/pcr/m/n/10 "AvantGarde"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Bookman"[]\T1
/ptm/m/n/10 , []\T1/pcr/m/n/10 "Courier"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "He
lvetica"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Helvetica-Narrow"[]\T1/ptm/m/n/10
,
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[]\T1/pcr/m/n/10 "NewCenturySchoolbook"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Pal
atino" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "Times"[]\T1/ptm/m/n/10 ; []\T1/pc
r/m/n/10 "URWGothic"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 "URWBookman"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "NimbusMon"[]\
T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "NimbusSan" []\T1/ptm/m/n/10 (syn-onym []\T1/p
cr/m/n/10 "URWHelvetica"[]\T1/ptm/m/n/10 ),
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[]\T1/ptm/m/n/10 There are also map-pings for []\T1/pcr/m/n/10 "ComputerModern"
[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ComputerModernItalic" []\T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/10 "Japan1"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Japan1HeiMin"[]\T
1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Japan1GothicBBB"[]\T1/ptm/m/n/10 , and []\T1/p
cr/m/n/10 "Japan1Ryumin" []\T1/ptm/m/n/10 for
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[]\T1/pcr/m/n/10 BousungEG-Light-GB []\T1/ptm/m/n/10 can be found at [][]$\T1/p
cr/m/n/10 https : / / ftp . gnu . org / pub / non-[]gnu /
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[]\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[]
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[]\T1/ptm/m/n/10 Calling []\T1/pcr/m/n/10 quartz() []\T1/ptm/m/n/10 sets [][][]
\T1/pcr/m/n/10 .Device[][][] []\T1/ptm/m/n/10 to []\T1/pcr/m/n/10 "quartz" []\T
1/ptm/m/n/10 for on-screen de-vices and to
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[] \T1/pcr/m/n/9 quartzFonts("mono") # the list(mono = ..) sublist o
f quartzFonts()[]
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\T1/ptm/m/n/10 play List", [][]$\T1/pcr/m/n/10 https : / / stattech . wordpress
. fos . auckland . ac . nz / 2015 / 12 / 21 /
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[]\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15,
sep = "."))[]
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[]\T1/pcr/m/n/10 rgb2hsv []\T1/ptm/m/n/10 trans-forms col-ors from RGB space (r
ed/green/blue) into HSV space
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[]\T1/pcr/m/n/9 p <- persp(x, y, fxy <- outer(x,y), phi = 20, theta = 15, r =
3, ltheta = -75,[]
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[]\T1/pcr/m/n/9 ## now some "horizontal rays" (going from center to very left
or very right):[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 6895--6895
[] \T1/pcr/m/n/9 lines(trans3d(x=seq(x1, x2, by=0.5), y= -0.7, z = z, pmat
= p, continuous = CNT),[]
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[]\T1/pcr/m/n/9 doHor(-10, 0, z = -0.5, col = 2) # x in [-10, 0] -- to the v
ery left : fine[]
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[]\T1/pcr/m/n/9 doHor(-.5, 2, z = -0.52,col = 4) # x in [-0.5, 2] only {to th
e right} --> all fine[]
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[]\T1/pcr/m/n/9 ## but now, x in [-0.5, 20] -- "too far" ==> "wrap around" pro
blem (without \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 continuous=TRUE\TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 ):[]
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[]\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp
inch,
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[]\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize
= 12,[]
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[]\T1/ptm/m/n/10 arguments []\T1/pcr/m/n/10 width[]\T1/ptm/m/n/10 , []\T1/pcr/m
/n/10 height[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pointsize[]\T1/ptm/m/n/10 , []\
T1/pcr/m/n/10 record[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 rescale[]\T1/ptm/m/n/10
,
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[]\T1/pcr/m/n/10 xpinch[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 ypinch[]\T1/ptm/m/n/
10 , []\T1/pcr/m/n/10 bg[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 canvas[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 gamma[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 xpos[]\T1/ptm/m
/n/10 , []\T1/pcr/m/n/10 ypos[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 buffered[]\T1/
ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 restoreConsole[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 clickToConfi
rm[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 title[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10
fillOddEven []\T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/9 windows() # make sure we have the right device type (availabl
e on Windows only)[]
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[]\T1/ptm/m/n/10 The \T1/phv/m/n/10 R \T1/ptm/m/n/10 func-tion is a wrap-per fo
r two de-vices, one based on Xlib ([][]$\T1/pcr/m/n/10 https : / /
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\T1/pcr/m/n/10 en . wikipedia . org / wiki / Xlib$[][]\T1/ptm/m/n/10 ) and one
us-ing cairo-graph-ics ([][]$\T1/pcr/m/n/10 https : / / www .
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[] \T1/pcr/m/n/10 fonts, family, xpos, ypos, title, type, antialias, symbol
family)[]
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[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
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[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" []\T1/ptm/m/n/10 for CJ
K lan-guages and
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[]\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of []
\T1/pcr/m/n/10 quote(pi) []\T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/10 expression(10^degree)[]\T1/ptm/m/n/10 ) have been seen on Linu
x sys-tems which have the Wine
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[]\T1/pcr/m/n/10 type = "Xlib" []\T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-d
o-Color', `GrayScale', []\T1/pcr/m/n/10 StaticGray []\T1/ptm/m/n/10 and
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[] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
= 6, xpos = 0,[]
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[]\T1/pcr/m/n/9 op <- options(warn = 2)# ==> warnings would be errors, we supp
ress the one "we know":[]
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[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., []\T1/pcr/m/n/10
number[i] []\T1/ptm/m/n/10 is the mul-ti-plic-ity of
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[]\T1/pcr/m/n/9 xy <- data.frame(x = round(sort(stats::rnorm(100))), y = stats
::rnorm(100))[]
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[903]) (./graphics-pkg.tex
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Chapter 5.
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[]\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag
es, use []\T1/pcr/m/n/10 library(help =
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[] \T1/pcr/m/n/10 gap.axis <- if(perpendicular(side, las)) 0.25 else 1[]
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[]\T1/ptm/m/n/10 When []\T1/pcr/m/n/10 at = NULL[]\T1/ptm/m/n/10 , pretty tick
mark lo-ca-tions are com-puted in-ter-nally (the same way
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[]\T1/pcr/m/n/9 ## now shrink the window (in x- and y-direction) and observe t
he axis labels drawn[]
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[]\T1/pcr/m/n/9 axis.Date(3, at = as.integer(as.Date("2023-04-01")), col.axis
= "darkgreen")[]
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[]\T1/pcr/m/n/9 axis.POSIXct(3, at = as.POSIXct("2022-10-01 00:01:30"), col.ax
is = "orange")[]
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[]\T1/pcr/m/n/9 axis.POSIXct(3, at = as.numeric(as.POSIXct("2022-10-01 00:00:3
0")) + 0.25,[]
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[] \T1/pcr/m/n/9 col.axis = "forestgreen", col = "darkgreen", m
gp = c(3,2,0))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 725--725
[]\T1/pcr/m/n/9 plot(data.frame(HST, y = 1), xaxt = "n", xlab = "Hawaii Standa
rd Time (HST)")[]
Underfull \hbox (badness 10000) in paragraph at lines 752--756
[]\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][][]\T1/pcr
/m/n/10 par[][][]("xaxp") []\T1/ptm/m/n/10 or
Underfull \hbox (badness 3250) in paragraph at lines 752--756
[][][]\T1/pcr/m/n/10 par[][][]("yaxp") []\T1/ptm/m/n/10 de-pend-ing on the []\T
1/pcr/m/n/10 side []\T1/ptm/m/n/10 ar-gu-ment ([]\T1/pcr/m/n/10 par("xaxp") []\
T1/ptm/m/n/10 if
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[] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[]
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[] \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend =
NULL, ...)[]
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[][][]\T1/pcr/m/n/10 plot[][][](..., type = "h")[]\T1/ptm/m/n/10 , [][][]\T1/pc
r/m/n/10 dotchart[][][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 hist[][][] []\T1
/ptm/m/n/10 for bars of a \T1/ptm/m/it/10 con-tin-u-ous \T1/ptm/m/n/10 vari-abl
e.
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[] \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = "
# {passengers}", legend.text = TRUE)[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1040--1040
[]\T1/pcr/m/n/9 (xt <- xtabs(Freq ~ Survived + Class + Sex, d.Titanic, subset
= Age=="Adult"))[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 1042--1042
[]\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur
vived, *)", color=TRUE)[]
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[]\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches ..
outside hinges"):[]
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\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 horizontal []\T1/ptm/m/n/10 is false, and
[]\T1/pcr/m/n/10 xlim []\T1/ptm/m/n/10 hor-i-zon-tally. []\T1/pcr/m/n/10 xaxt[]
\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 yaxt[]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 whisker line type (de-fault: []\T1/pcr/m/n/10 "dashed"[]\T1/pt
m/m/n/10 ),
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Overfull \hbox (20.58041pt too wide) in paragraph at lines 1594--1594
[]\T1/pcr/m/n/9 boxplot(z, col.axis = "skyblue3", main = "boxplot(*, col.axi
s=..,main=..)")[]
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[]\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main = "plot(*, col.axi
s=..,main=..)")[]
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[]\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill
= "grey40",[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1602--1602
[] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 1635--1635
[] \T1/pcr/m/n/10 yaxlabels = NULL, xlim = NULL, ylim = c(0, 1), weights = NU
LL, ...)[]
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Underfull \hbox (badness 10000) in paragraph at lines 1908--1914
[][][]\T1/pcr/m/n/10 contourLines[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
filled.contour[][][] []\T1/ptm/m/n/10 for color-filled con-tours, [][][]\T1/pcr
/m/n/10 contourplot[][][] []\T1/ptm/m/n/10 (and
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1928--1928
[]\T1/pcr/m/n/9 contour(x, x, z, ylim = c(-6, 6), nlevels = 20, lty = 2, metho
d = "simple",[]
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[]\T1/pcr/m/n/9 contour(z, levels=levs[-c(1,length(levs))], col = 1:5, lwd = 1
:3 *1.5, lty = 1:3)[]
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[]\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1965--1965
[]\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[]
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[]\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns,
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[]\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.values = given
.depth, rows = 1)[]
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[]\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c(
TRUE, FALSE))[]
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[]\T1/pcr/m/n/10 dotchart(x, labels = NULL, groups = NULL, gdata = NULL, offse
t = 1/8,
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[] \T1/pcr/m/n/10 ann = par("ann"), xaxt = par("xaxt"), frame.plot = T
RUE, log = "",[]
[941]
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[]\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use []\T1/pcr/m/n/10
"n" []\T1/ptm/m/n/10 to sup-press and see also
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[] \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO
rRd", rev = TRUE),[]
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[] \T1/pcr/m/n/10 plot.title, plot.axes, key.title, key.axes, ke
y.border = NULL,[]
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\T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n
ot ap-ply to
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[][][]\T1/pcr/m/n/10 contour[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 image
[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 hcl.colors[][][][]\T1/ptm/m/n/10
, [][][]\T1/pcr/m/n/10 gray.colors[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
palette[][][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 contourplot[][][] []\T1/p
tm/m/n/10 and
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[]\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c
(mx, my, 7))[]
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[]\T1/pcr/m/n/9 plot(8:270, log="xy") ; grid() # at (1, 10, 100); if preferrin
g "all" grid lines:[]
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[] \T1/pcr/m/n/10 density = NULL, angle = 45, col = "lightgray", border =
NULL,[]
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\T1/pcr/m/n/10 1)[]\T1/ptm/m/n/10 , they are the rel-a-tive fre-quen-cies []\T1
/pcr/m/n/10 counts/n []\T1/ptm/m/n/10 and in gen-eral sat-isfy
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[]\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe
r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[]
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[]\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a
suggestion only"[]
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[][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][][]\T1
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[953]
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[]\T1/pcr/m/n/9 ## The default fuzz in hist.default() "kills" this, with a "w
rong" message:[]
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[]\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL
SE, pch = 19, ...)[]
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[] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel)
, n = 1, plot = plot, ...)[]
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 useRaster []\T1/ptm/m/n/10 is not spec-i-f
ied, raster im-ages are used when the
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[][][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") []\T1/ptm/m/n/10 is true,
the grid is reg-u-lar and ei-ther
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[][][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage []\T1/pt
m/m/n/10 is []\T1/pcr/m/n/10 "yes" []\T1/ptm/m/n/10 or it is
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[]\T1/pcr/m/n/9 # Visualize as matrix. Need to transpose matrix and then flip
it horizontally:[]
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[]\T1/pcr/m/n/9 imageM <- function(m, grid = max(dim(m)) <= 25, asp = (nrow(m)
-1)/(ncol(m)-1), ...) {[]
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[] \T1/pcr/m/n/9 axis(side, at=at, labels=as.character(j+1L), col="gray
", col.axis=1, ...)[]
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[]\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space =
0, horiz = TRUE)[]
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[] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col =
par("fg"),[]
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[] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
FALSE,[]
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[] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c
ex = 0.8, adj = 0)[]
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[] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[]
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[] \T1/pcr/m/n/9 cex = 1+(-1:2)/8, trace = TRUE)# trace: show computed l
engths & coords[]
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[] \T1/pcr/m/n/9 title("legend(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 top\TS1/pcr/m/n/
9 '\T1/pcr/m/n/9 , lty = c(2, -1, 1), pch = c(NA, 3, 4), merge = TRUE)",[]
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[] \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj
= c(0, 0.3))[]
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[]\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Filled\TS1/pcr/m/n/9 ' \T1/pc
r/m/n/9 boxes -- see also example(barplot) which may call legend(*, fill=)[]
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[]\T1/pcr/m/n/9 legend("topright", rownames(VADeaths), fill = gray.colors(nrow
(VADeaths)))[]
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[]\T1/pcr/m/n/9 legend("bottomright", paste("sin(", 1:7, "pi * x)"), col = 1:7
, lty = 1:7,[]
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[]\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c
ol = "blue")[]
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[]\T1/pcr/m/n/9 legend("topleft", "(x,y)", pch=1, title= "topleft, inset =
.05", inset = .05)[]
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[]\T1/pcr/m/n/9 legend("topright", "(x,y)", pch=1, title= "topright, inset
= .02",inset = .02)[]
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[] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[]
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[]\T1/pcr/m/n/9 legend("bottomleft", c("This legend", "has", "optimally sized"
, "columns."),[]
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[][][]\T1/pcr/m/n/10 lines.formula[][][] []\T1/ptm/m/n/10 for the for-mula meth
od; [][][]\T1/pcr/m/n/10 points[][][][]\T1/ptm/m/n/10 , par-tic-u-larly for []\
T1/pcr/m/n/10 type %in%
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[] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb
ose"))[]
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[]\T1/pcr/m/n/9 nd <- length(dv <- seq(as.Date("1959-02-21"), by = "weeks", le
ngth.out = 100))[]
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[]\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a
mul-ti-ple of
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[]\T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify []\T1/pcr/m/n
/10 oma []\T1/ptm/m/n/10 when chang-ing
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[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are
to be used, see
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[]\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel
= panel.cor,[]
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[] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma
=c(2,2,3,2))[]
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\T1/ptm/m/n/10 func-tions such as [][][]\T1/pcr/m/n/10 plot.default[][][][]\T1/
ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.window[][][][]\T1/ptm/m/n/10 , [][][]\T1
/pcr/m/n/10 points[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lines[][][][]\T
1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 abline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc
r/m/n/10 axis[][][][]\T1/ptm/m/n/10 ,
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[984 </build/r/src/R-4.5.1/library/graphics/help/figures/mai.pdf>]
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[986 </build/r/src/R-4.5.1/library/graphics/help/figures/oma.pdf>]
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[]\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9,
physicians = 9,[]
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[] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[]
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[]\T1/pcr/m/n/9 points(trans3d(xy[,1], xy[,2], z = 6, pmat = res), co
l = 2, pch = 16)[]
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[]\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p
yramid" = 5),[]
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[] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow
3"), border = FALSE)[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot}) ha
s been already used, duplicate ignored
<to be read again>
\relax
l.6120 \aliasA{plot}{plot.default}{plot}
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[]\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext
remely silly[]
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[] \T1/pcr/m/n/10 main = paste("Histogram of", paste(x$xname, co
llapse = "\n")),[]
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[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
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[]\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th
is works as a mul-ti-ple of
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[][]
[1009 </build/r/src/R-4.5.1/library/graphics/help/figures/pch.pdf>]
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[]\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b
lue", cex = .6,[]
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[]\T1/pcr/m/n/9 ## Illustration of pch = 0:25 (as in the figure shown above in
PDF/HTML help)[]
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[]\T1/pcr/m/n/9 ## Not run: png("pch.png", height = 0.7, width = 7, res = 100,
units = "in")[]
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[] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab =
"", main = main)[]
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[]\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev
in Buhr
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[] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b
order = "red")[]
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[]\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats::
rnorm(n)))))[]
[1013]
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[]\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther []\T
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[]\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7
, end = 0.1))[]
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[]\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
ace = "Lab")[]
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[]\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit
h obs.number):[]
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[]\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE),[]
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[] \T1/pcr/m/n/10 xlim = NULL, ylim = c(0, 1), axes = TRUE, weights =
NULL, ...)[]
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[] \T1/pcr/m/n/10 subset = NULL, weights = NULL, drop.unused.levels =
FALSE)[]
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[]\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us = FALSE,[]
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[]\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us = FALSE,[]
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[] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
, key.loc = 0:1,[]
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[]\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont =
NULL, ...)
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[]\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont =
NULL, ...)[]
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[]\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL,
...,[]
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[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 number[i] == 1[]\T1/ptm/m/n/10 , a (sligh
tly en-larged) usual plot-ting sym-bol ([]\T1/pcr/m/n/10 pch[]\T1/ptm/m/n/10 )
is drawn. For
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[]\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035
, seg.lwd = .8)[]
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[]\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100,
lambda = 2),[]
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[]\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[]
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[] \T1/pcr/m/n/9 "Le fran�ais, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est facile:
R�gles, Libert�, Egalit�, Fraternit�...")[]
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[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color []\T1/pcr/m
/n/10 par(c("font.sub",
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[]\T1/ptm/m/n/10 The po-si-tions of []\T1/pcr/m/n/10 xlab[]\T1/ptm/m/n/10 , []\
T1/pcr/m/n/10 ylab []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 sub []\T1/ptm/m/n/10 a
re []\T1/pcr/m/n/10 line []\T1/ptm/m/n/10 (de-fault for []\T1/pcr/m/n/10 xlab [
]\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 ylab []\T1/ptm/m/n/10 be-ing
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l.9222 \HeaderA{units}{Graphical Units}{units}
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[]\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th
e poly-gon. See
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[]\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code =
2, length = 0.1)[]
[1046]) (./grid-pkg.tex
Chapter 6.
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[]\T1/ptm/m/n/10 Modification of the view-port (should all be valid ar-gu-ments
to the
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[] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un
it(1, "inches")))[]
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[] \T1/pcr/m/n/9 vpList(vpStack(viewport(x=0.1, y=0.1, width=0.5
, height=0.5,[]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="B"),[]
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[] \T1/pcr/m/n/9 viewport(x=0.1, y=0.1, width=0.5
, height=0.5,[]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="C"),[]
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[] \T1/pcr/m/n/9 viewport(x=0.1, y=0.1, width=0.5
, height=0.5,[]
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[] \T1/pcr/m/n/9 just=c("left", "bottom"
), name="D")),[]
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject
de-scrib-ing a cir-cle), but only
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[] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[]
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[]\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla
ck"), name="r1")[]
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[]\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey"
), name="r2")[]
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[]\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi
te"), name="r3")[]
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[]\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio
ns []\T1/pcr/m/n/10 preDrawDetails[]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 Both func-tions call []\T1/pcr/m/n/10 editDetails []\T1/ptm/m/
n/10 to al-low a grob to per-form cus-tom ac-tions and
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de
-scrib-ing a frame), but only
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[]\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global =
FALSE)[]
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[]\T1/ptm/m/n/10 The jus-ti-fi-ca-tion of the glyphs rel-a-tive to the ([]\T1/p
cr/m/n/10 x[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 ) lo-ca-tion.
Can be
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[]\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs =
FALSE,[]
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[] \T1/pcr/m/n/9 children=gList(grob(name="child", vp
="vp1::vp2")),[]
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[] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp =
NULL)[]
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[]\T1/ptm/m/n/10 A func-tion that re-turns an affine trans-for-ma-tion ma-trix;
see
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[]\T1/ptm/m/n/10 Another pos-si-ble use of []\T1/pcr/m/n/10 grid.group() []\T1/
ptm/m/n/10 is to spec-ify both []\T1/pcr/m/n/10 src []\T1/ptm/m/n/10 and []\T1/
pcr/m/n/10 dst []\T1/ptm/m/n/10 and com-bine
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[]\T1/ptm/m/n/10 is only drawn where it is NOT over-lapped by []\T1/pcr/m/n/10
src[]\T1/ptm/m/n/10 . The fol-low-ing (ex-tended) Porter-
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[]\T1/pcr/m/n/10 "multiply"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "screen"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "overlay"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "darke
n"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lighten"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n
/10 "color.dodge"[]\T1/ptm/m/n/10 ,
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[] \T1/pcr/m/n/9 mask <- as.mask(rectGrob(gp=gpar(col=NA, fill="grey50")), ty
pe="luminance")[]
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[] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[]
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[] \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[]
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[]\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, width=0.25, height=0.25, just=
c("left", "bottom")))[]
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[]\T1/ptm/m/n/10 There are two hooks called []\T1/pcr/m/n/10 "before.grid.newpa
ge" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "grid.newpage" []\T1/ptm/m/n/10 (see
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[] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
NULL,[]
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[] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
NULL,[]
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[] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant
i-clockwise")[]
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[] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other
anti-clockwise")[]
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[]\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s
ame path, thus[]
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec
t de-scrib-ing seg-ments), but only
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[] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un
it(1, "inches")))[]
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[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
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[]\T1/pcr/m/n/9 grid.text(quote(frac(e^{-x^2/2}, sqrt(2*pi))), x=x, y=y, rot=s
tats::runif(20, -45,45),[]
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[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 gridCoords []\T1/ptm/m/n/10 a nu-meric ve
c-tor. For []\T1/pcr/m/n/10 gridGrobCoords []\T1/ptm/m/n/10 a list
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\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 "GridCoords" []\T1/ptm/m/n/10 ob-jects. For
[]\T1/pcr/m/n/10 gridGTreeCoords []\T1/ptm/m/n/10 a list of ei-ther
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[]\T1/ptm/m/n/10 Either a []\T1/pcr/m/n/10 "GridGrobCoords" []\T1/ptm/m/n/10 ob
-ject (a list of lists with com-po-nents []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 an
d []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 ) or a
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[]\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 grid.legend()[]\T1/ptm/m/n/10 : all the a
r-gu-ments above are passed to
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[]\T1/pcr/m/n/9 unitType(min(unit(1, "in"), unit(1, "npc") + unit(1, "mm")), r
ecurse=TRUE)[]
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[]\T1/pcr/m/n/10 viewportTransform(group, shear=groupShear(), flip=groupFlip()
, device=TRUE)
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[]\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for
use in []\T1/pcr/m/n/10 downViewport []\T1/ptm/m/n/10 or
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[][][]\T1/pcr/m/n/10 viewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 push
Viewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 popViewport[][][][]\T1/pt
m/m/n/10 , [][][]\T1/pcr/m/n/10 downViewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/
pcr/m/n/10 seekViewport[][][][]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp
ar(col="red"))))[]
[1167]) (./methods-pkg.tex
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Chapter 7.
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[]\T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how
co-erce meth-ods work. Use
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[][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] []\T1/ptm/m/n/10 for other in-
for-ma-tion about group generic func-tions; [][]Meth-
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[]\T1/pcr/m/n/9 ## vector. The next method will always be the default, usuall
y a primitive.[]
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[]\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w
ith no arguments[]
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[]\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho
ut arguments[]
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[]\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th
e default method[]
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[]\T1/pcr/m/n/9 ## call f() with 1 argument: the default "B0" is not passed b
y callNextMethod[]
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[]\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the
"B0" method[]
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[]\T1/pcr/m/n/9 ## Although the argument here is numeric, it\TS1/pcr/m/n/9 '\T
1/pcr/m/n/9 s still the "B0" method that\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s called[
]
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[]\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N
umber" method[]
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[]\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE))
) # the default[]
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[]\T1/ptm/m/n/10 The ar-gu-ment to []\T1/pcr/m/n/10 insertSource []\T1/ptm/m/n/
10 can be an ob-ject of class
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[]\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age
, use []\T1/pcr/m/n/10 where =
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[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an [][][]\T1/pcr/m/n/10 environment
[][][][]\T1/ptm/m/n/10 ) used for meth-ods dis-patch, call
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[]\T1/pcr/m/n/10 getMethods(f, where, table = FALSE) # deprecated -> use getMe
thodsForDispatch()[]
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[]\T1/ptm/m/n/10 As you might ex-pect [][][]\T1/pcr/m/n/10 setGeneric[][][] []\
T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 setGroupGeneric[][][] []\T1/ptm/m/n/10 c
re-ate ob-jects of class
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[]\T1/ptm/m/n/10 Object of class []\T1/pcr/m/n/10 "optionalMethod" []\T1/ptm/m/
n/10 (a union of classes []\T1/pcr/m/n/10 "function" []\T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[]
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[]\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[]
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[]\T1/ptm/m/n/10 Function []\T1/pcr/m/n/10 implicitGeneric() []\T1/ptm/m/n/10 r
e-turns the im-plicit generic ver-sion,
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[]\T1/pcr/m/n/10 setGenericImplicit() []\T1/ptm/m/n/10 turns a generic im-plici
t, []\T1/pcr/m/n/10 prohibitGeneric() []\T1/ptm/m/n/10 pre-vents
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[]\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][][]\T1/pcr/m/n/10
getClass[][][] []\T1/ptm/m/n/10 and the de-scrip-tion of class
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[]
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[] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longit
ude =
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[]\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) {
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[]\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character")
,
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[]\T1/ptm/m/n/10 A call to [][][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) []
\T1/ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to
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[]\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char
acter(),
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[] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac
cess,[]
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[]\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here)
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[]\T1/ptm/m/n/10 For ad-di-tional in-for-ma-tion see doc-u-men-ta-tion for the
im-por-tant steps: ([][][]\T1/pcr/m/n/10 setMethod[][][]()[]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha
t eval-u-ates a call to
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[]\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
inheritance[]
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[]\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli
er fails here)[]
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[]\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho
d for classB[]
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[]\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...)
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[]\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p
assed to
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[]\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o
ds for this class are found (us-ing
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[]\T1/ptm/m/n/10 The de-fault method for []\T1/pcr/m/n/10 $initialize() []\T1/p
tm/m/n/10 is equiv-a-lent to in-vok-ing the method
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[]\T1/ptm/m/n/10 Typically, a spe-cial-ized []\T1/pcr/m/n/10 $initialize() []\T
1/ptm/m/n/10 method car-ries out its own com-pu-ta-tions,
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\T1/ptm/m/n/10 then in-vokes []\T1/pcr/m/n/10 $initFields() []\T1/ptm/m/n/10 to
per-form stan-dard ini-tial-iza-tion, as shown in the
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[]\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func-
tion re-turned by
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[]\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen
se as any S4 class (see
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[][][]\T1/pcr/m/n/10 setValidity[][][][]\T1/ptm/m/n/10 ). Such meth-ods are of-
ten a good idea; they will be called by call-ing
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pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has
been already used, duplicate ignored
<to be read again>
\relax
l.6911 \aliasA{S4}{S3Part}{S4}
[1259]
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[]\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement
version of as().[]
[1260]
[1261]
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[]\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data =
datasets::iris)[]
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[]\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con
tains = "mlm")[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Complex})
has been already used, duplicate ignored
<to be read again>
\relax
l.7167 \aliasA{Complex}{S4groupGeneric}{Complex}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Logic}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.7169 \aliasA{Logic}{S4groupGeneric}{Logic}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) ha
s been already used, duplicate ignored
<to be read again>
\relax
l.7170 \aliasA{Math}{S4groupGeneric}{Math}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.matrixOps
}) has been already used, duplicate ignored
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l.7172 ...sA{matrixOps}{S4groupGeneric}{matrixOps}
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l.7173 \aliasA{Ops}{S4groupGeneric}{Ops}
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l.7174 \aliasA{Summary}{S4groupGeneric}{Summary}
[1262]
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[]\T1/ptm/m/n/10 There are also S3 groups []\T1/pcr/m/n/10 Math[]\T1/ptm/m/n/10
, []\T1/pcr/m/n/10 Ops[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Summary[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 Complex []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 matrixOps[
]\T1/ptm/m/n/10 , see
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[]\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic
can be ob-tained by call-ing
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[]\T1/pcr/m/n/10 "abs"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sign"[]\T1/ptm/m/n/1
0 , []\T1/pcr/m/n/10 "sqrt"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ceiling"[]\T1/p
tm/m/n/10 , []\T1/pcr/m/n/10 "floor"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "trunc"
[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cummax"[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 2012) in paragraph at lines 7249--7261
[]\T1/pcr/m/n/10 "acosh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "asin"[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 "asinh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "atan"[]\T1/p
tm/m/n/10 , []\T1/pcr/m/n/10 "atanh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "exp"[]
\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "expm1"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "c
os"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 "cosh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cospi"[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 "sin"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sinh"[]\T1/ptm
/m/n/10 , []\T1/pcr/m/n/10 "sinpi"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tan"[]\T
1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tanh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tanp
i"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 selectMethod("Re", signature = "testComplex") # shows Generic:
.. "Re" & .."Complex"[]
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[]\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t
ion ob-ject (see
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[]\T1/ptm/m/n/10 The typ-i-cal user level func-tion is []\T1/pcr/m/n/10 selectS
uperClasses() []\T1/ptm/m/n/10 which calls
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[]\T1/pcr/m/n/9 selectSuperClasses("C", dropVirtual=TRUE, directOnly=FALSE)# d
itto w/o "Root"[]
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[]\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(),
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[] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[]
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[]\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[]
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[] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
"setCount")[]
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[]\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo
rmal arguments[]
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[]\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre
es of freedom[]
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[]\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][]
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[]\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][]
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[]\T1/ptm/m/n/10 Chambers, John M. (2009) \T1/ptm/m/it/10 Class In-her-i-tance
in R [][]$\T1/pcr/m/n/10 https : / / johnmchambers . su .
[1305]
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[]\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., []\T1/pcr/m/n/10 "functi
on" []\T1/ptm/m/n/10 for class
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[]\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl
ass, from the data part; e.g.,
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[]\T1/pcr/m/n/10 "functionWithTrace" []\T1/ptm/m/n/10 ex-tends []\T1/pcr/m/n/10
"function"[]\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends
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[1309]) (./parallel-pkg.tex
[1310]
Chapter 8.
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[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `[]\T1/p
cr/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"[]\T1/ptm/m/n/10 ' [][]
RNG[][][]: see
[1311]
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[]\T1/ptm/m/n/10 a vec-tor for []\T1/pcr/m/n/10 clusterApply []\T1/ptm/m/n/10 a
nd []\T1/pcr/m/n/10 clusterApplyLB[]\T1/ptm/m/n/10 , a ma-trix for
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[]\T1/ptm/m/n/10 Two ex-cep-tions: []\T1/pcr/m/n/10 parLapply []\T1/ptm/m/n/10
has ar-gu-ment []\T1/pcr/m/n/10 X []\T1/ptm/m/n/10 not []\T1/pcr/m/n/10 x []\T1
/ptm/m/n/10 for con-sis-tency with [][][]\T1/pcr/m/n/10 lapply[][][][]\T1/ptm/m
/n/10 , and
[1314]
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[]\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD,
So-laris and Win-dows.
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[]\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for []\T1/pcr/m/
n/10 Rscript []\T1/ptm/m/n/10 such as
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[]\T1/pcr/m/n/10 mcfork []\T1/ptm/m/n/10 re-turns an ob-ject of the class []\T1
/pcr/m/n/10 "childProcess" []\T1/ptm/m/n/10 to the mas-ter and of class
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[]\T1/pcr/m/n/10 "masterProcess" []\T1/ptm/m/n/10 to the child: both the classe
s in-herit from class []\T1/pcr/m/n/10 "process"[]\T1/ptm/m/n/10 . If
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[] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini
ty.list = NULL)[]
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[]\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit
y.list = affL)[]
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[]\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch
eduled to suitable CPUs[]
[1327]
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[]\T1/pcr/m/n/10 mcparallel []\T1/ptm/m/n/10 re-turns an ob-ject of the class [
]\T1/pcr/m/n/10 "parallelJob" []\T1/ptm/m/n/10 which in-her-its from
[1328]
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[]\T1/ptm/m/n/10 The be-haviour with []\T1/pcr/m/n/10 mc.set.seed = TRUE []\T1/
ptm/m/n/10 is dif-fer-ent only if
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1258--1258
[]\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin
ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[]
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[] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[]
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[]\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format =
"%Y-%m-%d")))[]
[1331]
Underfull \hbox (badness 1577) in paragraph at lines 1416--1419
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by []\T1/pcr/m/n/10
.Random.seed []\T1/ptm/m/n/10 when the
Underfull \hbox (badness 3375) in paragraph at lines 1463--1465
[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 nextRNGStream []\T1/ptm/m/n/10 and []\T1/
pcr/m/n/10 nextRNGSubStream[]\T1/ptm/m/n/10 , a value which can be as-signed to
[1332]
[1333]) (./splines-pkg.tex
[1334]
Chapter 9.
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[]\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
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[]\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl
ine = TRUE))[]
[1343]
Underfull \hbox (badness 1043) in paragraph at lines 599--601
[]\T1/ptm/m/n/10 An in-te-ger be-tween 0 and []\T1/pcr/m/n/10 splineOrder(objec
t) - 1 []\T1/ptm/m/n/10 spec-i-fy-ing the
[1344]
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[]\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37,
sparse = TRUE)))[]
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[1347]
[1348]) (./stats-pkg.tex
Chapter 10.
[1349]
Underfull \hbox (badness 1077) in paragraph at lines 71--74
[]\T1/pcr/m/n/10 .MFclass() []\T1/ptm/m/n/10 re-turns a char-ac-ter string, one
of []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ordered"[]\T
1/ptm/m/n/10 , []\T1/pcr/m/n/10 "factor"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 (xl <- .getXlevels(terms(mf), mf)) # a list with one entry " $
Species" with 3 levels:[]
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[] \T1/pcr/m/n/9 identical(.getXlevels(terms(mc), mc), xl[0]) # a empty named
list, as no factors[]
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[]\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[]
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[]\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet =
FALSE)
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Underfull \hbox (badness 1024) in paragraph at lines 901--903
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from []\T1/pcr/m/n/10 l
m []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 aov[]\T1/ptm/m/n/10 , or a for-mula for
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[] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm
= TRUE)[]
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[] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm
= TRUE)[]
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[] \T1/pcr/m/n/9 approx(xn, yn, xout=xout, method=M, rule=R, n
a.rm=na.)$y),[]
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[]\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$y) # warning, can be avoided by
specifying \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ties=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[
]
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[]\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE)
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[]\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[]
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Underfull \hbox (badness 10000) in paragraph at lines 3295--3297
[]\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Bartlett test of homo
geneity of
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[]\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p =
FALSE)[]
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[]\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p =
FALSE)[]
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Package amsmath Warning: Foreign command \atopwithdelims;
(amsmath) \frac or \genfrac should be used instead
(amsmath) on input line 3684.
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[]\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[]
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[]\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0)
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[]\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p
= FALSE)[]
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[]\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p
= FALSE)[]
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[]\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful
, but is ok![]
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[] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
df, ncp = L)),[]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10
(\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/
it/10 g[] \OT1/cmr/m/n/10 =
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[]\T1/pcr/m/n/10 confint(object, parm, level = 0.95, trace = FALSE, test=c("LR
T", "Rao"), ...)[]
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[]\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1))
, ci = c(-1,-1))[]
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[]\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci
= c(-0.9,0.1))[]
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[]\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works
with these :[]
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[]\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter"))
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[]\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i
ng co-vari-ances
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\T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi
-a-tion of)
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\T1/ptm/m/n/10 one of the strings []\T1/pcr/m/n/10 "everything"[]\T1/ptm/m/n/10
, []\T1/pcr/m/n/10 "all.obs"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "complete.obs"
[]\T1/ptm/m/n/10 ,
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[] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
...)[]
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[]\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
TRUE,
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[]\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
NULL)
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[]\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en
v = parent.frame())[]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor in-dex-ing []\T1/pcr/m/n/10 labels(termobj)
[]\T1/ptm/m/n/10 (that is, the
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
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[]\T1/ptm/m/n/10 Objects of class []\T1/pcr/m/n/10 "hclust" []\T1/ptm/m/n/10 ca
n be con-verted to class []\T1/pcr/m/n/10 "dendrogram" []\T1/ptm/m/n/10 us-ing
method
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[]\T1/pcr/m/n/10 rev.dendrogram []\T1/ptm/m/n/10 sim-ply re-turns the den-dro-g
ram []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 with re-versed nodes, see also
Underfull \hbox (badness 1655) in paragraph at lines 6702--6707
\T1/ptm/m/n/10 has []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 y [
]\T1/ptm/m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be-
fore \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.1.2,
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Underfull \hbox (badness 7238) in paragraph at lines 6738--6741
[][][]\T1/pcr/m/n/10 dendrapply[][][] []\T1/ptm/m/n/10 for ap-ply-ing a func-ti
on to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][][]\T1/pcr/m/n/10 order.dend
rogram[][][] []\T1/ptm/m/n/10 and
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[]\T1/pcr/m/n/9 str(dend1, max.level = 2, last.str = "\TS1/pcr/m/n/9 '\T1/pcr
/m/n/9 ") # only the first two sub-levels[]
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[]\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE,
type = "tr")[]
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[]\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p
cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6803--6803
[]\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[]
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[]\T1/pcr/m/n/9 abline(h = 1/1022, v = range(x), lty=2); axis(2, at=1/1022, "1
/(2n-2)", las=1)[]
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[] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[]
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[]\T1/pcr/m/n/10 "maximum"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "manhattan"[]\T1/
ptm/m/n/10 , []\T1/pcr/m/n/10 "canberra"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "bi
nary" []\T1/ptm/m/n/10 or
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[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from []\T1/
pcr/m/n/10 dist()[]\T1/ptm/m/n/10 , the
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[]\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht
tps : / / CRAN . R-[]project . org / view =
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[]\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences []
\T1/pcr/m/n/10 x[t][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 x[t-1][]\T1/ptm/m/n/10 ,
...,
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[]\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 na.action[][][] []\T1/ptm/m/n/10 to b
e used if []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 is used as a for-mula, in which c
ase
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[]\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q
uasipoisson())[]
Underfull \vbox (badness 10000) has occurred while \output is active
[1482]
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[]\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link
= "log")) # fails[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 9018--9018
[]\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[]
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[] \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4
0k", "> 40k"),[]
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[] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod
erateS", "VeryS")))[]
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Underfull \hbox (badness 7291) in paragraph at lines 9772--9774
[]\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Fligner-Killeen test
of homogeneity of
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Underfull \hbox (badness 6944) in paragraph at lines 10265--10271
[][][]\T1/pcr/m/n/10 ftable.formula[][][] []\T1/ptm/m/n/10 for the for-mula in-
ter-face (which al-lows a []\T1/pcr/m/n/10 data = . []\T1/ptm/m/n/10 ar-gu-ment
);
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[]\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org
/ wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or
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Overfull \hbox (6.78088pt too wide) in paragraph at lines 10724--10724
[] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL
, ...)[]
Underfull \hbox (badness 4518) in paragraph at lines 10750--10755
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
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Underfull \hbox (badness 4132) in paragraph at lines 10789--10793
[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
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[]\T1/ptm/m/n/10 A spec-i-fi-ca-tion of the form []\T1/pcr/m/n/10 first:second
[]\T1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak-
[1509]
Underfull \hbox (badness 10000) in paragraph at lines 10895--10898
[]\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][][]\T1/pcr/m/n/10 coeffic
ients[][][][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 effects[]\T1/ptm/m/n/10 , []\T1/
pcr/m/n/10 fitted.values []\T1/ptm/m/n/10 and
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[1512]
Underfull \hbox (badness 2142) in paragraph at lines 11112--11115
[]\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p
tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1
0 dev \OMS/cmsy/m/n/10 ^^@
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Underfull \hbox (badness 1708) in paragraph at lines 11193--11197
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
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Underfull \hbox (badness 10000) in paragraph at lines 11235--11241
[][][]\T1/pcr/m/n/10 glm[][][] []\T1/ptm/m/n/10 for com-put-ing []\T1/pcr/m/n/1
0 glm.obj[]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 anova.glm[][][][]\T1/ptm/m/n/1
0 ; the cor-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions,
Underfull \hbox (badness 1418) in paragraph at lines 11273--11278
[]\T1/pcr/m/n/10 "average" []\T1/ptm/m/n/10 (= UP-GMA), []\T1/pcr/m/n/10 "mcqui
tty" []\T1/ptm/m/n/10 (= WPGMA), []\T1/pcr/m/n/10 "median" []\T1/ptm/m/n/10 (=
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[1516]
Underfull \hbox (badness 2635) in paragraph at lines 11406--11409
\T1/ptm/m/n/10 There are [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/n/10 , [][
][]\T1/pcr/m/n/10 plot[][][] []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 identify []\
T1/ptm/m/n/10 (see [][][]\T1/pcr/m/n/10 identify.hclust[][][][]\T1/ptm/m/n/10 )
meth-ods and the
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[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these
de-fault to
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[1521]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11704--11704
[]\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11737--11737
[] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma =
0.1),[]
Underfull \hbox (badness 10000) in paragraph at lines 11750--11754
[]\T1/ptm/m/n/10 Character string to se-lect an []\T1/pcr/m/n/10 "additive" []\
T1/ptm/m/n/10 (the de-fault) or
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[1524]
[1525]
[1526]
[1527]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 12074--12074
[]\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has
been already used, duplicate ignored
<to be read again>
\relax
l.12089 \aliasA{hat}{influence.measures}{hat}
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Overfull \hbox (0.78088pt too wide) in paragraph at lines 12152--12152
[]\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12164--12164
[]\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
...)[]
[1529]
Underfull \hbox (badness 1062) in paragraph at lines 12217--12222
[]\T1/ptm/m/n/10 The op-tional []\T1/pcr/m/n/10 infl[]\T1/ptm/m/n/10 , []\T1/pc
r/m/n/10 res []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 sd []\T1/ptm/m/n/10 ar-gu-me
nts are there to en-cour-age the use of these di-
Underfull \hbox (badness 1052) in paragraph at lines 12234--12236
[]\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 hat() []\T1/ptm/m/n/10 ex-ists
mainly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
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[1533]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 12470--12470
[]\T1/pcr/m/n/9 integrate(dnorm, 0, 20000) ## "fails" on many systems -- "wron
gly" giving \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 0\TS1/pcr/m/n/9 '[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12489--12489
[] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend =
TRUE,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12490--12490
[] \T1/pcr/m/n/10 trace.label = deparse1(substitute(trace.fact
or)),[]
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[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][][]\T1/pcr/m/n/10 solve.de
fault[][][] []\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 SSinit =
Underfull \hbox (badness 4739) in paragraph at lines 12844--12846
[]\T1/ptm/m/n/10 the es-ti-mate at time $\OML/cmm/m/it/10 t \OMS/cmsy/m/n/10 ^^
@ \OT1/cmr/m/n/10 1$ \T1/ptm/m/n/10 of the state un-cer-tainty ma-trix $\OML/cm
m/m/it/10 Q$ \T1/ptm/m/n/10 (not up-dated by
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[]\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class []\T1/pcr/
m/n/10 "kmeans"[]\T1/ptm/m/n/10 , typ-i-cally the re-sult []\T1/pcr/m/n/10 ob [
]\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 ob <-
Underfull \hbox (badness 2894) in paragraph at lines 13163--13167
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
Underfull \hbox (badness 1038) in paragraph at lines 13163--13167
\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 "Hartigan-Wong"[]\T1/ptm/m/n/10 ): if pos-i-ti
ve (or true), trac-ing in-for-ma-tion on the
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Underfull \hbox (badness 1496) in paragraph at lines 13591--13597
[]\T1/ptm/m/n/10 Gunar Schr�er and Di-et-rich Tren-kler (1995). Ex-act and Ran-
dom-iza-tion Dis-tri-bu-tions of
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[1553]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13846--13846
[]\T1/pcr/m/n/9 lag.plot(sqrt(sunspots), set.lags = c(1:4, 9:12), pch = ".", c
ol = "gold")[]
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[1555]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13946--13946
[]\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep
t", "slope"))[]
Underfull \hbox (badness 4518) in paragraph at lines 13994--13999
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
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[]\T1/ptm/m/n/10 More []\T1/pcr/m/n/10 lm() []\T1/ptm/m/n/10 ex-am-ples are ava
il-able e.g., in [][][]\T1/pcr/m/n/10 anscombe[][][][]\T1/ptm/m/n/10 , [][][]\T
1/pcr/m/n/10 attitude[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 freeny[][][]
[]\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 els, [][][]\T1/pcr/m/n/10 influence[][][] []\T1/ptm/m/n/10 (etc
on that page) for re-gres-sion di-ag-nos-tics, [][][]\T1/pcr/m/n/10 weighted.re
siduals[][][][]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
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[]\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p =
FALSE)[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14874--14874
[]\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
FALSE)[]
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Overfull \hbox (6.78088pt too wide) in paragraph at lines 15218--15218
[]\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p =
FALSE)[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 15219--15219
[]\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p =
FALSE)[]
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[]\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x)))
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[]\T1/ptm/m/n/10 character; one of []\T1/pcr/m/n/10 "logit"[]\T1/ptm/m/n/10 , [
]\T1/pcr/m/n/10 "probit"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cauchit"[]\T1/ptm/
m/n/10 , []\T1/pcr/m/n/10 "cloglog"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i
n R <= 3.5.0[]
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Overfull \hbox (42.78088pt too wide) in paragraph at lines 16072--16072
[] \T1/pcr/m/n/10 T = Thin.row(Proj(M) - Proj(X)), M = diag(nrow =
p), X = ~0,[]
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[]\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph)
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\T1/ptm/m/n/10 those spec-i-fied in []\T1/pcr/m/n/10 ... []\T1/ptm/m/n/10 which
are re-cy-cled to the num-ber of data frame rows. Un-like
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[]\T1/pcr/m/n/9 model.frame(dist ~ speed, data = cars, subset = speed < 10, z
= log(dist))[]
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[]\T1/ptm/m/n/10 a data frame cre-ated with [][][]\T1/pcr/m/n/10 model.frame[][
][][]\T1/ptm/m/n/10 . If an-other sort of ob-ject,
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[]\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts.arg = list(a = "contr.sum"
, b = contr.poly))[]
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[]\T1/pcr/m/n/9 m.orth <- model.matrix(~a+b, dd, contrasts.arg = list(a = "con
tr.helmert"))[]
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[]\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3)) # does not affect objects
with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[]
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[]\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x,
s, prob = 0.4)),[]
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[]\T1/pcr/m/n/9 ## adjusting the convergence test by adding \TS1/pcr/m/n/9 '\T
1/pcr/m/n/9 scaleOffset\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 to its denominator RSS:[]
Underfull \vbox (badness 10000) has occurred while \output is active
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Overfull \hbox (74.58035pt too wide) in paragraph at lines 18279--18279
[]\T1/pcr/m/n/9 ## Here, requiring close convergence, must use more accurate n
umerical differentiation,[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 18280--18280
[]\T1/pcr/m/n/9 ## as this typically gives Error: "step factor .. reduced belo
w \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 minFactor\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 .."[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 18284--18284
[]\T1/pcr/m/n/9 ## central differencing works here typically (PR#18165: not co
nverging on *some*):[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18285--18285
[]\T1/pcr/m/n/9 ctr2 <- nls.control(nDcentral=TRUE, tol = 8e-8, # <- even smal
ler than above[]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 18288--18288
[] \T1/pcr/m/n/9 (grepl("^aarch64.*linux", R.version$platform) && grepl
("^NixOS", osVersion)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18320--18320
[] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[]
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[]\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[]
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Overfull \hbox (20.58041pt too wide) in paragraph at lines 18543--18543
[]\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18590--18590
[]\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[]
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[] \T1/pcr/m/n/10 eps = .Machine$double.eps ^ (1/if(central) 3 els
e 2), central = FALSE)[]
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[]\T1/ptm/m/n/10 Method []\T1/pcr/m/n/10 "Brent" []\T1/ptm/m/n/10 is for one-di
mensional prob-lems only, us-ing [][][]\T1/pcr/m/n/10 optimize[][][](<ff>,
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[]\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma
-tion to the gra-di-ent, on
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[]\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i
t is un-able to re-duce
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\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 control$trace []\T1/ptm/m/n/10 is pos-i-tive
. De-faults to ev-ery 10 it-er-a-tions for []\T1/pcr/m/n/10 "BFGS" []\T1/ptm/m/
n/10 and
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Underfull \hbox (badness 2042) in paragraph at lines 19207--19209
[]\T1/ptm/m/n/10 indicates an er-ror from the []\T1/pcr/m/n/10 "L-BFGS-B" []\T1
/ptm/m/n/10 method; see com-po-nent
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Overfull \hbox (15.18042pt too wide) in paragraph at lines 19313--19313
[] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[]
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[] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem",
axes = FALSE)[]
Overfull \hbox (123.1803pt too wide) in paragraph at lines 19374--19374
[]\T1/pcr/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b
ut NM may be ok and "unavoidable",[]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 19377--19377
[]\T1/pcr/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[]
[1637]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 19397--19397
[]\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max
(interval),
Overfull \hbox (36.78088pt too wide) in paragraph at lines 19400--19400
[]\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max
(interval),[]
Underfull \hbox (badness 2564) in paragraph at lines 19435--19446
[]\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 f []\T1/ptm/m/n/10 is never eva
l-u-ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m
/n/10 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/
10 tol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1082) in paragraph at lines 19435--19446
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately
[]\T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) []\T1/ptm/m/n/10 and $\OML
/cmm/m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa
[1638]
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[]\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x -
1)), 10), 10)[]
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[1640]
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[]\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp =
1, lty = 1:6,[]
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[1643]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
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[1648]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 20157--20157
[] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd =
1.5),[]
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[1650]
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[] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist
vs Leverage* " * h[ii] / (1 - h[ii]))),[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 20246--20246
[] \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else
points,[]
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[] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[]
[1651]
Underfull \hbox (badness 10000) in paragraph at lines 20308--20314
\T1/pcr/m/n/10 "bottomleft", legend = "Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s di
stance", lty = cook.lty,
Underfull \hbox (badness 10000) in paragraph at lines 20308--20314
\T1/pcr/m/n/10 col = cook.col, text.col = cook.col, bty = "n", x.intersp
Underfull \hbox (badness 10000) in paragraph at lines 20316--20322
[]\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment []\T
1/pcr/m/n/10 iter []\T1/ptm/m/n/10 in
Underfull \hbox (badness 10000) in paragraph at lines 20327--20330
[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 1 or 2, to be used in []\T1/pcr/m
/n/10 ylim <-
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[]\T1/pcr/m/n/9 nlmod <- nls(y ~ Const + A * exp(B * x), start=list(Const=100
, A=10, B=1))[]
[1656]
[1657]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 20725--20725
[] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
...)[]
[1658]
Underfull \hbox (badness 1194) in paragraph at lines 20735--20738
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
of the con-fi-dence
[1659]
Underfull \hbox (badness 1107) in paragraph at lines 20793--20795
[]\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate []
\T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . De-faults to
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20848--20848
[]\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[]
[1660]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 20855--20855
[]\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty =
1, y.intersp = 1)[]
[1661]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20949--20949
[]\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[]
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[1663]
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[] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no
cancellation[]
[1664]
Underfull \hbox (badness 7740) in paragraph at lines 21140--21142
[]\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Exact Poisson test" [
]\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 "Comparison of
[1665]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 21188--21188
[]\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple =
FALSE)
Underfull \hbox (badness 10000) in paragraph at lines 21244--21246
[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 poly(*, simple=TRUE)[]\T1/ptm/m/n/10 , []
\T1/pcr/m/n/10 polym(*, coefs=<non-NULL>)[]\T1/ptm/m/n/10 , and
[1666]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 21281--21281
[] \T1/pcr/m/n/9 zm <- zapsmall(polym ( 1:4, c(1, 4:6), degree = 3)) # or
just poly():[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 21286--21286
[]\T1/pcr/m/n/9 ## poly(<matrix>, df) --- used to fail till July 14 (vive la F
rance!), 2017:[]
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[] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tolerance = 1e-15)) # e
xactly equal typically[]
[1680]
Underfull \hbox (badness 6859) in paragraph at lines 22207--22214
[][][]\T1/pcr/m/n/10 predict.glm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 p
redict.lm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.loess[][][][]\T1
/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.nls[][][][]\T1/ptm/m/n/10 , [][][]\T
1/pcr/m/n/10 predict.poly[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 22218--22224
[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][][]\T1/pcr/m/n/10 predict.ar[
][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.Arima[][][][]\T1/ptm/m/n/1
0 , [][][]\T1/pcr/m/n/10 predict.arima0[][][][]\T1/ptm/m/n/10 ,
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Overfull \hbox (54.78088pt too wide) in paragraph at lines 22506--22506
[] \T1/pcr/m/n/10 rankdeficient = c("warnif", "simple", "non-estim", "N
A", "NAwarn"),[]
Underfull \hbox (badness 10000) in paragraph at lines 22532--22535
[]\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string
spec-i-fy-ing what should hap-pen in the
Underfull \hbox (badness 10000) in paragraph at lines 22532--22535
\T1/ptm/m/n/10 case of a rank de-fi-cient model, i.e., when []\T1/pcr/m/n/10 ob
ject$rank <
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Underfull \hbox (badness 5832) in paragraph at lines 22537--22542
\T1/ptm/m/n/10 cases, i.e., vec-tors not in the same pre-dic-tor sub-space as t
he
Underfull \hbox (badness 8151) in paragraph at lines 22537--22542
\T1/ptm/m/n/10 orig-i-nal data (with tol-er-ance []\T1/pcr/m/n/10 tol[]\T1/ptm/
m/n/10 ). In that case, the non-
Underfull \hbox (badness 1184) in paragraph at lines 22537--22542
\T1/ptm/m/n/10 estimable in-dices are also re-turned as at-tribute []\T1/pcr/m/
n/10 "non-estim" []\T1/ptm/m/n/10 (see
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Overfull \hbox (48.78088pt too wide) in paragraph at lines 23005--23005
[] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign
= TRUE, ...)[]
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Overfull \hbox (0.78088pt too wide) in paragraph at lines 23289--23289
[] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x
)) &&[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 23290--23290
[] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr("
, "p-v"),[]
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Underfull \hbox (badness 1337) in paragraph at lines 23694--23700
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
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[1708]
[1709]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 24006--24006
[]\T1/pcr/m/n/9 with(d, qqplot(Female, Male, pch = 19, xlim = c(-31, 31), ylim
= c(-31, 31),[]
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Underfull \hbox (badness 10000) in paragraph at lines 24338--24340
[]\T1/ptm/m/n/10 Wicklin, R. (2017) Sam-ple quan-tiles: A com-par-i-son of 9 de
f-i-ni-tions;
Underfull \hbox (badness 10000) in paragraph at lines 24338--24340
\T1/ptm/m/n/10 SAS Blog. [][]$\T1/pcr/m/n/10 https : / / blogs . sas . com / co
ntent / iml / 2017 / 05 / 24 /
Underfull \hbox (badness 10000) in paragraph at lines 24341--24342
[]\T1/ptm/m/n/10 Wikipedia: [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . or
g / wiki / Quantile # Estimating _
[1714]
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Overfull \hbox (48.78088pt too wide) in paragraph at lines 24452--24452
[] \T1/pcr/m/n/10 method = c("non.compact", "row.compact", "col.compact"
, "compact"),[]
[1716]
Underfull \hbox (badness 1028) in paragraph at lines 24510--24513
[]\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for []\T
1/pcr/m/n/10 write() []\T1/ptm/m/n/10 and
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[1718]
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[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
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[]\T1/ptm/m/n/10 This, as [][][]\T1/pcr/m/n/10 reorder[][][]()[]\T1/ptm/m/n/10
, is a spe-cial case of sim-ply call-ing [][][]\T1/pcr/m/n/10 factor[][][](x, l
evels =
[1720]
Underfull \hbox (badness 7099) in paragraph at lines 24744--24746
[]\T1/ptm/m/n/10 This, as [][][]\T1/pcr/m/n/10 relevel[][][]()[]\T1/ptm/m/n/10
, is a spe-cial case of sim-ply call-ing [][][]\T1/pcr/m/n/10 factor[][][](x, l
evels =
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[]\T1/pcr/m/n/9 bymedianR <- with(InsectSprays, reorder(spray, count, median,
decreasing=TRUE))[]
[1721]
[1722]
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[]\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd,
10:1, mean)")[]
[1723]
[1724]
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[]\T1/pcr/m/n/10 # varying = ___, # list / matrix / vector (use with
care)[]
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[]\T1/pcr/m/n/10 # v.names = ___, # vector of variable names in long
format[]
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[]\T1/pcr/m/n/10 # timevar, times, # name / values of constructed time
variable[]
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[]\T1/pcr/m/n/10 # idvar, ids) # name / values of constructed id v
ariable[]
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[][][]\T1/pcr/m/n/10 stack[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 aperm[]
[][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 relist[][][] []\T1/ptm/m/n/10 for r
e-shap-ing the re-sult of [][][]\T1/pcr/m/n/10 unlist[][][][]\T1/ptm/m/n/10 . [
][][]\T1/pcr/m/n/10 xtabs[][][] []\T1/ptm/m/n/10 and
Underfull \hbox (badness 2495) in paragraph at lines 25132--25137
[][][]\T1/pcr/m/n/10 as.data.frame.table[][][] []\T1/ptm/m/n/10 for cre-at-ing
con-tin-gency ta-bles and con-vert-ing them back to
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[]\T1/pcr/m/n/9 ## long to wide (direction = "wide") requires idvar and timeva
r at a minimum[]
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[]\T1/pcr/m/n/9 reshape(Indometh, direction = "wide", idvar = "Subject", timev
ar = "time")[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 25165--25165
[]\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[]
[1727]
[1728]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 25270--25270
[] \T1/pcr/m/n/10 na.action = c("+Big_alternate", "-Big_alternate", "na.
omit", "fail"),[]
Underfull \hbox (badness 1033) in paragraph at lines 25313--25319
\T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10
where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/
m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where
[1729]
Underfull \hbox (badness 10000) in paragraph at lines 25334--25337
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult []\T1/pcr/m/n/10 y = r
unmed(x, k) []\T1/ptm/m/n/10 sim-ply has []\T1/pcr/m/n/10 y[j] =
[1730]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 25412--25412
[]\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 25438--25438
[]\T1/pcr/m/n/9 ## An example with initial NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s -
used to fail badly (notably for "Turlach"):[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 25450--25450
[]\T1/pcr/m/n/9 matplot(y = cbind(x15, rT15), type = "b", ylim = c(1,9), pch=1
:5, xlab = NA,[]
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Underfull \vbox (badness 10000) has occurred while \output is active
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Underfull \hbox (badness 6268) in paragraph at lines 25909--25914
[][][]\T1/pcr/m/n/10 SSasympOrig[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 S
Sbiexp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSfol[][][][]\T1/ptm/m/n/10
, [][][]\T1/pcr/m/n/10 SSfpl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSgo
mpertz[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSlogis[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 SSmicmen[][][][]\T1/ptm/m/n/10 ,
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[1740]
[1741]
Underfull \hbox (badness 1867) in paragraph at lines 26119--26121
[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods.
Passed to
Underfull \hbox (badness 10000) in paragraph at lines 26135--26139
[]\T1/ptm/m/n/10 where []\T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallba
ck = use.fallback) []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 PP
Underfull \hbox (badness 10000) in paragraph at lines 26135--26139
\T1/pcr/m/n/10 <- sum(!is.na([][]coef[][][](object))) []\T1/ptm/m/n/10 -- where
in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was
[1742]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 26177--26177
[]\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr
om summary(lm1)[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 26184--26184
[]\T1/pcr/m/n/9 stopifnot(all.equal(sigma(fm.DN1), summary(fm.DN1)$sigma, tole
rance=1e-15))[]
[1743]
[1744]
[1745]
Underfull \hbox (badness 2495) in paragraph at lines 26366--26375
[]\T1/ptm/m/n/10 For an in-verse gaus-sian GLM the model as-sumed is $\OML/cmm/
m/it/10 IG\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^V[]; ^^Uw[]\OT1/cmr/m/n/10 )$ \T1
/ptm/m/n/10 (see [][]$\T1/pcr/m/n/10 https : / / en .
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[1747]
Underfull \hbox (badness 2197) in paragraph at lines 26512--26515
[]\T1/pcr/m/n/10 psmirnov []\T1/ptm/m/n/10 gives the dis-tri-bu-tion func-tion,
[]\T1/pcr/m/n/10 qsmirnov []\T1/ptm/m/n/10 gives the quan-tile func-tion, and
Overfull \hbox (24.78088pt too wide) in paragraph at lines 26532--26532
[] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
= FALSE)[]
Underfull \hbox (badness 1412) in paragraph at lines 26539--26541
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1748]
[1749]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 26624--26624
[]\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 26649--26649
[]\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda
= NULL, cv = FALSE,
Overfull \hbox (66.78088pt too wide) in paragraph at lines 26652--26652
[] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee
p.stuff = FALSE)[]
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[1751]
[1752]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 26877--26877
[] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / t
ol) ))[]
Underfull \hbox (badness 2547) in paragraph at lines 26881--26887
[]\T1/ptm/m/n/10 The de-fault []\T1/pcr/m/n/10 all.knots = FALSE []\T1/ptm/m/n/
10 and []\T1/pcr/m/n/10 nknots = .nknots.smspl[]\T1/ptm/m/n/10 , en-tails us-in
g only
[1753]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26928--26928
[]\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi
ng splines")[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 26949--26949
[]\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # =
= unique(cars$speed)[]
[1754]
[1755]
[1756]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 27141--27141
[]\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail,
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[1758]
[1759]
[1760]
Underfull \hbox (badness 10000) in paragraph at lines 27406--27411
\T1/ptm/m/n/10 This makes the spec-tral den-sity a den-sity over the range []\T
1/pcr/m/n/10 (-frequency(x)/2,
[1761]
[1762]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 27520--27520
[] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[]
[1763]
[1764]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 27702--27702
[]\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi
* x) + rnorm(30)/10, 3)[]
[1765]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 27708--27708
[]\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean))
for when x has ties")[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 27717--27717
[]\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c
ol = 3, n = 1001)[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 27718--27718
[]\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c
ol = 4, n = 1001)[]
[1766]
Underfull \hbox (badness 2922) in paragraph at lines 27787--27792
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (9.78043pt too wide) in paragraph at lines 27824--27824
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim
= c(-.3, 5),[]
[1767]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 27827--27827
[] \T1/pcr/m/n/9 {f[phi](x) == phi[1] + (phi[2]-phi[1])*~e^
{-e^{phi[3]}*~x}}))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 27836--27836
[] \T1/pcr/m/n/9 c(0 , 1 ), 1, length = 0.08, angle = 25); text(0.
5, 1, quote(1))[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 27837--27837
[] \T1/pcr/m/n/9 y0 <- 1 + 4*exp(-3/4) ; t.5 <- log(2) / exp(-3/4) ; AR2 <- 3
# (Asym + R0)/2[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 27841--27841
[] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi
[1]+phi[2],2), phi[1]),[]
[1768]
Underfull \hbox (badness 3240) in paragraph at lines 27895--27898
[][][]\T1/pcr/m/n/10 nls[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 selfStart
[][][][]\T1/ptm/m/n/10 ; []\T1/pcr/m/n/10 example(SSasympOff) []\T1/ptm/m/n/10
gives graph show-ing the []\T1/pcr/m/n/10 SSasympOff
Overfull \hbox (36.7804pt too wide) in paragraph at lines 27916--27916
[] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOff(xx, Asym = 5, lrc = log(
0.4), c0 = 3/4)) )[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27919--27919
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim
= c(-1, 8),[]
[1769]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28002--28002
[] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOrig(xx, Asym = 5, lrc = log
(log(2)))) )[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28006--28006
[] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim =
c(-1/4, 5),[]
[1770]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 28016--28016
[] \T1/pcr/m/n/9 axis(2, at = 5*c(1/2,1), labels= expression(frac(phi[1],2),
phi[1]), pos=0, las=1)[]
Overfull \hbox (106.98032pt too wide) in paragraph at lines 28021--28021
[] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
== frac(log(2), e^{phi[2]})}),[]
Underfull \hbox (badness 2922) in paragraph at lines 28057--28063
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1771]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28079--28079
[]\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28095--28095
[] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 =
1.5 * exp(-x)"),[]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 28109--28109
[]\T1/pcr/m/n/9 ## Fails by default (scaleOffset=0) on most platforms {also af
ter increasing maxiter !}[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28111--28111
[] \T1/pcr/m/n/9 nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d
atN, trace=TRUE)[]
Overfull \hbox (128.58029pt too wide) in paragraph at lines 28117--28117
[] \T1/pcr/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol=
1e-11, nDcentral=TRUE), trace=TRUE)[]
[1772]
[1773]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 28228--28228
[]\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input))
[1774]
Underfull \hbox (badness 2922) in paragraph at lines 28290--28295
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1775]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 28328--28328
[] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm
id", phi[4] == "scal")))[]
Underfull \hbox (badness 2922) in paragraph at lines 28377--28382
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1776]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28408--28408
[]\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = "
red", lwd=2)[]
Underfull \hbox (badness 2922) in paragraph at lines 28442--28447
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1777]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28467--28467
[]\T1/pcr/m/n/9 ## Initial values are in fact the converged one here, "Number
of iter...: 0" :[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 28471--28471
[]\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR
UE), trace = TRUE)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28491--28491
[] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3]
== "scal")))[]
[1778]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 28501--28501
[] \T1/pcr/m/n/9 segments(c(2,2.6,2.6), c(0, 2.5,3.5), # NB. SSlogis(x =
xmid = 2) = 2.5[]
Underfull \hbox (badness 2922) in paragraph at lines 28536--28541
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu
t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28558--28558
[]\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
digits = 3)[]
[1779]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 28576--28576
[] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS
micmen model")[]
[1780]
Underfull \hbox (badness 6493) in paragraph at lines 28628--28633
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 x[]\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28656--28656
[]\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 28658--28658
[]\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 28662--28662
[]\T1/pcr/m/n/9 plot(weight ~ Time, Chick.6, xlim = c(0, 21), main = "SSweibul
l() fit to Chick.6")[]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 28665--28665
[]\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f
m1)[["Drop"]]), lty = 3)[]
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[]\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.glm"[]\T1/ptm/m/
n/10 , usu-ally, a re-sult of a call to
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[1796]
[1797]
Underfull \hbox (badness 2237) in paragraph at lines 29725--29727
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1
/pcr/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if
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[1799]
Underfull \hbox (badness 2591) in paragraph at lines 29889--29891
[]\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.nls"[]\T1/ptm/m/
n/10 , usu-ally the re-sult of a call to
[1800]
Underfull \hbox (badness 2237) in paragraph at lines 29935--29938
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1
/pcr/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if
[1801]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 30008--30008
[]\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t
race = FALSE)
[1802]
[1803]
Underfull \hbox (badness 3407) in paragraph at lines 30117--30121
[]\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m
ented\T1/ptm/m/n/10 , see []\T1/pcr/m/n/10 corr []\T1/ptm/m/n/10 be-low)
[1804]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 30187--30187
[]\T1/pcr/m/n/9 symnum(ii, cutpoints = 2*(0:4), symbols = c(".", "-", "+", "$
"), show.max = TRUE)[]
[1805]
Underfull \hbox (badness 1337) in paragraph at lines 30250--30254
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
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[1807]
[1808]
[1809]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 30524--30524
[]\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200,
main = t.tit,[]
[1810]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 30567--30567
[] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com
mon",[]
Underfull \hbox (badness 1616) in paragraph at lines 30593--30596
[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
resid-u-als, when
[1811]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 30672--30672
[]\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[]
[1812]
Underfull \hbox (badness 10000) in paragraph at lines 30710--30715
[]\T1/ptm/m/n/10 There are meth-ods for classes []\T1/pcr/m/n/10 "aovlist"[]\T1
/ptm/m/n/10 , []\T1/pcr/m/n/10 "terms"[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 "
formula" []\T1/ptm/m/n/10 (see
[1813]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 30750--30750
[]\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out =
TRUE,[]
[1814]
[1815]
[1816]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 30984--30984
[]\T1/pcr/m/n/10 toeplitz2(x, nrow = length(x) +1 - ncol, ncol = length(x) +1
- nrow)[]
Underfull \hbox (badness 2913) in paragraph at lines 30990--30994
[]\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 toeplitz(x, *)[]\T1/ptm/m/n/10 : the firs
t col-umn of the Toeplitz ma-trix; for
[1817]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 31027--31027
[]\T1/pcr/m/n/9 # Matrix of character (could also have logical, raw, complex .
.) {also warning}:[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 31040--31040
[] \T1/pcr/m/n/9 colnames(W) <- paste0(",", if(n <= 9) 1:n else c(1:9, lette
rs[seq_len(n-9)]))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 31051--31051
[]\T1/pcr/m/n/9 y.hat <- W. %*% y # y.hat := smoothed(y) ("mass preserving" ->
longer than y)[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 31053--31053
[]\T1/pcr/m/n/9 plot(x,y, type="b", xlim=c(1,m)); curve(f(x), 1,n, col="gray",
lty=2, add=TRUE)[]
[1818]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 31085--31085
[] \T1/pcr/m/n/10 class = if(nseries > 1) c("mts", "ts", "matrix", "array")
else "ts",[]
[1819]
Underfull \hbox (badness 1655) in paragraph at lines 31162--31165
[]\T1/pcr/m/n/10 is.mts(x) []\T1/ptm/m/n/10 tests if an ob-ject []\T1/pcr/m/n/1
0 x []\T1/ptm/m/n/10 is a mul-ti-vari-ate time se-ries, i.e., ful-fills []\T1/p
cr/m/n/10 is.ts(x)[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 utils:: methods(class = "ts") # all functions with methods ava
ilable for "ts"[]
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[]\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
FALSE)
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[]\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
FALSE)[]
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[] \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con
v = FALSE,[]
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[] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace
= 0)[]
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[]\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature
s: --------------[]
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[]\T1/pcr/m/n/9 ## where as \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 simply first enlarges the search interval:[]
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[]\T1/pcr/m/n/9 wilcox.test( 4:2, 3:1, paired=TRUE) # Warning: canno
t compute exact p-value with ties[]
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[]\T1/pcr/m/n/9 wilcox.test((4:2)/10, (3:1)/10, paired=TRUE, digits.rank = 9)
# same ties as (4:2, 3:1)[]
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[] \T1/pcr/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps
= getOption("ts.eps"), ...)[]
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[]\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE,
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[] \T1/pcr/m/n/10 exclude = if(!addNA) c(NA, NaN), drop.unused.levels = F
ALSE)[]
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Chapter 11.
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[] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[]
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[]\T1/pcr/m/n/9 ## Boundary case: This works, but fails if limits are set clos
er to 0 and 1[]
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Chapter 12.
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[]\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all.names = TRUE) # .Tcl.args put a ca
llback ref in here[]
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[]\T1/pcr/m/n/10 tcl []\T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-i
ng any Tk or Tcl com-mand by sim-ply run-ning
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[]\T1/pcr/m/n/9 eval.txt <- function() eval(str2lang(tclvalue(tkget(txt.w, "0.
0", "end"))))[]
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[][][]\T1/pcr/m/n/10 select.list[][][] []\T1/ptm/m/n/10 (a text ver-sion ex-cep
t on Win-dows and the ma-cOS GUI), [][][]\T1/pcr/m/n/10 menu[][][] []\T1/ptm/m/
n/10 (whose
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Chapter 13.
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[]\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
new methods.[]
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[]\T1/pcr/m/n/10 assertWarning() []\T1/ptm/m/n/10 as-serts that a warn-ing will
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[]\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
ing warning)[]
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[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
o ren-der each of the 12
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\T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][][]\T1/pcr/m/n
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\T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named []\T1/pcr/m/n
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,
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[]\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta
ngle = TRUE,
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[]\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gin
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\T1/ptm/m/n/10 If given, vi-gnette source files are by de-fault looked for in s
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\T1/ptm/m/n/10 by \T1/pcr/m/n/10 \donttest\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \dont
diff \T1/ptm/m/n/10 or \T1/pcr/m/n/10 \dontshow\T1/ptm/m/n/10 , and \T1/pcr/m/n
/10 \title \T1/ptm/m/n/10 re-placed by \T1/pcr/m/n/10 \section \T1/ptm/m/n/10 o
r
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[]\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", "
xz"),[]
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[]\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co
mpress == "none")[]
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[] \T1/pcr/m/n/10 outputs = FALSE, sources = FALS
E, ...)[]
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[]\T1/pcr/m/n/10 check_packages_in_dir_details(dir, logs = NULL, drop_ok = TRU
E, ...)[]
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[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v
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[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-
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[]\T1/pcr/m/n/10 check_packages_in_dir []\T1/ptm/m/n/10 re-turns an ob-ject in-
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[]\T1/pcr/m/n/10 codocClasses []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 codocData [
]\T1/ptm/m/n/10 re-turn ob-jects of class []\T1/pcr/m/n/10 "codocClasses" []\T1
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[]\T1/pcr/m/n/10 CRAN_package_db() []\T1/ptm/m/n/10 re-turns a data frame with
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' meta-data for the cu
r-rent pack-ages in the CRAN pack-age repos-i-
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\T1/ptm/m/n/10 tory, in-clud-ing in par-tic-u-lar the De-scrip-tion and Main-ta
iner in-for-ma-tion not pro-vided by
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[]\T1/ptm/m/n/10 Functions []\T1/pcr/m/n/10 CRAN_current_db()[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 CRAN_aliases_db()[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 CRAN_rdx
refs_db()[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 CRAN_authors_db() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 CRAN_a
rchive_db() []\T1/ptm/m/n/10 (also used by []\T1/pcr/m/n/10 R CMD check[]\T1/pt
m/m/n/10 )
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T1/pcr/m/n/10 R_CRAN_WEB[]\T1/ptm/m/n/10 . The mir-ror to be used is re-ported
by
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[] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En
hances"))[]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
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\T1/pcr/m/n/10 "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string []\T1/pcr/m/n/1
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[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 loadPkgRdMacros []\T1/ptm/m/n/10 func-tio
n first looks for an []\T1/pcr/m/n/10 "RdMacros" []\T1/ptm/m/n/10 en-try in the
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[]\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user
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\T1/ptm/m/n/10 tion set-tings also for com-pi-la-tions not us-ing \T1/phv/m/n/1
0 R\T1/ptm/m/n/10 's mech-a-nisms (in par-tic-u-lar, cus-tom com-
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\T1/ptm/m/n/10 pi-la-tions in sub-di-rec-to-ries of `\T1/pcr/m/n/10 src\T1/ptm/
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[]\T1/ptm/m/n/10 The de-fault method of []\T1/pcr/m/n/10 as.Rconcordance []\T1/
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[]\T1/pcr/m/n/10 followConcordance []\T1/ptm/m/n/10 is used when a file is tran
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\T1/ptm/m/n/10 trans-for-ma-tion records a con-cor-dance in the file which is r
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[]\T1/pcr/m/n/10 package_dependencies(packages = NULL, db = NULL, which = "str
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\T1/pcr/m/n/10 "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string []\T1/pcr/m/n/1
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[]\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster"
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[] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations
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[] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system
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[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion 3.2.0, User-d
efined macros may be given in a sep-a-rate file us-ing
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[] \T1/pcr/m/n/10 stylesheet = file.path(R.home("doc"), "html", "R-nav
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[] \T1/pcr/m/n/10 hooks = list(pkg_href = function(pkg) sprintf("%s.ht
ml", pkg)),[]
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[] \T1/pcr/m/n/10 mathjax_config = file.path(R.home("doc"), "html", "m
athjax-config.js"),[]
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[] \T1/pcr/m/n/10 fragment = FALSE, ..., writeEncoding = outputEncodin
g != "UTF-8",[]
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[]\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-
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[] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro
s", "system.Rd"))[]
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[]\T1/ptm/m/n/10 By de-fault, the tags \T1/pcr/m/n/10 \S3method\T1/ptm/m/n/10 ,
\T1/pcr/m/n/10 \S4method\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \command\T1/ptm/m/n/10
, \T1/pcr/m/n/10 \docType\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \email\T1/ptm/m/n/10
,
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[] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett
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[]\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter
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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
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[]\T1/pcr/m/n/9 (prio <- sapply(as.vector(pNms), packageDescription, fields =
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[]\T1/pcr/m/n/9 toTitleCase("ensemble tool for predictions from species distri
bution models")[]
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[]\T1/pcr/m/n/9 toTitleCase("a small fox is jumping") # "a Small Fox is .."
(the \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 a\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 may cha
nge)% i.e. BUG[]
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[]\T1/pcr/m/n/9 toTitleCase("asking -- \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 is a smal
l fox jumping?\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ") # ".. -- Is a Small ..." (fi
ne)[]
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[]\T1/ptm/m/n/10 optional char-ac-ter strings for the `[]\T1/pcr/m/n/10 Copyrig
ht[]\T1/ptm/m/n/10 ' and
Underfull \hbox (badness 6859) in paragraph at lines 5200--5205
[]\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory []\T1/pcr/m/n/10 po []\T1/
ptm/m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\
T1/ptm/m/n/10 ' are up-dated from
Underfull \hbox (badness 1184) in paragraph at lines 5208--5214
[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po
/\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T
he
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\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t
he pack-age are ex-am-ined to cre-ate a file
[1965]
[1966]
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[]\T1/pcr/m/n/9 parse_URI_reference(c("foo://example.com:8042/over/there?name=
ferret#nose",[]
[1967]
[1968]
[1969]
Underfull \hbox (badness 10000) in paragraph at lines 5513--5515
[]\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 vignetteEngine[][][][]\T1/ptm/m/n/10
, such as []\T1/pcr/m/n/10 "utils::Sweave" []\T1/ptm/m/n/10 or
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5542--5542
[] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F
ALSE,[]
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[] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr
ess = "xz",[]
Underfull \hbox (badness 3240) in paragraph at lines 5556--5559
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T
1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ',
Underfull \hbox (badness 1742) in paragraph at lines 5560--5570
[]\T1/pcr/m/n/10 "Package"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Version"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "Priority"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Depe
nds"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Imports"[]\T1/ptm/m/n/10 ,
[1970]
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[]\T1/pcr/m/n/10 write_PACKAGES []\T1/ptm/m/n/10 scans the named di-rec-tory fo
r R pack-ages, ex-tracts in-for-ma-tion from
Underfull \hbox (badness 1635) in paragraph at lines 5598--5604
\T1/ptm/m/n/10 each pack-age's `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file
, and writes this in-for-ma-tion into the `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/1
0 ',
Underfull \hbox (badness 1571) in paragraph at lines 5626--5630
[]\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down-
load speed and time spent by
[1971]
Underfull \hbox (badness 2772) in paragraph at lines 5652--5657
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 PACKAGES.gz\T1/ptm/m/n/10 ' files. See [][][
]\T1/pcr/m/n/10 update_PACKAGES[][][] []\T1/ptm/m/n/10 for ef-fi-ciently up-dat
-ing ex-ist-ing
[1972]
[1973]
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[] \T1/pcr/m/n/9 " stop(errorCondition(gettext(\TS1/pcr/m/n/9 '\T1/pcr/m/n
/9 needs Deep Thought\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ), class=\TS1/pcr/m/n/9 '\T1
/pcr/m/n/9 myError\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ))",[]
[1974]) (./utils-pkg.tex
Chapter 14.
Underfull \hbox (badness 1072) in paragraph at lines 47--52
[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[]
\T1/pcr/m/n/10 insertions[]\T1/ptm/m/n/10 ',
[1975]
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[1978]
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[]\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with
these names[]
[1979]
[1980]
Underfull \hbox (badness 10000) in paragraph at lines 378--383
\T1/ptm/m/n/10 are []\T1/pcr/m/n/10 c("vertical", "horizontal", "cascade", "min
imize",
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[]\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 list[][][] []\T1/ptm/m/n/10 of win-dow
han-dles, by de-fault pro-duced by
[1981]
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[]\T1/pcr/m/n/9 # This default is useful only in SDI mode: it will tile any F
irefox window[]
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[]\T1/pcr/m/n/9 .arrangeWindowsDefaults <- list(c("R", "all"), pattern = c("",
"Firefox"))[]
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[] \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No
", "Cancel"))),[]
[1982]
[1983]
[1984]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 691--691
[]\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l
ist(),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 692--692
[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 693--693
[]\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l
ist(),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 694--694
[] \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[]
[1985]
Underfull \hbox (badness 10000) in paragraph at lines 728--734
[]\T1/ptm/m/n/10 Functions []\T1/pcr/m/n/10 aspell_package_Rd_files[]\T1/ptm/m/
n/10 , []\T1/pcr/m/n/10 aspell_package_vignettes[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 4416) in paragraph at lines 728--734
[]\T1/pcr/m/n/10 aspell_package_R_files []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 a
spell_package_C_files []\T1/ptm/m/n/10 per-form spell check-
[1986]
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[] \T1/pcr/m/n/10 fields = getOption("available_packages_fie
lds"),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 802--802
[] \T1/pcr/m/n/10 str2logical(Sys.getenv("R_PACKAGES_CAC
HE_USER_DIR",[]
Underfull \hbox (badness 10000) in paragraph at lines 842--845
[][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 in-di-cat-ing if caching sh
ould hap-pen in \T1/ptm/b/n/10 tools\T1/ptm/m/n/10 '
[1987]
Underfull \hbox (badness 1552) in paragraph at lines 936--942
[]\T1/ptm/m/n/10 A char-ac-ter ma-trix with one row per pack-age, row names the
pack-age names and col-
[1988]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 963--963
[]\T1/pcr/m/n/9 db <- available.packages(repos = findCRANmirror("web"), filter
s = "duplicates")[]
[1989]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1065--1065
[]\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
NULL,
[1990]
[1991]
Underfull \hbox (badness 7649) in paragraph at lines 1139--1145
[][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 in-di-cat-ing if Bib-TeX co
de should be given ad-di-tion-ally;
Underfull \hbox (badness 5533) in paragraph at lines 1139--1145
\T1/ptm/m/n/10 cur-rently ap-plies only to []\T1/pcr/m/n/10 style = "citation"[
]\T1/ptm/m/n/10 . The de-fault for
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\T1/ptm/m/n/10 the []\T1/pcr/m/n/10 print() []\T1/ptm/m/n/10 method de-pends on
the num-ber of (bib) en-tries and
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\T1/ptm/m/n/10 For ex-am-ple, to see no Bib-TeX at all, you can change the de-f
ault by
Underfull \hbox (badness 10000) in paragraph at lines 1148--1150
[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1992]
Underfull \hbox (badness 10000) in paragraph at lines 1266--1269
[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org
/ wiki / Digital _ Object _
[1993]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1349--1349
[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
[1994]
[1995]
[1996]
[1997]
[1998]
[1999]
Underfull \hbox (badness 1859) in paragraph at lines 1758--1767
[]\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b
e quite large the com-
Underfull \hbox (badness 2042) in paragraph at lines 1758--1767
\T1/ptm/m/n/10 mand []\T1/pcr/m/n/10 data.frame(x, y, z, monday, tuesday) []\T1
/ptm/m/n/10 never re-turns. Do not re-port that
[2000]
[2001]
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[] \T1/pcr/m/n/9 data = infert, family = b
inomial())))[]
[2002]
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[] \T1/pcr/m/n/10 md5sum = FALSE, digest = NULL, full.names = length(path)
> 1,[]
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[]\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[]
[2003]
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[]\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[]
[2004]
Underfull \hbox (badness 2277) in paragraph at lines 2113--2118
[]\T1/pcr/m/n/10 charClass []\T1/ptm/m/n/10 was added in \T1/phv/m/n/10 R \T1/p
tm/m/n/10 4.1.0. A less di-rect way to ex-am-ine char-ac-ter classes
[2005]
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[]\T1/pcr/m/n/9 cl <- c("alnum", "alpha", "blank", "digit", "graph", "punct",
"upper", "xdigit")[]
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[]\T1/pcr/m/n/9 X <- as.data.frame(X); row.names(X) <- sQuote(intToUtf8(x, mul
tiple = TRUE))[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2155--2155
[]\T1/pcr/m/n/9 ## How many printable characters are there? (Around 280,000 in
Unicode 13.)[]
[2006]
[2007]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2303--2303
[]\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
NULL,
[2008]
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[]\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
NULL,
[2009]
[2010]
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[]\T1/ptm/m/n/10 If the ob-ject re-turned by []\T1/pcr/m/n/10 citation() []\T1/
ptm/m/n/10 con-tains only one ref-er-ence, the as-so-ci-ated print
Underfull \hbox (badness 1400) in paragraph at lines 2481--2488
\T1/ptm/m/n/10 method shows both a text ver-sion and a Bib-TeX en-try for it. I
f a pack-age has more
[2011]
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[]\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
NULL,[]
[2012]
[2013]
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[] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 2724--2724
[]\T1/pcr/m/n/10 citEntry(entry, textVersion = NULL, header = NULL, footer = N
ULL, ...)
[2014]
Underfull \hbox (badness 1082) in paragraph at lines 2753--2757
[][][]\T1/pcr/m/n/10 citation[][][] []\T1/ptm/m/n/10 for more in-for-ma-tion ab
out cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file
s;
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard
}) has been already used, duplicate ignored
<to be read again>
\relax
l.2758 ... the Clipboard in MS Windows}{clipboard}
[2015]
[2016]
Underfull \hbox (badness 10000) in paragraph at lines 2882--2884
[]\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/
phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see
[2017]
[2018]
[2019]
[2020]
Underfull \hbox (badness 10000) in paragraph at lines 3103--3105
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[2021]
[2022]
[2023]
[2024]
Underfull \hbox (badness 1762) in paragraph at lines 3396--3399
[]\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re
c-tory of the cur-rent work-ing di-rec-tory, set []\T1/pcr/m/n/10 package =
[2025]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 3484--3484
[]\T1/pcr/m/n/9 try(data(package = "rpart"), silent = TRUE) # list the data se
ts in the rpart package[]
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[]\T1/pcr/m/n/9 data(USArrests, "VADeaths") # load the data sets \TS1/pcr/m
/n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9
'\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[]
[2026]
Underfull \hbox (badness 2452) in paragraph at lines 3559--3562
[]\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class []\
T1/pcr/m/n/10 R_dataentry[]\T1/ptm/m/n/10 . Re-sources
[2027]
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[2032]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 3987--3987
[] \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf
orm$r_arch, "stats.dll"))[]
[2033]
[2034]
Underfull \hbox (badness 4779) in paragraph at lines 4068--4073
[]\T1/ptm/m/n/10 Support for method []\T1/pcr/m/n/10 "libcurl" []\T1/ptm/m/n/10
was op-tional on Win-dows prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0: use
Underfull \hbox (badness 1072) in paragraph at lines 4131--4135
[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
the []\T1/pcr/m/n/10 quiet []\T1/ptm/m/n/10 ar-gu-ment and the
[2035]
Underfull \hbox (badness 7238) in paragraph at lines 4192--4197
[]\T1/ptm/m/n/10 For the []\T1/pcr/m/n/10 "libcurl" []\T1/ptm/m/n/10 and []\T1/
pcr/m/n/10 "curl" []\T1/ptm/m/n/10 meth-ods, prox-ies can be set \T1/ptm/m/it/1
0 via \T1/ptm/m/n/10 the en-vi-ron-
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\T1/ptm/m/n/10 ment vari-ables []\T1/pcr/m/n/10 http_proxy []\T1/ptm/m/n/10 or
[]\T1/pcr/m/n/10 ftp_proxy[]\T1/ptm/m/n/10 . See [][]$\T1/pcr/m/n/10 https : /
/ curl . se / libcurl / c /
Underfull \hbox (badness 1184) in paragraph at lines 4207--4223
\T1/ptm/m/n/10 string con-tain-ing `[]\T1/pcr/m/n/10 "Schannel"[]\T1/ptm/m/n/10
'. If it does not, for ver-i-fi-ca-tion to be on the en-vi-ron-
[2036]
[2037]
Underfull \hbox (badness 4660) in paragraph at lines 4333--4336
\T1/ptm/m/n/10 able at the repos-i-to-ries, or []\T1/pcr/m/n/10 NULL []\T1/ptm/
m/n/10 which makes an in-ter-nal call to
Underfull \hbox (badness 10000) in paragraph at lines 4357--4359
[]\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][][]\T1/pcr/m/n/10 do
wnload.file[][][] []\T1/ptm/m/n/10 and
[2038]
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[]\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c
har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of
[2041]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4627--4627
[] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[]
[2042]
Underfull \hbox (badness 1910) in paragraph at lines 4662--4669
\T1/ptm/m/n/10 is saved, then ini-tial-ized to a spec-i-fied state, the ex-am-p
le is run and
Underfull \hbox (badness 1655) in paragraph at lines 4662--4669
\T1/ptm/m/n/10 the (saved) state is re-stored. []\T1/pcr/m/n/10 setRNG = TRUE [
]\T1/ptm/m/n/10 sets the same state as
Underfull \hbox (badness 2846) in paragraph at lines 4662--4669
[]\T1/pcr/m/n/10 R CMD [][]check[][][] []\T1/ptm/m/n/10 does for run-ning a pac
k-age's ex-am-ples. This is cur-
Underfull \hbox (badness 3460) in paragraph at lines 4662--4669
\T1/ptm/m/n/10 rently equiv-a-lent to []\T1/pcr/m/n/10 setRNG = {RNGkind("defau
lt", "default",
Underfull \hbox (badness 1931) in paragraph at lines 4669--4676
[]\T1/ptm/m/n/10 logical (or []\T1/pcr/m/n/10 "default"[]\T1/ptm/m/n/10 ) in-di
-cat-ing if [][][]\T1/pcr/m/n/10 devAskNewPage[][][](ask = TRUE)
[2043]
[2044]
[2045]
[2046]
Underfull \hbox (badness 5939) in paragraph at lines 4922--4924
[]\T1/ptm/m/n/10 An en-try in []\T1/pcr/m/n/10 getOption("repos") []\T1/ptm/m/n
/10 named `[]\T1/pcr/m/n/10 CRAN[]\T1/ptm/m/n/10 ' which is not the de-fault
[2047]
[2048]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5065--5065
[]\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[]
[2049]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format})
has been already used, duplicate ignored
<to be read again>
\relax
l.5136 ...mat Unordered and Ordered Lists}{format}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format.1}
) has been already used, duplicate ignored
<to be read again>
\relax
l.5136 ...mat Unordered and Ordered Lists}{format}
[2050]
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Underfull \hbox (badness 1622) in paragraph at lines 5659--5663
[]\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing
to ex-ter-nal GUIs or to the
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[2060]
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[2062]
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[]\T1/ptm/m/n/10 External pointer ob-jects are com-pared as ref-er-ence ob-ject
s, cor-re-spond-ing to call-ing
[2063]
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[2065]
Overfull \hbox (96.78088pt too wide) in paragraph at lines 6193--6193
[]\T1/pcr/m/n/10 ## NB: The methods for \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 data.f
rame\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 and \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 array\
TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 are identical to the \TS1/pcr/m/n/10 '\T1/pcr/
m/n/10 matrix\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 one[]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 6205--6205
[]\T1/pcr/m/n/10 tail(x, n = 6L, keepnums = TRUE, addrownums, ...) # exported
as tail.matrix()[]
[2066]
[2067]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6347--6347
[] \T1/pcr/m/n/9 ## BUT if I use "useAttrib(.)", this is *not* ok, when n i
s of length 2:[]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 6348--6348
[] \T1/pcr/m/n/9 ## --- because [i,j]-indexing of data frames *also* drops
"other" attributes ..[]
[2068]
[2069]
[2070]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6558--6558
[] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[]
[2071]
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[]\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 https : / / www . r-[]
project . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also
[2072]
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[]\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words
'. `Key-
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\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are
listed in file
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[]\T1/pcr/m/n/9 help.search("linear models") # In case you forgot how to fit
linear models[]
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[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-
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\T1/ptm/m/n/10 dex, `\T1/ptm/m/sl/10 R_DOC_DIR\T1/pcr/m/n/10 /html/packages.htm
l\T1/ptm/m/n/10 ', which can be re-made by
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion
to search. See
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Underfull \hbox (badness 5175) in paragraph at lines 6949--6952
[]\T1/pcr/m/n/10 hsearch_db() []\T1/ptm/m/n/10 builds and caches the help searc
h database for sub-se-quent use by
[2077]
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[]\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion `
Lock-ing' in the help for
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[]\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 means to use []\T1/pcr/m/n/10 c("Depends
", "Imports", "LinkingTo",
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\T1/pcr/m/n/10 "Suggests") []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pkgs []\T1/ptm
/m/n/10 and []\T1/pcr/m/n/10 c("Depends", "Imports",
Underfull \hbox (badness 1270) in paragraph at lines 7276--7283
\T1/pcr/m/n/10 "LinkingTo") []\T1/ptm/m/n/10 for added de-pen-den-cies: this in
-stalls all the pack-ages
Underfull \hbox (badness 1270) in paragraph at lines 7291--7301
\T1/ptm/m/n/10 for the `[]\T1/pcr/m/n/10 --configure-args[]\T1/ptm/m/n/10 ' fla
g in the call to []\T1/pcr/m/n/10 R CMD INSTALL[]\T1/ptm/m/n/10 . If
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[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
be passed to []\T1/pcr/m/n/10 R
Underfull \hbox (badness 4913) in paragraph at lines 7334--7338
\T1/pcr/m/n/10 CMD INSTALL []\T1/ptm/m/n/10 for a source pack-age in-stall. E.g
., []\T1/pcr/m/n/10 c("--html",
Underfull \hbox (badness 10000) in paragraph at lines 7334--7338
\T1/pcr/m/n/10 "--no-multiarch", "--no-test-load") []\T1/ptm/m/n/10 or, for ma-
cOS,
Underfull \hbox (badness 1424) in paragraph at lines 7343--7346
[]\T1/ptm/m/n/10 logical: if true, re-duce the amount of out-put. This is \T1/p
tm/m/it/10 not \T1/ptm/m/n/10 passed to
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[]\T1/ptm/m/n/10 further ar-gu-ments to be passed to [][][]\T1/pcr/m/n/10 downl
oad.file[][][][]\T1/ptm/m/n/10 ,
[2082]
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[]\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is []\T1/pcr/m/n
/10 "both" []\T1/ptm/m/n/10 which means `use bi-nary if avail-
Underfull \hbox (badness 5175) in paragraph at lines 7424--7431
\T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there
are source pack-ages
Underfull \hbox (badness 1342) in paragraph at lines 7424--7431
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by
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[]\T1/ptm/m/n/10 Using pack-ages with []\T1/pcr/m/n/10 type = "source" []\T1/pt
m/m/n/10 al-ways works pro-vided the pack-age con-tains no
[2083]
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[]\T1/pcr/m/n/10 install.packages []\T1/ptm/m/n/10 needs to be able to com-pute
all the de-pen-den-cies of []\T1/pcr/m/n/10 pkgs []\T1/ptm/m/n/10 from
[2084]
Underfull \hbox (badness 10000) in paragraph at lines 7594--7599
[][][]\T1/pcr/m/n/10 update.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 download.pac
kages[][][][]\T1/ptm/m/n/10 ,
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7617--7617
[] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 7635--7635
[] \T1/pcr/m/n/10 str2logical(Sys.getenv("R_PACKAGES_CAC
HE_USER_DIR",[]
[2085]
Underfull \hbox (badness 10000) in paragraph at lines 7656--7659
[][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 in-di-cat-ing if caching sh
ould hap-pen in \T1/ptm/b/n/10 tools\T1/ptm/m/n/10 '
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each
pack-age's
Underfull \hbox (badness 1983) in paragraph at lines 7674--7677
[]\T1/pcr/m/n/10 installed.packages []\T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10
DESCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along
[2086]
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[]\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
= "License")[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7726--7726
[]\T1/pcr/m/n/9 ## Keep packages that come with R (priority="high") and all ot
hers separate![]
[2087]
[2088]
Underfull \hbox (badness 4132) in paragraph at lines 7852--7854
[]\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion
of []\T1/pcr/m/n/10 libtool []\T1/ptm/m/n/10 in-stalled at
[2089]
[2090]
[2091]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8019--8019
[]\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h
ave defined?[]
[2092]
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Overfull \hbox (0.78088pt too wide) in paragraph at lines 8162--8162
[]\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE)
[2094]
Underfull \hbox (badness 10000) in paragraph at lines 8202--8204
[]\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/
phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see
[2095]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8294--8294
[] \T1/pcr/m/n/10 methods(generic.function, class, all.names = FALSE, dropPa
th = FALSE)[]
Overfull \hbox (132.78088pt too wide) in paragraph at lines 8296--8296
[] \T1/pcr/m/n/10 all.names = FALSE, dropPa
th = FALSE, useEnv = FALSE)[]
Underfull \hbox (badness 10000) in paragraph at lines 8309--8311
[]\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if
Underfull \hbox (badness 10000) in paragraph at lines 8327--8329
[]\T1/ptm/m/n/10 typically the re-sult of []\T1/pcr/m/n/10 methods(..)[]\T1/ptm
/m/n/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of S3 class
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Underfull \hbox (badness 1859) in paragraph at lines 8559--8562
[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
[2100]
[2101]
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[]\T1/pcr/m/n/9 db4 <- news(Version == "4.0.0" & grepl("^BUG", Category) & gre
pl("PR#", Text),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8693--8693
[]\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri
x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8701--8701
[]\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[]
[2102]
Underfull \hbox (badness 1917) in paragraph at lines 8788--8790
[]\T1/pcr/m/n/10 "B"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "KiB"[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 "MiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "GiB"[]\T1/ptm/m/n/1
0 , []\T1/pcr/m/n/10 "TiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "PiB"[]\T1/ptm/m/
n/10 ,
Underfull \hbox (badness 1331) in paragraph at lines 8796--8800
[]\T1/ptm/m/n/10 For all stan-dards, []\T1/pcr/m/n/10 units = "auto" []\T1/ptm/
m/n/10 is also al-lowed. If []\T1/pcr/m/n/10 standard =
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[]\T1/ptm/m/n/10 optionally a [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/
n/10 string with an en-cod-ing for an op-tional
[2106]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 9062--9062
[] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica
tion", "Built"),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 9063--9063
[] \T1/pcr/m/n/10 tryFormats = c("%Y-%m-%d", "%Y/%m/%d", "%D", "%m/
%d/%y"),[]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 9064--9064
[] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f
ields=date.fields))[]
[2107]
Underfull \hbox (badness 10000) in paragraph at lines 9092--9094
[]\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 asDateBuilt()[]\T1/ptm/m/n/10 , a [][][]\
T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string as from
Underfull \hbox (badness 10000) in paragraph at lines 9106--9108
[]\T1/pcr/m/n/10 packageVersion() []\T1/ptm/m/n/10 is a con-ve-nience short-cut
, al-low-ing things like []\T1/pcr/m/n/10 if
Underfull \hbox (badness 1259) in paragraph at lines 9114--9119
[]\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the
given pack-age is found and can suc-cess-fully be read,
[2108]
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[] \T1/pcr/m/n/9 identical(pu, packageDate("stats"))) # as "utils" an
d "stats" are[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9159--9159
[] \T1/pcr/m/n/9 # both \TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 base R\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and "Built" at same time[]
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[2110]
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[]\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 "Status"[]\T1/ptm/m/n/10 , a fac-tor wit
h lev-els []\T1/pcr/m/n/10 c("ok", "upgrade",
Underfull \hbox (badness 10000) in paragraph at lines 9292--9295
[]\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 "Status"[]\T1/ptm/m/n/10 , a fac-tor wit
h lev-els []\T1/pcr/m/n/10 c("installed", "not
[2111]
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[] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 9410--9410
[] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<",
">"),[]
[2113]
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 9597--9597
[] \T1/pcr/m/n/9 "S original, <http://statwww.epfl.ch/davison/BMA/libr
ary.html>"),[]
[2115]
[2116]
[2117]
Underfull \hbox (badness 1789) in paragraph at lines 9769--9771
[]\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for
more dis-cus-sion of the
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[2119]
[2120]
[2121]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the name of the help topic;
de-faults to
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Overfull \hbox (30.78088pt too wide) in paragraph at lines 10616--10616
[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[]
[2130]
[2131]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 10777--10777
[]\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[]
[2132]
[2133]
[2134]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10958--10958
[]\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23
456 98 76 54[]
[2135]
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[] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
"no.loss"),[]
[2136]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 11045--11045
[] \T1/pcr/m/n/10 row.names, col.names, as.is = !stringsAsFactors, t
ryLogical = TRUE,[]
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[] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 11052--11052
[] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[]
[2137]
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[]\T1/ptm/m/n/10 Using []\T1/pcr/m/n/10 row.names = NULL []\T1/ptm/m/n/10 force
s row num-ber-ing. Miss-ing or []\T1/pcr/m/n/10 NULL
Underfull \hbox (badness 2435) in paragraph at lines 11147--11151
[]\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 de-ter-m
in-ing if columns con-sist-ing en-tirely of []\T1/pcr/m/n/10 "F"[]\T1/ptm/m/n/1
0 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1824) in paragraph at lines 11147--11151
[]\T1/pcr/m/n/10 "FALSE"[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 "TRUE" []\T1/pt
m/m/n/10 should be con-verted to [][][]\T1/pcr/m/n/10 logical[][][][]\T1/ptm/m/
n/10 ; passed to
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[2139]
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Overfull \hbox (12.78088pt too wide) in paragraph at lines 11409--11409
[]\T1/pcr/m/n/10 readRegistry(key, hive = c("HLM", "HCR", "HCU", "HU", "HCC",
"HPD"),
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[] \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64-
bit"))[]
Underfull \hbox (badness 10000) in paragraph at lines 11417--11422
[]\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are
Underfull \hbox (badness 10000) in paragraph at lines 11417--11422
\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 HKEY_LOCAL_MACHINE[]\T1/ptm/m/n/10 , []\T1/
pcr/m/n/10 HKEY_CLASSES_ROOT[]\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 11417--11422
[]\T1/pcr/m/n/10 HKEY_CURRENT_USER[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 HKEY_USER
S[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 HKEY_CURRENT_CONFIG
[2141]
[2142]
[2143]
[2144]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 11649--11649
[] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0)))
[2145]
[2146]
[2147]
[2148]
Underfull \hbox (badness 2469) in paragraph at lines 11915--11919
[]\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2024). Ro-man nu-mer-als. Wikipedia
, The Free En-cy-clo-pe-dia.
Underfull \hbox (badness 10000) in paragraph at lines 11915--11919
[][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / w / index . php ? title
= Roman _ numerals & oldid =
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Overfull \hbox (25.98041pt too wide) in paragraph at lines 11933--11933
[]\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:7))) # + NA with a warni
ng for the last.[]
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[]\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in
{1,2,..,4999} :[]
[2150]
[2151]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 12092--12092
[]\T1/pcr/m/n/10 4. | \-base:::tryCatchOne(expr, names, parentenv, handler
s[[1L]])[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 12093--12093
[]\T1/pcr/m/n/10 5. | \-base:::doTryCatch(return(expr), name, parentenv,
handler)[]
[2152]
Underfull \hbox (badness 10000) in paragraph at lines 12195--12197
[]\T1/ptm/m/n/10 The chap-ter on ``Tidy-ing and pro-fil-ing R code'' in `Writ-i
ng R Ex-ten-sions':
[2153]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12228--12228
[]\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
= 0)
[2154]
[2155]
Underfull \hbox (badness 1917) in paragraph at lines 12361--12364
[]\T1/ptm/m/n/10 If `[]\T1/pcr/m/n/10 --default-packages[]\T1/ptm/m/n/10 ' is n
ot used, then []\T1/pcr/m/n/10 Rscript []\T1/ptm/m/n/10 checks the en-vi-ron-me
nt vari-
Underfull \hbox (badness 4328) in paragraph at lines 12361--12364
\T1/ptm/m/n/10 able []\T1/pcr/m/n/10 R_SCRIPT_DEFAULT_PACKAGES[]\T1/ptm/m/n/10
. If this is set, then it takes prece-dence over
Overfull \hbox (106.98032pt too wide) in paragraph at lines 12384--12384
[]\T1/pcr/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr
aphics,stats -e \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 sessionInfo()\TS1/pcr/m/n/9 '[]
[2156]
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[] \T1/pcr/m/n/10 restrict = c("functions", "descriptions", "news",
"Rfunctions",[]
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[] \T1/pcr/m/n/10 "Rmanuals", "READMEs", "views", "vig
nettes"),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 12479--12479
[] \T1/pcr/m/n/10 sortby = c("score", "date:late", "date:early", "s
ubject",[]
[2157]
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[] \T1/pcr/m/n/10 "subject:descending", "size", "size:de
scending"),[]
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\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 score[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 date:
late []\T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first,
Underfull \hbox (badness 2662) in paragraph at lines 12503--12511
\T1/ptm/m/n/10 der, []\T1/pcr/m/n/10 subject:descending []\T1/ptm/m/n/10 for re
-verse al-pha-bet-i-cal or-der, []\T1/pcr/m/n/10 size []\T1/ptm/m/n/10 or
[2158]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12548--12548
[]\T1/pcr/m/n/9 fullquery <- RSiteSearch("lattice", restrict = c("vignettes","
Rfunctions"))[]
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[]\T1/ptm/m/n/10 Character string spec-i-fy-ing whether emacs style ([]\T1/pcr/
m/n/10 "etags"[]\T1/ptm/m/n/10 ) or vi style
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p
tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software /
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[] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F
ALSE, ...)[]
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[]\T1/ptm/m/n/10 The de-fault for []\T1/pcr/m/n/10 stylepath []\T1/ptm/m/n/10 i
s now taken from the en-vi-ron-ment vari-able
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[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
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[]\T1/ptm/m/n/10 The use of fancy quotes (see [][][]\T1/pcr/m/n/10 sQuote[][][]
[]\T1/ptm/m/n/10 ) can cause prob-lems when set-ting \T1/phv/m/n/10 R \T1/ptm/m
/n/10 out-put in
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[] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[]
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[]\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func-
tions can be ex-e-cuted. If
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[]\T1/ptm/m/n/10 The file `\T1/pcr/m/n/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ures
the R GUI ([]\T1/pcr/m/n/10 Rgui[]\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows
and
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[]\T1/ptm/m/n/10 At the time of writ-ing `\T1/pcr/m/n/10 Rdevga\T1/ptm/m/n/10 '
con-fig-ured the map-ping of font num-bers to fonts, and
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[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
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[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
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[]\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at
end of report[]
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[]\T1/ptm/m/n/10 Repository `[]\T1/pcr/m/n/10 CRAN[]\T1/ptm/m/n/10 ' is treated
spe-cially: the value is taken from the cur-rent set-ting of
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[]\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf
fix))
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[]\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t
o the Win-dows API call
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[]\T1/pcr/m/n/10 getSrcFilename []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 getSrcDir
ectory []\T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file-
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[] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
TRUE, ...))[]
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[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
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[][][]\T1/pcr/m/n/10 options[][][]("width")[]\T1/ptm/m/n/10 ; note that this ha
s only a weak ef-fect, un-less
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[]\T1/ptm/m/n/10 (see [][][]\T1/pcr/m/n/10 options[][][][]\T1/ptm/m/n/10 ) whic
h de-faults to []\T1/pcr/m/n/10 "no" []\T1/ptm/m/n/10 for back com-pat-i-bil-it
y rea-sons;
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[]\T1/ptm/m/n/10 numeric or []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 as by de-fau
lt, de-ter-min-ing the []\T1/pcr/m/n/10 nlines []\T1/ptm/m/n/10 ar-gu-ment to
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[]\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
of binary numbers[]
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[]\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo
ng" non-ASCII:[]
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[]\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of 2 in order to se
e 1 (in UTF-8!):[]
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[]\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N)))
# "1 is 1" here[]
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[]\T1/ptm/m/n/10 Options other than []\T1/pcr/m/n/10 memory = "none" []\T1/ptm/
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[]\T1/ptm/m/n/10 The chap-ter on `Tidy-ing and pro-fil-ing R code' in `Writ-ing
R Ex-ten-sions':
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[]\T1/ptm/m/n/10 further ar-gu-ments passed to the driver's setup func-tion. Se
e
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[][][]\T1/pcr/m/n/10 RweaveLatexSetup[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/
m/n/10 RtangleSetup[][][][]\T1/ptm/m/n/10 , re-spec-tively, for the ar-gu-
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[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 syntax = NULL []\T1/ptm/m/n/10 (the de-fau
lt) then the avail-able syn-tax ob-jects are con-sulted in
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\T1/ptm/m/n/10 turn, and se-lected if their []\T1/pcr/m/n/10 extension []\T1/pt
m/m/n/10 com-po-nent matches (as a reg-exp) the file
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\T1/ptm/m/n/10 name. Ob-jects []\T1/pcr/m/n/10 SweaveSyntaxNoweb []\T1/ptm/m/n/
10 (with []\T1/pcr/m/n/10 extension = "[.][rsRS]nw$"[]\T1/ptm/m/n/10 ) and
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\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `[]\T1/pcr/m/n/10 -h[]\T1/ptm/m/
n/10 ' (fol-low sym-bolic links, also `[]\T1/pcr/m/n/10 -L[]\T1/ptm/m/n/10 ' on
some plat-forms),
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\T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 --acls[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 --
exclude-backups[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 --exclude-vcs[]\T1/ptm/m/n
/10 ' (and sim-i-lar) and on Win-dows
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[]\T1/ptm/m/n/10 A con-ve-nient and ro-bust way to set op-tions for GNU []\T1/p
cr/m/n/10 tar []\T1/ptm/m/n/10 is via en-vi-ron-ment vari-able
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[]\T1/ptm/m/n/10 When ar-gu-ment []\T1/pcr/m/n/10 tar []\T1/ptm/m/n/10 is set t
o the com-mand []\T1/pcr/m/n/10 tar []\T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment
vari-able
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f
ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / pubs .
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\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _ 92 _
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[] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
...),[]
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[] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
...),[]
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\T1/ptm/m/n/10 able at the repos-i-to-ries, or []\T1/pcr/m/n/10 NULL []\T1/ptm/
m/n/10 which makes an in-ter-nal call to
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[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][][]\T1/pcr/m/n/10 ins
talled.packages[][][](lib.loc =
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[]\T1/ptm/m/n/10 Arguments such as []\T1/pcr/m/n/10 destdir []\T1/ptm/m/n/10 an
d []\T1/pcr/m/n/10 dependencies []\T1/ptm/m/n/10 to be
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\T1/ptm/m/n/10 passed to [][][]\T1/pcr/m/n/10 install.packages[][][] []\T1/ptm/
m/n/10 and []\T1/pcr/m/n/10 ignore_repo_cache[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 max_repo_cache_age []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 noCac
he []\T1/ptm/m/n/10 to [][][]\T1/pcr/m/n/10 available.packages[][][]
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[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
in-stall. See
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[]\T1/pcr/m/n/10 available = NULL []\T1/ptm/m/n/10 make a call to []\T1/pcr/m/n
/10 available.packages(contriburl =
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\T1/pcr/m/n/10 contriburl, method = method) []\T1/ptm/m/n/10 and hence by de-fa
ult fil-ters on \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion, OS type
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[]\T1/ptm/m/n/10 Take care when us-ing []\T1/pcr/m/n/10 dependencies []\T1/ptm/
m/n/10 (passed to [][][]\T1/pcr/m/n/10 install.packages[][][][]\T1/ptm/m/n/10 )
with
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[][][]\T1/pcr/m/n/10 install.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n
/10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 download.pa
ckages[][][][]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/9 ## Not run: url.show("https://www.stats.ox.ac.uk/pub/datasets/
csb/ch3a.txt")
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[][][]\T1/pcr/m/n/10 browseVignettes[][][] []\T1/ptm/m/n/10 for an HTML-based v
i-gnette browser; [][][]\T1/pcr/m/n/10 RShowDoc[][][]("\T1/ptm/m/sl/10 basename
\T1/pcr/m/n/10 ",
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[]\T1/pcr/m/n/9 ## Note that \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 package = *\TS1/pcr
/m/n/9 ' \T1/pcr/m/n/9 is much faster in the case of many installed packages:[]
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[] \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d
ata = DAT)))[]
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[] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal),
data = DD)))[]
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[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i
s se-lected, or
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[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 winMenuDel []\T1/ptm/m/n/10 func-tion wil
l delete a menu and all of its items and sub-menus.
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[]\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
" ",
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[]\T1/ptm/m/n/10 arguments to []\T1/pcr/m/n/10 write.table[]\T1/ptm/m/n/10 : []
\T1/pcr/m/n/10 append[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 col.names[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 sep[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 dec []\T1/ptm/m/n
/10 and
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[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion e.g. []\T1/pcr/m/n/10 file =
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[2217])
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[2220] (./KernSmooth-pkg.tex
Chapter 15.
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[]\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE)
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[]\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
= 0.05,
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[2230]) (./MASS-pkg.tex
Chapter 16.
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[]\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b
eav2$hours/24))[]
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pdfTeX warning (ext4): destination with the same identifier (name{Rfn.confint.g
lm}) has been already used, duplicate ignored
<to be read again>
\relax
l.1477 ...{confint.glm}{confint-MASS}{confint.glm}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.confint.n
ls}) has been already used, duplicate ignored
<to be read again>
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[]\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq",
"F"),[]
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[]\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq",
"F"),[]
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[]\T1/ptm/m/n/10 further ar-gu-ments for []\T1/pcr/m/n/10 plot []\T1/ptm/m/n/10
and graph-i-cal pa-ram-e-ters. Note that
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[]\T1/pcr/m/n/10 "gamma"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "geometric"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "log-normal"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lo
gnormal"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 "logistic"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "negative binomi
al"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "normal"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n
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[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
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[] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[]
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[]\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
"exponential")[]
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[]\T1/ptm/m/n/10 The va-ri-ety of bar-ley ([]\T1/pcr/m/n/10 "manchuria"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "svansota"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "velv
et"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "trebi" []\T1/ptm/m/n/10 and
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[] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
...)[]
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[]\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model
= FALSE,
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[]\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE)
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[]\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/
10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log")
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<to be read again>
\relax
l.6085 ...sical N, P, K Factorial Experiment}{npk}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.npk.1}) h
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\relax
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[] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[]
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[] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[]
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[] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[]
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[]\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea
s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c
mr/m/n/10 ) =
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[]\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[]
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[]\T1/ptm/m/n/10 the di-men-sion of the space to be used. If this is less than
[]\T1/pcr/m/n/10 min(p,
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[]\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[]
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[] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[]
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\relax
l.7513 ... for Profiling glm Objects}{profile.glm}
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[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
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[] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
NULL)[]
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[]\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if []\T1/pcr/m
/n/10 NA[]\T1/ptm/m/n/10 s are found. The
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[]\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[]
[2362]
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[]\T1/ptm/m/n/10 ``Fold your arms! Which is on top'' (Fac-tor, with lev-els []\
T1/pcr/m/n/10 "R on L"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "L on R"[]\T1/ptm/m/n
/10 ,
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[]\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els []\T1/pcr/m/n/
10 "Heavy"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Regul" []\T1/ptm/m/n/10 (reg-u-l
arly),
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[]\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub
le.eps^0.25)
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[]\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[]
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[]\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[]
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[]\T1/ptm/m/n/10 The orig-i-nal data are avail-able at [][]$\T1/pcr/m/n/10 http
s : / / lib . stat . cmu . edu / datasets / 1993 .
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[2376]) (./Matrix-pkg.tex
Chapter 17.
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[]\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec
t to change, and if you
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\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
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[]\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o
wn code. Please con-tact us
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[]\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm
/m/n/10 ob-jects; here, when the first is
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\T1/ptm/m/n/10 an []\T1/pcr/m/n/10 "[][]abIndex[][][]" []\T1/ptm/m/n/10 vec-tor
, these ar-gu-ments will be con-cate-nated to a new
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.all.equal
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\relax
l.182 ...{all.equal}{all.equal-methods}{all.equal}
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[]\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing
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[]\T1/ptm/m/n/10 There are more meth-ods, no-tably also for []\T1/pcr/m/n/10 "[
][]sparseVector[][][]"[]\T1/ptm/m/n/10 's, see
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[]\T1/ptm/m/n/10 optional ar-gu-ments passed to the de-fault method for generic
func-tion
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[] \T1/pcr/m/n/9 band(sm5, -1, 1)# "dsyMatrix": symmetric band preserves sym
metry property[]
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[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class
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[][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/
m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc
r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse
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[]\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[]
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[]\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[]
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[]\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20, 1), rpois(20, 3))[
c(1:3, 2:3, 3:2)],[]
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[]\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Fast version of Matrix :: .bd
iag() -- for the case of *many* (k x k) matrices:[]
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[]\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(<mat1>, <mat
2>, ....., <mat_N>) where each mat_j is a k x k \TS1/pcr/m/n/9 '\T1/pcr/m/n/9
matrix\TS1/pcr/m/n/9 '[]
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[]\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @return a sparse (N*k x N*k)
matrix of class \code{"\linkS4class{dgCMatrix}"}.[]
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[] \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 i :\TS1/pcr/m/n/9 ' \
T1/pcr/m/n/9 maybe there\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s a faster way (w/o matri
x indexing), but elegant?[]
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[] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len(
N), each=k)]),[]
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[]\T1/pcr/m/n/9 L. <- L; L.[1:2,1] <- TRUE; L.@x[1:2] <- FALSE; L. # has "zero
s" to drop0()[]
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[]\T1/pcr/m/n/10 new("pBunchKaufman", ...)[]\T1/ptm/m/n/10 , but they are more
typ-i-cally ob-tained as the value of
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[]\T1/pcr/m/n/10 signature(from = "BunchKaufman", to = "dtrMatrix")[]\T1/ptm/m/
n/10 : re-turns a
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[]\T1/pcr/m/n/10 signature(from = "pBunchKaufman", to = "dtpMatrix")[]\T1/ptm/m
/n/10 : re-turns a
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[]\T1/pcr/m/n/10 signature(from = "p?BunchKaufman", logarithm =
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[]\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m
atrix"), ...)[]
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[]\T1/ptm/m/n/10 An ob-ject rep-re-sent-ing the fac-tor-iza-tion, in-her-it-ing
from vir-tual class
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[]\T1/pcr/m/n/9 stopifnot(all.equal(as(A, "matrix"), as(Reduce(\TS1/cmtt/m/n/9
`\T1/pcr/m/n/9 %*%\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 , e.bk.A), "matrix")))[]
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\relax
l.1185 ... on cbind2/rbind2}{cbind2.Rdash.methods}
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l.1186 \aliasA{cbind2}{cbind2-methods}{cbind2}
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l.1195 \aliasA{rbind2}{cbind2-methods}{rbind2}
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l.1204 ...s}{cbind2-methods}{rbind2.Rdash.methods}
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[]\T1/ptm/m/n/10 Our class def-i-ni-tion help pages men-tion-ing []\T1/pcr/m/n/
10 cbind2() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 rbind2() []\T1/ptm/m/n/10 met
h-ods:
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[]\T1/ptm/m/n/10 The im-ple-men-ta-tion of class []\T1/pcr/m/n/10 CHMfactor []\
T1/ptm/m/n/10 is based on CHOLMOD's C-level
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[]\T1/pcr/m/n/10 signature(from = "CHMfactor", logarithm = "logical")[]\T1/ptm/
m/n/10 : be-
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[]\T1/pcr/m/n/10 signature(update = ., C = ., object = "CHMfactor")[]\T1/ptm/m/
n/10 : see
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[]\T1/ptm/m/n/10 The CHOLMOD source code; see [][]$\T1/pcr/m/n/10 https : / / g
ithub . com / DrTimothyAldenDavis /
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\T1/pcr/m/n/10 SuiteSparse$[][]\T1/ptm/m/n/10 , no-tably the header file `\T1/p
cr/m/n/10 CHOLMOD/Include/cholmod.h\T1/ptm/m/n/10 ' defin-ing
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[]\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m
atrix"), ...)[]
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[] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(list(
NULL), dn[2L]),[]
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[] \T1/pcr/m/n/9 ae2(A[ch.A@perm + 1L, ch.A@perm + 1L], with(e.ch.A, L1 %*%
D %*% L1.))[]
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[] \T1/pcr/m/n/9 ae2(A[ch.A@perm + 1L, ch.A@perm + 1L], with(E.ch.A, L %*%
L. ))[]
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[]\T1/pcr/m/n/9 u2 <- update(ch.A, t(M), mult = sqrt(2)) # updating with cross
prod(M), not M[]
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\T1/pcr/m/n/10 double / dpstrf . f$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 htt
ps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and
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[]\T1/ptm/m/n/10 The CHOLMOD source code; see [][]$\T1/pcr/m/n/10 https : / / g
ithub . com / DrTimothyAldenDavis /
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l.1854 ...sA{chol2inv}{chol2inv-methods}{chol2inv}
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of length []\T1/pcr/m/n/10 n*n []\T1/ptm/m/
n/10 ([]\T1/pcr/m/n/10 Cholesky[]\T1/ptm/m/n/10 ) or []\T1/pcr/m/n/10 n*(n+1)/2
[]\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 pCholesky[]\T1/ptm/m/n/10 ), where
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[]\T1/ptm/m/n/10 Class [][][]\T1/pcr/m/n/10 CholeskyFactorization[][][][]\T1/pt
m/m/n/10 , di-rectly. Class [][][]\T1/pcr/m/n/10 MatrixFactorization[][][][]\T1
/ptm/m/n/10 , by class
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[]\T1/ptm/m/n/10 Objects can be gen-er-ated di-rectly by calls of the form []\T
1/pcr/m/n/10 new("Cholesky", ...) []\T1/ptm/m/n/10 or
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0 : re-turns a
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[]\T1/pcr/m/n/10 signature(from = "p?Cholesky", logarithm = "logical")[]\T1/ptm
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ps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and
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[]\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m
atrix"), ...)[]
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[] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(list(
NULL), dn[2L]),[]
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[]\T1/ptm/m/n/10 a [][]fi-nite[][][] num-ber. The ma-trix that is fac-tor-ized
is []\T1/pcr/m/n/10 A + Imult *
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\T1/pcr/m/n/10 - diag(abs(A))) []\T1/ptm/m/n/10 en-sures that []\T1/pcr/m/n/10
A + Imult * diag(nrow(A)) []\T1/ptm/m/n/10 is di-
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[]\T1/ptm/m/n/10 An ob-ject rep-re-sent-ing the fac-tor-iza-tion, in-her-it-ing
from vir-tual class
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\T1/pcr/m/n/10 double / dpstrf . f$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 htt
ps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and
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[]\T1/ptm/m/n/10 The CHOLMOD source code; see [][]$\T1/pcr/m/n/10 https : / / g
ithub . com / DrTimothyAldenDavis /
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\T1/pcr/m/n/10 SuiteSparse$[][]\T1/ptm/m/n/10 , no-tably the header file `\T1/p
cr/m/n/10 CHOLMOD/Include/cholmod.h\T1/ptm/m/n/10 ' defin-ing
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[] \T1/pcr/m/n/9 list(simpl1 = Cholesky(A4, perm = TRUE, super = FALSE, L
DL = TRUE),[]
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[] \T1/pcr/m/n/9 simpl0 = Cholesky(A4, perm = TRUE, super = FALSE, L
DL = FALSE),[]
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[] \T1/pcr/m/n/9 super0 = Cholesky(A4, perm = TRUE, super = TRUE
)),[]
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[] \T1/pcr/m/n/9 list(simpl1 = Cholesky(A4, perm = FALSE, super = FALSE, L
DL = TRUE),[]
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[] \T1/pcr/m/n/9 simpl0 = Cholesky(A4, perm = FALSE, super = FALSE, L
DL = FALSE),[]
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[] \T1/pcr/m/n/9 super0 = Cholesky(A4, perm = FALSE, super = TRUE
)))[]
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[]\T1/pcr/m/n/9 rapply2 <- function(object, f, ...) rapply(object, f, , , how
= "list", ...)[]
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[] \T1/pcr/m/n/9 x = c(1, 6, 38, 10, 60, 103, -4, 6, -32, -247, -2, -
16, -128, -2, -67))[]
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[] \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4), j=c(2:4,1), x = 2,
dimnames=dns))[]
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[] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
dimnames=dns))[]
[2410]
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[] \T1/pcr/m/n/9 a. <- sparseMatrix(i=4:1, j=1:4, dimnames=list(n4, n4), repr
="T") # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[]
[2411]
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) has been already used, duplicate ignored
<to be read again>
\relax
l.2696 ...asA{colMeans}{colSums-methods}{colMeans}
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has been already used, duplicate ignored
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\relax
l.2704 \aliasA{colSums}{colSums-methods}{colSums}
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) has been already used, duplicate ignored
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l.2711 ...asA{rowMeans}{colSums-methods}{rowMeans}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowSums})
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l.2719 \aliasA{rowSums}{colSums-methods}{rowSums}
Underfull \hbox (badness 2922) in paragraph at lines 2771--2775
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i
n-her-it-ing from
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\T1/ptm/m/n/10 class [][][]\T1/pcr/m/n/10 sparseVector[][][][]\T1/ptm/m/n/10 .
Only ap-pli-ca-ble when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 is in-her-it-ing fr
om a
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[][][]\T1/pcr/m/n/10 dimnames[][][](x) []\T1/ptm/m/n/10 are only kept (as [][][
]\T1/pcr/m/n/10 names[][][](v)[]\T1/ptm/m/n/10 ) when the re-sult-ing []\T1/pcr
/m/n/10 v []\T1/ptm/m/n/10 is [][][]\T1/pcr/m/n/10 numeric[][][][]\T1/ptm/m/n/1
0 , since
[2412]
[2413]
Underfull \hbox (badness 3547) in paragraph at lines 2888--2891
[]\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10
, the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when
[2414]
[2415]
[2416]
[2417]
[2418]
Underfull \hbox (badness 10000) in paragraph at lines 3290--3293
[]\T1/pcr/m/n/10 signature(from = "denseLU", logarithm = "logical")[]\T1/ptm/m/
n/10 : com-
[2419]
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[]\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m
atrix"), ...)[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 3352--3352
[] \T1/pcr/m/n/9 new( "pMatrix", Dim = c(n, n), Dimnames = c(dn[
1L], list(NULL)),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3355--3355
[] \T1/pcr/m/n/9 new("dtrMatrix", Dim = c(n, n), Dimnames = list(
NULL, NULL),[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 3358--3358
[] \T1/pcr/m/n/9 new("dtrMatrix", Dim = c(n, n), Dimnames = c(lis
t(NULL), dn[2L]),[]
[2420]
Underfull \hbox (badness 7379) in paragraph at lines 3486--3488
[]\T1/pcr/m/n/10 signature(x = "dgCMatrix")[]\T1/ptm/m/n/10 : com-putes the LU
de-com-po-si-tion of a square
[2421]
[2422]
[2423]
Underfull \hbox (badness 4846) in paragraph at lines 3707--3711
[]\T1/ptm/m/n/10 Note that both []\T1/pcr/m/n/10 new(.) []\T1/ptm/m/n/10 and []
[][]\T1/pcr/m/n/10 spMatrix[][][] []\T1/ptm/m/n/10 con-struc-tors for []\T1/pcr
/m/n/10 "dgTMatrix" []\T1/ptm/m/n/10 (and other
Underfull \hbox (badness 2717) in paragraph at lines 3712--3716
[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can be stored in
more than one pos-si-ble
[2424]
Underfull \hbox (badness 5231) in paragraph at lines 3757--3762
[]\T1/ptm/m/n/10 Construct a for-mally di-ag-o-nal [][][]\T1/pcr/m/n/10 Matrix[
][][][]\T1/ptm/m/n/10 , i.e., an ob-ject in-her-it-ing from vir-tual class
Overfull \hbox (84.78088pt too wide) in paragraph at lines 3768--3768
[]\T1/pcr/m/n/10 .sparseDiagonal(n, x = NULL, uplo = "U", shape = "t", unitri
= TRUE, kind, cols)[]
[2425]
Underfull \hbox (badness 10000) in paragraph at lines 3824--3827
[]\T1/pcr/m/n/10 .trDiagonal() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 .symDiagon
al() []\T1/ptm/m/n/10 are sim-ple wrap-pers, for
Underfull \hbox (badness 6792) in paragraph at lines 3824--3827
[]\T1/pcr/m/n/10 .sparseDiagonal(shape = "t") []\T1/ptm/m/n/10 and []\T1/pcr/m/
n/10 .sparseDiagonal(shape = "s")[]\T1/ptm/m/n/10 , re-spec-
[2426]
Underfull \hbox (badness 3646) in paragraph at lines 3901--3904
[]\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 dimnames[][][][]\T1/ptm/m/n/10 , a []
[][]\T1/pcr/m/n/10 list[][][][]\T1/ptm/m/n/10 , see the [][][]\T1/pcr/m/n/10 Ma
trix[][][] []\T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally
Underfull \hbox (badness 6542) in paragraph at lines 3936--3940
[]\T1/pcr/m/n/10 signature(x = "diagonalMatrix")[]\T1/ptm/m/n/10 : all these gr
oup meth-ods re-turn a
Underfull \hbox (badness 4518) in paragraph at lines 3945--3951
[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")[]\T1/ptm/m/n/10
: the re-sult is from class
[2427]
Underfull \hbox (badness 10000) in paragraph at lines 3952--3956
[]\T1/pcr/m/n/10 (object = "diagonalMatrix")[]\T1/ptm/m/n/10 : Re-turns an ob-j
ect of S3 class
Underfull \hbox (badness 2318) in paragraph at lines 3962--3966
[][][]\T1/pcr/m/n/10 Diagonal[][][]() []\T1/ptm/m/n/10 as con-struc-tor of thes
e ma-tri-ces, and [][][]\T1/pcr/m/n/10 isDiagonal[][][][]\T1/ptm/m/n/10 . [][][
]\T1/pcr/m/n/10 ddiMatrix[][][] []\T1/ptm/m/n/10 and
[2428]
[2429]
[2430]
Underfull \hbox (badness 10000) in paragraph at lines 4219--4221
[]\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")[]\T1/ptm/m/n/10 :
this group con-tains
[2431]
[2432]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 4360--4360
[]\T1/pcr/m/n/9 stopifnot(all.equal(S9p0, S9p))# same as as default, but diffe
rent from the random one[]
[2433]
Underfull \hbox (badness 2469) in paragraph at lines 4474--4477
[]\T1/pcr/m/n/10 signature(x = "dpoMatrix")[]\T1/ptm/m/n/10 : Re-turns the [][]
[]\T1/pcr/m/n/10 determinant[][][] []\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 x[]\T1/
ptm/m/n/10 , via
[2434]
Underfull \hbox (badness 10000) in paragraph at lines 4497--4502
[]\T1/ptm/m/n/10 Currently the va-lid-ity meth-ods for these classes such as
Underfull \hbox (badness 2020) in paragraph at lines 4497--4502
[][][]\T1/pcr/m/n/10 getValidity[][][](getClass("dpoMatrix")) []\T1/ptm/m/n/10
for ef-fi-ciency rea-sons only check the di-
Underfull \hbox (badness 1748) in paragraph at lines 4503--4512
\T1/pcr/m/n/10 error=identity), "error") []\T1/ptm/m/n/10 . In-deed, when \T1/p
tm/m/it/10 co-erc-ing \T1/ptm/m/n/10 to these classes, a ver-sion
Underfull \hbox (badness 1590) in paragraph at lines 4503--4512
\T1/ptm/m/n/10 of [][][]\T1/pcr/m/n/10 Cholesky[][][]() []\T1/ptm/m/n/10 or [][
][]\T1/pcr/m/n/10 chol[][][]() []\T1/ptm/m/n/10 is typ-i-cally used, e.g., see
[]\T1/pcr/m/n/10 selectMethod("coerce",
Underfull \hbox (badness 6675) in paragraph at lines 4559--4566
[]\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 Matrix[][][][]\T1/ptm/m/n/10 , typ-i-ca
lly in-her-it-ing from vir-tual class [][][]\T1/pcr/m/n/10 sparseMatrix[][][][]
\T1/ptm/m/n/10 .
Underfull \hbox (badness 6493) in paragraph at lines 4559--4566
[][][]\T1/pcr/m/n/10 denseMatrix[][][] []\T1/ptm/m/n/10 and tra-di-tional vec-t
ors and ma-tri-ces are co-erced to
[2435]
Underfull \hbox (badness 10000) in paragraph at lines 4574--4582
[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing if the re-sult must in-herit from vi
r-tual class
Underfull \hbox (badness 1365) in paragraph at lines 4574--4582
[][][]\T1/pcr/m/n/10 CsparseMatrix[][][][]\T1/ptm/m/n/10 . If []\T1/pcr/m/n/10
FALSE []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 in-her-its from
[][][]\T1/pcr/m/n/10 RsparseMatrix[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4597--4600
[]\T1/ptm/m/n/10 Function [][][]\T1/pcr/m/n/10 sparseMatrix[][][][]\T1/ptm/m/n/
10 , for con-struct-ing ob-jects in-her-it-ing from vir-tual class
[2436]
Underfull \hbox (badness 10000) in paragraph at lines 4641--4645
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10
new("dsCMatrix", ...) []\T1/ptm/m/n/10 or
Underfull \hbox (badness 2103) in paragraph at lines 4641--4645
[]\T1/pcr/m/n/10 new("dsTMatrix", ...)[]\T1/ptm/m/n/10 , or au-to-mat-i-cally v
ia e.g., []\T1/pcr/m/n/10 as(*, "symmetricMatrix")[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1571) in paragraph at lines 4691--4694
[]\T1/pcr/m/n/10 signature(x = "dsCMatrix", pivot = "logical")[]\T1/ptm/m/n/10
: Re-turns (and stores) the
[2437]
[2438]
Underfull \hbox (badness 1221) in paragraph at lines 4834--4837
[]\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "dMatrix"[]\T1/ptm/m/n/10 , by class []
\T1/pcr/m/n/10 "dsparseMatrix"[]\T1/ptm/m/n/10 ; class []\T1/pcr/m/n/10 "sparse
Matrix"[]\T1/ptm/m/n/10 , by classes
Underfull \hbox (badness 1400) in paragraph at lines 4844--4847
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")[]\T1/ptm/m/n/10
: if []\T1/pcr/m/n/10 uplo ==
[2439]
Underfull \hbox (badness 10000) in paragraph at lines 4896--4898
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10
new("dsyMatrix", ...) []\T1/ptm/m/n/10 or
Underfull \hbox (badness 1365) in paragraph at lines 4932--4935
[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")[]\T1/ptm/m/n/10
, or []\T1/pcr/m/n/10 x = "dsyMatrix"
[2440]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4978--4978
[]\T1/pcr/m/n/9 stopifnot(all(S1 == S2)) # equal "seen as matrix", but differ
internally :[]
[2441]
[2442]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5084--5084
[]\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim
= c(5L, 5L),[]
Underfull \hbox (badness 3635) in paragraph at lines 5139--5143
[]\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ddenseMatrix"[]\T1/ptm/m/n/10 , di-rec
tly. Class []\T1/pcr/m/n/10 "triangularMatrix"[]\T1/ptm/m/n/10 , di-rectly. Cla
ss
Underfull \hbox (badness 10000) in paragraph at lines 5148--5151
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")[]\T1/ptm/m/n/10 :
Ma-trix mul-ti-pli-ca-tion;
Underfull \hbox (badness 10000) in paragraph at lines 5151--5155
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")[]\T1/ptm/m/n
/10 : the
[2443]
[2444]
[2445]
[2446]
Underfull \hbox (badness 10000) in paragraph at lines 5399--5401
[]\T1/ptm/m/n/10 a ma-trix fac-tor-iza-tion, typ-i-cally in-her-it-ing from vir
-tual class
Overfull \hbox (29.27832pt too wide) in paragraph at lines 5418--5418
[] \T1/pcr/m/n/10 all.equal(as(x, "matrix"), as(Reduce(\TS1/cmtt/m/n/10 `\T
1/pcr/m/n/10 %*%\TS1/cmtt/m/n/10 `\T1/pcr/m/n/10 , expand2(y)), "matrix"))
Overfull \hbox (37.71342pt too wide) in alignment at lines 5449--5449
[] []
[2447]
Underfull \hbox (badness 7064) in paragraph at lines 5477--5494
[]\T1/pcr/m/n/10 signature(x = "p?BunchKaufman")[]\T1/ptm/m/n/10 : ex-pands the
fac-tor-iza-tion $\OML/cmm/m/it/10 A \OT1/cmr/m/n/10 =
Underfull \hbox (badness 3000) in paragraph at lines 5506--5513
[]\T1/pcr/m/n/10 signature(x = "denseLU")[]\T1/ptm/m/n/10 : ex-pands the fac-to
r-iza-tion $\OML/cmm/m/it/10 A \OT1/cmr/m/n/10 = \OML/cmm/m/it/10 P[]LU$ \T1/pt
m/m/n/10 as
Underfull \hbox (badness 2735) in paragraph at lines 5522--5529
[]\T1/pcr/m/n/10 signature(x = "CHMfactor")[]\T1/ptm/m/n/10 : as []\T1/pcr/m/n/
10 expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/pcr/m/n/10 list(P, L)[]\T1/p
tm/m/n/10 .
Underfull \hbox (badness 1337) in paragraph at lines 5529--5544
[]\T1/pcr/m/n/10 signature(x = "sparseLU")[]\T1/ptm/m/n/10 : as []\T1/pcr/m/n/1
0 expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/pcr/m/n/10 list(P, L, U,
Underfull \hbox (badness 2680) in paragraph at lines 5529--5544
\T1/pcr/m/n/10 Q)[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 expand(x)[["Q"]] []\T1/ptm
/m/n/10 and []\T1/pcr/m/n/10 expand2(x)[["P2."]] []\T1/ptm/m/n/10 rep-re-sent t
he same per-
Underfull \hbox (badness 5374) in paragraph at lines 5529--5544
\T1/ptm/m/n/10 mu-ta-tion ma-trix $\OML/cmm/m/it/10 P[]$ \T1/ptm/m/n/10 but hav
e op-po-site []\T1/pcr/m/n/10 margin []\T1/ptm/m/n/10 slots and in-verted []\T1
/pcr/m/n/10 perm []\T1/ptm/m/n/10 slots.
Underfull \hbox (badness 2073) in paragraph at lines 5544--5549
[]\T1/pcr/m/n/10 signature(x = "denseLU")[]\T1/ptm/m/n/10 : as []\T1/pcr/m/n/10
expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/pcr/m/n/10 list(L, U, P)[]\T1/
ptm/m/n/10 .
[2448]
[2449]
[2450]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5752--5752
[]\T1/pcr/m/n/9 str(pores <- readMM(system.file("external/pores_1.mtx", packag
e = "Matrix")))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5753--5753
[]\T1/pcr/m/n/9 str(utm <- readHB(system.file("external/utm300.rua" , packag
e = "Matrix")))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5754--5754
[]\T1/pcr/m/n/9 str(lundA <- readMM(system.file("external/lund_a.mtx" , packag
e = "Matrix")))[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5755--5755
[]\T1/pcr/m/n/9 str(lundA <- readHB(system.file("external/lund_a.rsa" , packag
e = "Matrix")))[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5756--5756
[]\T1/pcr/m/n/9 ## https://math.nist.gov/MatrixMarket/data/Harwell-Boeing/coun
terx/counterx.htm[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5757--5757
[]\T1/pcr/m/n/9 str(jgl <- readMM(system.file("external/jgl009.mtx" , packag
e = "Matrix")))[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5763--5763
[]\T1/pcr/m/n/9 u. <- url("https://www.cise.ufl.edu/research/sparse/RB/Boeing/
msc00726.tar.gz")[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5768--5768
[]\T1/pcr/m/n/9 ## Store as MatrixMarket (".mtx") file, here inside temporary
dir./folder:[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5771--5771
[]\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of
the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[]
[2451]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 5781--5781
[]\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume
nts to sparseMatrix():[]
[2452]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5843--5843
[] \T1/pcr/m/n/9 all.equal(facmul(x, nm, y, trans = TRUE, left = TRUE),
crossprod(L, y))[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5844--5844
[] \T1/pcr/m/n/9 all.equal(facmul(x, nm, y, trans = TRUE, left = FALSE), t
crossprod(y, L))[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5923--5923
[]\T1/pcr/m/n/10 .diag2dense(from, kind = ".", shape = "t", packed = FALSE, up
lo = "U")[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 5925--5925
[]\T1/pcr/m/n/10 .m2dense(from, class = ".ge", uplo = "U", diag = "N", trans =
FALSE)[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5928--5928
[]\T1/pcr/m/n/10 .diag2sparse(from, kind = ".", shape = "t", repr = "C", uplo
= "U")[]
[2453]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5930--5930
[]\T1/pcr/m/n/10 .m2sparse(from, class = ".gC", uplo = "U", diag = "N", trans
= FALSE)[]
Underfull \hbox (badness 10000) in paragraph at lines 6000--6002
[]\T1/ptm/m/n/10 a string in []\T1/pcr/m/n/10 c("trace", "sumLog", "prod", "min
", "max",
[2454]
Underfull \hbox (badness 10000) in paragraph at lines 6073--6079
[][]\T1/pcr/m/n/10 .solve.dgC.*(a, b)[]\T1/ptm/b/n/10 : []\T1/pcr/m/n/10 .solv
e.dgC.lu(a, b) []\T1/ptm/m/n/10 needs a square ma-trix []\T1/pcr/m/n/10 a[]\T1/
ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 6073--6079
[]\T1/pcr/m/n/10 .solve.dgC.qr(a, b) []\T1/ptm/m/n/10 needs a ``long'' ma-trix
[]\T1/pcr/m/n/10 a[]\T1/ptm/m/n/10 , with []\T1/pcr/m/n/10 nrow(a) >= ncol(a)[]
\T1/ptm/m/n/10 .
[2455]
Underfull \hbox (badness 10000) in paragraph at lines 6087--6096
[][]\T1/pcr/m/n/10 .updateCHMfactor(object, parent, mult)[]\T1/ptm/b/n/10 : []
\T1/pcr/m/n/10 .updateCHMfactor []\T1/ptm/m/n/10 up-
Underfull \hbox (badness 10000) in paragraph at lines 6087--6096
\T1/ptm/m/n/10 dates []\T1/pcr/m/n/10 object []\T1/ptm/m/n/10 with the re-sult
of Cholesky fac-tor-iz-ing []\T1/pcr/m/n/10 F(parent) + mult[1] *
Underfull \hbox (badness 2443) in paragraph at lines 6087--6096
\T1/pcr/m/n/10 diag(nrow(parent))[]\T1/ptm/m/n/10 , i.e., []\T1/pcr/m/n/10 F(pa
rent) []\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 mult[1] []\T1/ptm/m/n/10 times the
iden-tity ma-trix,
[2456]
[2457]
[2458]
[2459]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.image}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.6399 \aliasA{image}{image-methods}{image}
[2460]
[2461]
Underfull \hbox (badness 4120) in paragraph at lines 6495--6498
[]\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][
][]\T1/pcr/m/n/10 dgTMatrix[][][] []\T1/ptm/m/n/10 class. Use
Overfull \hbox (47.58038pt too wide) in paragraph at lines 6514--6514
[]\T1/pcr/m/n/9 stopifnot(!is.null(leg <- imgC$legend), is.list(leg$right)) #
failed for 2 days ..[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6534--6534
[]\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col
/row) indices:[]
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[] \T1/pcr/m/n/9 I2 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE,
border.col=NA)[]
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[] \T1/pcr/m/n/9 I3 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd
=2, border.col=NA)[]
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[]\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor
der.col = adjustcolor("skyblue", 1/2))[]
[2462]
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[]\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a
nti-aliasing[]
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[] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[]
[2463]
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[]\T1/pcr/m/n/10 signature(x = "indMatrix", y = "Matrix") []\T1/ptm/m/n/10 and
oth-ers listed by
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[]\T1/pcr/m/n/10 showMethods("%*%", classes = "indMatrix")[]\T1/ptm/m/n/10 : ma
-trix prod-ucts im-ple-mented
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[]\T1/pcr/m/n/10 signature(from = "numeric", to = "indMatrix")[]\T1/ptm/m/n/10
: sup-port-ing typ-i-cal
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[]\T1/pcr/m/n/10 signature(from = "list", to = "indMatrix")[]\T1/ptm/m/n/10 : s
up-port-ing []\T1/pcr/m/n/10 indMatrix
[2464]
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[]\T1/pcr/m/n/10 signature(x = "indMatrix")[]\T1/ptm/m/n/10 : row and
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[]\T1/pcr/m/n/10 signature(X = "indMatrix", Y = "indMatrix")[]\T1/ptm/m/n/10 :
Kro-necker prod-uct of
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[]\T1/ptm/m/n/10 Fabian Scheipl at `\T1/pcr/m/n/10 uni-muenchen.de\T1/ptm/m/n/1
0 ', build-ing on the ex-ist-ing class [][][]\T1/pcr/m/n/10 pMatrix[][][] []\T1
/ptm/m/n/10 af-ter
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\T1/ptm/m/n/10 a nice hike's con-ver-sa-tion with Mar-tin Maech-ler. Meth-ods f
or [][][]\T1/pcr/m/n/10 crossprod[][][](x, y) []\T1/ptm/m/n/10 and
[2465]
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[]\T1/ptm/m/n/10 an in-te-ger off-set, in-di-cat-ing that the re-sult should be
a per-mu-ta-tion of
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[]\T1/pcr/m/n/10 invertPerm(p) []\T1/ptm/m/n/10 re-turns an in-te-ger vec-tor o
f length []\T1/pcr/m/n/10 length(p) []\T1/ptm/m/n/10 such that
Underfull \hbox (badness 4441) in paragraph at lines 6837--6841
[]\T1/pcr/m/n/10 p[invertPerm(p)] []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 invertP
erm(p)[p] []\T1/ptm/m/n/10 are both []\T1/pcr/m/n/10 seq_along(p)[]\T1/ptm/m/n/
10 , i.e., the
[2466]
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[]\T1/pcr/m/n/9 ## Product of transpositions (1 2)(2 1)(4 3)(6 8)(10 1) = (3 4
)(6 8)(1 10)[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.anyNA}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.6888 \aliasA{anyNA}{is.na-methods}{anyNA}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.finite
}) has been already used, duplicate ignored
<to be read again>
\relax
l.6895 ...asA{is.finite}{is.na-methods}{is.finite}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.infini
te}) has been already used, duplicate ignored
<to be read again>
\relax
l.6903 ...is.infinite}{is.na-methods}{is.infinite}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.na}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.6911 \aliasA{is.na}{is.na-methods}{is.na}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.nan})
has been already used, duplicate ignored
<to be read again>
\relax
l.6918 \aliasA{is.nan}{is.na-methods}{is.nan}
[2467]
[2468]
[2469]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.isSymmetr
ic}) has been already used, duplicate ignored
<to be read again>
\relax
l.7077 ...etric}{isSymmetric-methods}{isSymmetric}
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[]\T1/pcr/m/n/10 isSymmetric(object, checkDN = TRUE, tol = 100 * .Machine$doub
le.eps, tol1 = 8 * tol, ...)[]
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[]\T1/pcr/m/n/10 isSymmetric(object, checkDN = TRUE, tol = 100 * .Machine$doub
le.eps, ...)[]
[2470]
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[]\T1/pcr/m/n/9 isSymmetric(as(M, "generalMatrix")) # still symmetric, even if
not "formally"[]
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[]\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs = TRUE) # includes S3 g
eneric from base[]
[2471]
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[]\T1/pcr/m/n/9 isTriangular(as(M, "generalMatrix")) # still triangular, even
if not "formally"[]
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[]\T1/pcr/m/n/10 KhatriRao(X, Y = X, FUN = "*", sparseY = TRUE, make.dimnames
= FALSE)
[2472]
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[]\T1/pcr/m/n/9 stopifnot(all(K1 <- KhatriRao(nd, zm) == 0), identical(dim(K1)
, c(12L, 4L)),[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7372--7372
[] \T1/pcr/m/n/9 all(K2 <- KhatriRao(zm, nd) == 0), identical(dim(K2)
, c(12L, 4L)))[]
[2473]
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[] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), d
imnames(Kmd)))[]
[2474]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.kronecker
}) has been already used, duplicate ignored
<to be read again>
\relax
l.7453 ...kronecker}{kronecker-methods}{kronecker}
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[]\T1/pcr/m/n/10 ldenseMatrix []\T1/ptm/m/n/10 is the vir-tual class of all den
se \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2475]
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[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-call
y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2476
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.*,ndiMatr
ix,Matrix.Rdash.method}) has been already used, duplicate ignored
<argument> ...shipout:D \box_use:N \l_shipout_box
\__shipout_drop_firstpage_...
l.7691 C
lass \code{"\LinkA{sparseMatrix}{sparseMatrix.Rdash.class}"}, by cla...
]
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[]\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ldenseMatrix"[]\T1/ptm/m/n/10 , di-rec
tly. Class []\T1/pcr/m/n/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/
10 "ldenseMatrix"[]\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "denseMatrix"[]\T1/ptm/m/n/10 , by class
[]\T1/pcr/m/n/10 "ldenseMatrix"[]\T1/ptm/m/n/10 . Class []\T1/pcr/m/n/10 "Matri
x"[]\T1/ptm/m/n/10 , by class
Underfull \hbox (badness 10000) in paragraph at lines 7746--7749
[]\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n
/10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/
10 ); use, e.g.,
[2477]
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[]\T1/pcr/m/n/10 lsTMatrix[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 ltTMatrix[]\T
1/ptm/m/n/10 ) or in com-pressed column-oriented form (class
Underfull \hbox (badness 1242) in paragraph at lines 7804--7814
[][][]\T1/pcr/m/n/10 CsparseMatrix[][][][]\T1/ptm/m/n/10 , sub-classes []\T1/pc
r/m/n/10 lgCMatrix[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lsCMatrix[]\T1/ptm/m/n/10
, and []\T1/pcr/m/n/10 ltCMatrix[]\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\
T1/ptm/m/n/10 --in
[2478]
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[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cal
ly equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2479]
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[]\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n
/10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/
10 ; use, e.g.,
[2480]
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[]\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n
/10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/
10 ; use, e.g.,
[2481]
[2482]
[2483]
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[]\T1/ptm/m/n/10 vector of all non-zero en-tries of []\T1/pcr/m/n/10 x[]\T1/ptm
/m/n/10 ; ex-ists \T1/ptm/b/n/10 only \T1/ptm/m/n/10 when []\T1/pcr/m/n/10 as(x
,
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[]\T1/pcr/m/n/10 mat2triplet() []\T1/ptm/m/n/10 is con-cep-tu-ally the \T1/ptm/
m/it/10 in-verse \T1/ptm/m/n/10 func-tion of [][][]\T1/pcr/m/n/10 spMatrix[][][
] []\T1/ptm/m/n/10 and (one case of)
[2484]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rpcent.*
.Rpcent.}) has been already used, duplicate ignored
<to be read again>
\relax
l.8313 ...*\%}{matmult-methods}{.Rpcent.*.Rpcent.}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.crossprod
}) has been already used, duplicate ignored
<to be read again>
\relax
l.8387 ...A{crossprod}{matmult-methods}{crossprod}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tcrosspro
d}) has been already used, duplicate ignored
<to be read again>
\relax
l.8463 ...tcrossprod}{matmult-methods}{tcrossprod}
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\T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][][]\T1/
pcr/m/n/10 t[][][](.)[]\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn
[2485]
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[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")[]\T1/ptm/m/n/10 :
Ma-trix mul-ti-pli-ca-tion;
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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and
other sig-na-tures (use
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[]\T1/pcr/m/n/10 showMethods("%*%", class="dtrMatrix")[]\T1/ptm/m/n/10 ): ma-tr
ix mul-ti-pli-ca-tion. Mul-ti-
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\T1/ptm/m/n/10 sig-na-tures, use []\T1/pcr/m/n/10 showMethods("crossprod", clas
s = "dgeMatrix")[]\T1/ptm/m/n/10 , ma-trix
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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and
other sig-na-
[2486]
[2487]
[2488]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det}) has
been already used, duplicate ignored
<to be read again>
\relax
l.8859 \aliasA{det}{Matrix-class}{det}
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[]\T1/pcr/m/n/10 signature(x = "Matrix", value = "list")[]\T1/ptm/m/n/10 : set
the []\T1/pcr/m/n/10 dimnames []\T1/ptm/m/n/10 to a
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[2489]
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[]\T1/pcr/m/n/10 signature(from = "ANY", to = "Matrix")[]\T1/ptm/m/n/10 : This
re-lies on a cor-rect
[2490]
[2491]
Underfull \hbox (badness 10000) in paragraph at lines 9128--9132
[]\T1/pcr/m/n/10 CholeskyFactorization[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Bunch
KaufmanFactorization[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 signature(x = "MatrixFactorization", logarithm =
Underfull \hbox (badness 10000) in paragraph at lines 9168--9171
[]\T1/pcr/m/n/10 signature(obj = "MatrixFactorization")[]\T1/ptm/m/n/10 : re-tu
rns []\T1/pcr/m/n/10 obj []\T1/ptm/m/n/10 with
Underfull \hbox (badness 3019) in paragraph at lines 9177--9180
[]\T1/ptm/m/n/10 Classes ex-tend-ing []\T1/pcr/m/n/10 CholeskyFactorization[]\T
1/ptm/m/n/10 , namely [][][]\T1/pcr/m/n/10 Cholesky[][][][]\T1/ptm/m/n/10 , [][
][]\T1/pcr/m/n/10 pCholesky[][][][]\T1/ptm/m/n/10 , and
[2492]
Underfull \hbox (badness 10000) in paragraph at lines 9181--9183
[]\T1/ptm/m/n/10 Classes ex-tend-ing []\T1/pcr/m/n/10 BunchKaufmanFactorization
[]\T1/ptm/m/n/10 , namely [][][]\T1/pcr/m/n/10 BunchKaufman[][][] []\T1/ptm/m/n
/10 and
Underfull \hbox (badness 10000) in paragraph at lines 9196--9199
[]\T1/ptm/m/n/10 Generic func-tions [][][]\T1/pcr/m/n/10 expand1[][][] []\T1/pt
m/m/n/10 and [][][]\T1/pcr/m/n/10 expand2[][][] []\T1/ptm/m/n/10 for con-struct
-ing ma-trix fac-tors from
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[]\T1/pcr/m/n/10 ndenseMatrix []\T1/ptm/m/n/10 is the vir-tual class of all den
se \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
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[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-call
y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2493]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if []\T1/pcr/m/n/10 X <- (X + t(X))/2 []
\T1/ptm/m/n/10 should be done, af-ter []\T1/pcr/m/n/10 X <-
[2494]
[2495]
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[] \T1/pcr/m/n/9 all.equal(n.A.m, unname(as.matrix(n.A$mat)), tolerance = 1e
-15)# seen rel.d.= 1.46e-16[]
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[]\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a
ll in this example[]
[2496]
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[]\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ndenseMatrix"[]\T1/ptm/m/n/10 , di-rec
tly. Class []\T1/pcr/m/n/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/
10 "ndenseMatrix"[]\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "denseMatrix"[]\T1/ptm/m/n/10 , by class
[]\T1/pcr/m/n/10 "ndenseMatrix"[]\T1/ptm/m/n/10 . Class []\T1/pcr/m/n/10 "Matri
x"[]\T1/ptm/m/n/10 , by class
Underfull \hbox (badness 10000) in paragraph at lines 9518--9521
[]\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n
/10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/
10 ); use, e.g.,
[2497]
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[]\T1/pcr/m/n/10 signature(from = "matrix", to = "nMatrix")[]\T1/ptm/m/n/10 : N
ote that these co-er-cions
[2498]
Underfull \hbox (badness 1867) in paragraph at lines 9699--9701
[]\T1/ptm/m/n/10 fast sim-
[2499]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.norm}) ha
s been already used, duplicate ignored
<to be read again>
\relax
l.9741 \aliasA{norm}{norm-methods}{norm}
[2500]
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[]\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x) ## 8 x 10
"dgCMatrix"[]
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[]\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
"dsCMatrix"[]
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[]\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
"dtCMatrix"[]
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[]\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][][]\T1/pcr/m/n
/10 TsparseMatrix[][][][]\T1/ptm/m/n/10 , sub-classes []\T1/pcr/m/n/10 ngTMatri
x[]\T1/ptm/m/n/10 ,
[2501]
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[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cal
ly equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2502]
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[]\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n
/10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/
10 ; use, e.g.,
[2503]
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[]\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n
/10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/
10 ; use, e.g.,
[2504]
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[]\T1/ptm/m/n/10 typically a []\T1/pcr/m/n/10 "packedMatrix"[]\T1/ptm/m/n/10 ,
though
[2505]
[2506]
[2507]
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[]\T1/pcr/m/n/10 signature(x = "pMatrix", y = "Matrix") []\T1/ptm/m/n/10 and ot
h-ers listed by
Underfull \hbox (badness 8189) in paragraph at lines 10386--10389
[]\T1/pcr/m/n/10 showMethods("%*%", classes = "pMatrix")[]\T1/ptm/m/n/10 : ma-t
rix prod-ucts im-ple-mented
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[]\T1/pcr/m/n/10 signature(from = "numeric", to = "pMatrix")[]\T1/ptm/m/n/10 :
sup-port-ing typ-i-cal
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[]\T1/pcr/m/n/10 signature(a = "pMatrix", b = "missing")[]\T1/ptm/m/n/10 : the
in-verse per-mu-ta-tion ma-trix,
[2508]
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[] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD
iag = TRUE,[]
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[]\T1/pcr/m/n/10 printSpMatrix(x, digits = NULL, maxp = max(100L, getOption("m
ax.print")),[]
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[] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[]
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[]\T1/pcr/m/n/10 printSpMatrix2(x, digits = NULL, maxp = max(100L, getOption("
max.print")),[]
[2509]
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[] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[]
Underfull \hbox (badness 3989) in paragraph at lines 10502--10512
[]\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of []
\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 should
Underfull \hbox (badness 10000) in paragraph at lines 10502--10512
\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2510]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr}) has
been already used, duplicate ignored
<to be read again>
\relax
l.10604 \aliasA{qr}{qr-methods}{qr}
[2511]
[2512]
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[] \T1/pcr/m/n/9 all.equal(qr.coef(qr.A1, b), drop(solve(crossprod(A1), cro
ssprod(A1, b))))[]
[2513]
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[] \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 qr.coef\TS1/pcr/m/n/9 ' \
T1/pcr/m/n/9 computes unique least squares solution of "nearby" problem[]
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[] \T1/pcr/m/n/9 ## Z x = b for some full rank Z ~ A, currently without war
ning {FIXME} ![]
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[]\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m
atrix"), ...)[]
Underfull \vbox (badness 10000) has occurred while \output is active
[2514]
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[]\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of [][][]\T1/pcr/m/n/10
qr[][][](x, tol,
Underfull \hbox (badness 10000) in paragraph at lines 10865--10868
[]\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense []\T1/pcr/m/n/10 x[]\
T1/ptm/m/n/10 , it cor-re-sponds to
[2515]
[2516]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 10962--10962
[]\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/
n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale
free"[]
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[]\T1/pcr/m/n/9 sapply(meths, function(.m.) rankMatrix(M15, method = .m., tol
= 1e-7)) # all 14[]
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[]\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L))) # war
ning+ ~1.5 sec (2013)[]
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[]\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con
siderably faster![]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.11005 \aliasA{rcond}{rcond-methods}{rcond}
[2517]
[2518]
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[]\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
have full rank[]
[2519]
[2520]
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\T1/ptm/m/n/10 dices, if not []\T1/pcr/m/n/10 symmetric [][]sample.int[][][](nr
ow*ncol, nnz)[]\T1/ptm/m/n/10 , then---if []\T1/pcr/m/n/10 rand.x []\T1/ptm/m/n
/10 is not
[2521]
[2522]
Underfull \hbox (badness 5147) in paragraph at lines 11444--11447
[]\T1/ptm/m/n/10 Class [][][]\T1/pcr/m/n/10 SchurFactorization[][][][]\T1/ptm/m
/n/10 , di-rectly. Class [][][]\T1/pcr/m/n/10 MatrixFactorization[][][][]\T1/pt
m/m/n/10 , by class
[2523]
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[]\T1/pcr/m/n/10 signature(from = "Schur", logarithm = "logical")[]\T1/ptm/m/n/
10 : com-putes
[2524]
[2525]
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[] \T1/pcr/m/n/9 all.equal(e1, e3[order(Mod(e3), decreasing = TRUE)], toler
ance = 1e-13)[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solve}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.11633 \aliasA{solve}{solve-methods}{solve}
[2526]
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[]\T1/pcr/m/n/10 solve(a, b, system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "
D", "P", "Pt"), ...)[]
Underfull \hbox (badness 1147) in paragraph at lines 11769--11775
[]\T1/ptm/m/n/10 a vec-tor, [][][]\T1/pcr/m/n/10 sparseVector[][][][]\T1/ptm/m/
n/10 , ma-trix, or [][][]\T1/pcr/m/n/10 Matrix[][][] []\T1/ptm/m/n/10 sat-is-fy
-ing []\T1/pcr/m/n/10 NROW(b) ==
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[]\T1/ptm/m/n/10 Methods for dense []\T1/pcr/m/n/10 a []\T1/ptm/m/n/10 are buil
t on 14 LA-PACK rou-tines: class []\T1/pcr/m/n/10 d..Matrix[]\T1/ptm/m/n/10 , w
here
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[]\T1/ptm/m/n/10 Methods for sparse []\T1/pcr/m/n/10 a []\T1/ptm/m/n/10 are bui
lt on CXS-parse rou-tines []\T1/pcr/m/n/10 cs_lsolve[]\T1/ptm/m/n/10 , []\T1/pc
r/m/n/10 cs_usolve[]\T1/ptm/m/n/10 , and
[2527]
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[]\T1/pcr/m/n/9 image(ia0 <- solve(a, tol = 0)) # checker board, dense [but re
ally, a is singular!][]
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[] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on
[FIXME ??] only[]
[2528]
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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, from a for-mu
la and data frame
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[] \T1/pcr/m/n/10 drop.unused.levels = TRUE, repr = c("C", "R", "T"), giveC
sparse)[]
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[] \T1/pcr/m/n/10 drop.unused.levels = TRUE, repr = c("C", "R", "T"), giveC
sparse,[]
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[]\T1/ptm/m/n/10 a data frame cre-ated with [][][]\T1/pcr/m/n/10 model.frame[][
][][]\T1/ptm/m/n/10 . If an-other sort of ob-ject,
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[]\T1/ptm/m/n/10 character string or []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or
(co-er-ca-ble to)
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[]\T1/pcr/m/n/10 "[][]sparseMatrix[][][]"[]\T1/ptm/m/n/10 , spec-i-fy-ing the c
on-trasts to be ap-plied to the
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[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for
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[]\T1/pcr/m/n/10 sparse.model.matrix []\T1/ptm/m/n/10 has been changed to []\T1
/pcr/m/n/10 FALSE[]\T1/ptm/m/n/10 , 2010-07, for
[2529]
Underfull \hbox (badness 1668) in paragraph at lines 11981--11986
[][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/
m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc
r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse
Underfull \hbox (badness 3291) in paragraph at lines 12008--12013
[]\T1/pcr/m/n/10 model.Matrix(sparse = TRUE) []\T1/ptm/m/n/10 from pack-age [][
]\T1/ptm/b/n/10 Ma-trix-Mod-els[][] \T1/ptm/m/n/10 may be nowa-days be
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\T1/ptm/m/n/10 prefer-able to []\T1/pcr/m/n/10 sparse.model.matrix[]\T1/ptm/m/n
/10 , as []\T1/pcr/m/n/10 model.Matrix []\T1/ptm/m/n/10 re-turns an ob-ject of
class
[2530]
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[] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M)
== c(0, 0),[]
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[] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M)
== c(3, 0),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12063--12063
[] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
== c(0,12),[]
[2531]
Underfull \hbox (badness 2961) in paragraph at lines 12125--12128
[]\T1/pcr/m/n/10 signature(from = "sparseLU", logarithm = "logical")[]\T1/ptm/m
/n/10 : com-
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[]\T1/pcr/m/n/9 A <- as(readMM(system.file("external", "pores_1.mtx", package
= "Matrix")),[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12179--12179
[]\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m
atrix"), ...)[]
[2532]
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[] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(dn[1L
], list(NULL)),[]
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[] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(list(
NULL), dn[2L]),[]
Underfull \hbox (badness 10000) in paragraph at lines 12214--12216
[]\T1/ptm/m/n/10 This in-ter-face is rec-om-mended over di-rect con-struc-tion
via calls such as
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12221--12221
[] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 =
TRUE,[]
[2533]
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\T1/ptm/m/n/10 of the sparse ma-trix re-sult, i.e., spec-i-fy-ing one of the vi
r-tual classes
[2534]
Underfull \hbox (badness 10000) in paragraph at lines 12348--12351
[]\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][][]\T1/pcr/m/n/10 xtabs[][][
](*, sparse=TRUE)[]\T1/ptm/m/n/10 , for sparse ta-bles and
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12361--12361
[]\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x)) ## 8 x 10
"dgCMatrix"[]
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[]\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
"dsCMatrix"[]
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[]\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
"dtCMatrix"[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12371--12371
[]\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims
= c(10,20)))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12374--12374
[]\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[]
[2535]
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[]\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
if necessary:[]
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[]\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x =
1:6, dimnames = dn)[]
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[]\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep
resentations.[]
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[] \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack
age = "SparseM"))) {[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12429--12429
[] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
X@dimension)[]
[2536]
Underfull \hbox (badness 6842) in paragraph at lines 12519--12522
[]\T1/pcr/m/n/10 (x = "sparseMatrix", logarithm=TRUE)[]\T1/ptm/m/n/10 : [][][]\
T1/pcr/m/n/10 determinant[][][]() []\T1/ptm/m/n/10 meth-ods
Underfull \hbox (badness 10000) in paragraph at lines 12554--12558
[][][]\T1/pcr/m/n/10 sparseMatrix[][][][]\T1/ptm/m/n/10 , and its ref-er-ences,
such as [][][]\T1/pcr/m/n/10 xtabs[][][](*, sparse=TRUE)[]\T1/ptm/m/n/10 , or
[2537]
[2538]
Underfull \hbox (badness 2961) in paragraph at lines 12738--12741
[]\T1/pcr/m/n/10 signature(from = "sparseQR", logarithm = "logical")[]\T1/ptm/m
/n/10 : com-
[2539]
Underfull \hbox (badness 3229) in paragraph at lines 12816--12820
[]\T1/ptm/m/n/10 The many aux-il-iary func-tions for QR fac-tor-iza-tions: [][]
[]\T1/pcr/m/n/10 qr.Q[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 qr.R[][][][]
\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 qr.X[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc
r/m/n/10 qr.coef[][][][]\T1/ptm/m/n/10 ,
[2540]
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[]\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m
atrix"), ...)[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 12864--12864
[] \T1/pcr/m/n/9 new("pMatrix", Dim = c(m, m), Dimnames = c(dn[1L
], list(NULL)),[]
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[] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(list(
NULL), dn[2L]),[]
Underfull \vbox (badness 10000) has occurred while \output is active
[2541]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 12886--12886
[] \T1/pcr/m/n/9 ae2(qrc <- qr.coef (qr.A, b), with(e.qr.A, solve(R1 %*% P
2., t(qrQ)) %*% b))[]
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[]\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case
a
[2542]
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[]\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class []\T1/pcr/m/
n/10 "sparseVector" []\T1/ptm/m/n/10 has the five ac-
Underfull \hbox (badness 3679) in paragraph at lines 13044--13050
\T1/ptm/m/n/10 tual daugh-ter classes []\T1/pcr/m/n/10 "dsparseVector"[]\T1/ptm
/m/n/10 , []\T1/pcr/m/n/10 "isparseVector"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "
lsparseVector"[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 13089--13092
[]\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") []\T1/ptm/m/
n/10 co-erces sparse
[2543]
Underfull \hbox (badness 10000) in paragraph at lines 13123--13128
[]\T1/pcr/m/n/10 (x = "nsparseVector")[]\T1/ptm/m/n/10 : re-turn [][][]\T1/pcr/
m/n/10 logical[][][] []\T1/ptm/m/n/10 or
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[][][]\T1/pcr/m/n/10 sparseVector[][][]() []\T1/ptm/m/n/10 for friendly con-str
uc-tion of sparse vec-tors (apart from []\T1/pcr/m/n/10 as(*,
[2544]
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[2545]
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[]\T1/pcr/m/n/10 spMatrix(nrow, ncol, i = integer(0L), j = integer(0L), x = do
uble(0L))
Underfull \hbox (badness 2310) in paragraph at lines 13264--13270
[][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) []\T1/ptm/m/n/10 for the more
usual con-struc-tor of such ma-tri-ces. Then,
[2546]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.[<.Rdash.
}) has been already used, duplicate ignored
<to be read again>
\relax
l.13316 ...\Rdash{}}{subassign-methods}{[<.Rdash.}
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[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2547]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.[}) has b
een already used, duplicate ignored
<to be read again>
\relax
l.13450 \aliasA{[}{subscript-methods}{[}
[2548]
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\T1/ptm/m/n/10 Classes [][][]\T1/pcr/m/n/10 triangularMatrix[][][][]\T1/ptm/m/n
/10 , and, e.g., [][][]\T1/pcr/m/n/10 dsyMatrix[][][] []\T1/ptm/m/n/10 for nu-m
eric \T1/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or
[2549]
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[]\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe
r-ent ma-trix classes, use e.g.,
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[]\T1/pcr/m/n/10 symmpart(x) []\T1/ptm/m/n/10 re-turns a sym-met-ric ma-trix, i
n-her-it-ing from [][][]\T1/pcr/m/n/10 symmetricMatrix[][][] []\T1/ptm/m/n/10 o
r
[2550]
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[]\T1/pcr/m/n/10 skewpart(x) []\T1/ptm/m/n/10 re-turns a skew-symmetric ma-trix
, in-her-it-ing from [][][]\T1/pcr/m/n/10 generalMatrix[][][][]\T1/ptm/m/n/10 ,
[2551]
Underfull \hbox (badness 6641) in paragraph at lines 13752--13755
[]\T1/ptm/m/n/10 Currently, [][][]\T1/pcr/m/n/10 Schur[][][][]\T1/ptm/m/n/10 ,
[][][]\T1/pcr/m/n/10 isSymmetric[][][] []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 as
() []\T1/ptm/m/n/10 (i.e. [][][]\T1/pcr/m/n/10 coerce[][][][]\T1/ptm/m/n/10 ) h
ave meth-ods with
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[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 "TsparseMatrix" []\T1/ptm/m/n/10 class is
the vir-tual class of all sparse ma-tri-ces coded in
Underfull \hbox (badness 2818) in paragraph at lines 13788--13792
\T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c
re-ated from it. See
[2552]
[2553]
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[][][]\T1/pcr/m/n/10 pack[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 unpac
k[][][][]\T1/ptm/m/n/10 ; its vir-tual "com-ple-ment" []\T1/pcr/m/n/10 "[][]pac
kedMatrix[][][]"[]\T1/ptm/m/n/10 ; its proper sub-classes
[2554]
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[]\T1/ptm/m/n/10 GAL lat-tice file `\T1/pcr/m/n/10 usc_q.GAL\T1/ptm/m/n/10 ' (r
e-trieved in 2008 from
[2555]
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[2557]) (./boot-pkg.tex
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Chapter 18.
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[]\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"),
[2566]
Underfull \hbox (badness 1325) in paragraph at lines 570--577
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r
e-quired. Pos-si-ble
Underfull \hbox (badness 1275) in paragraph at lines 585--590
[]\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m
ulti-sample prob-
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[2568]
[2569]
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[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
Underfull \hbox (badness 6493) in paragraph at lines 853--857
[][][]\T1/pcr/m/n/10 boot.array[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 bo
ot.ci[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 censboot[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 empinf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 j
ack.after.boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 tilt.boot[][][][]\T
1/ptm/m/n/10 ,
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 887--887
[]\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt,
data = nuke)[]
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[]\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari-
ance of the
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\T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i
n-ter-vals. If it
Underfull \hbox (badness 2343) in paragraph at lines 1084--1093
\T1/ptm/m/n/10 is not sup-plied and []\T1/pcr/m/n/10 length(index) []\T1/ptm/m/
n/10 is 2 then []\T1/pcr/m/n/10 var.t0 []\T1/ptm/m/n/10 de-faults to
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[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
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[]\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An
al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis-
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[2580]
[2581]
[2582]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1738--1738
[]\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2),
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[2584]
[2585]
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[2586]
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[]\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
+ strata(ulcer),[]
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[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
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[2590]
Underfull \hbox (badness 1565) in paragraph at lines 2338--2343
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori
g-i-nal data set
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Underfull \hbox (badness 4595) in paragraph at lines 2363--2368
\T1/ptm/m/n/10 are passed un-changed ev-ery time []\T1/pcr/m/n/10 boot.out$stat
istic []\T1/ptm/m/n/10 is called.
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[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
Underfull \hbox (badness 2057) in paragraph at lines 2440--2441
[][][]\T1/pcr/m/n/10 boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 empinf[]
[][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 k3.linear[][][][]\T1/ptm/m/n/10 , [
][][]\T1/pcr/m/n/10 linear.approx[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
saddle.distn[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 smooth.spline[][][][]
\T1/ptm/m/n/10 ,
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[2593]
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[]\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of []\T1/pcr/m
/n/10 n/((n-1)*(n-2)) []\T1/ptm/m/n/10 where []\T1/pcr/m/n/10 n []\T1/ptm/m/n/1
0 is the sam-ple
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\T1/ptm/m/n/10 size, if []\T1/pcr/m/n/10 unbiased []\T1/ptm/m/n/10 is []\T1/pcr
/m/n/10 FALSE []\T1/ptm/m/n/10 then a mul-ti-plier of []\T1/pcr/m/n/10 1/n []\T
1/ptm/m/n/10 is used. This is mul-ti-plied by
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[2598]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2895--2895
[]\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t
= 25,
Overfull \hbox (18.78088pt too wide) in paragraph at lines 2897--2897
[]\T1/pcr/m/n/10 EL.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t
= 25,[]
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[2600]
[2601]
Underfull \hbox (badness 3861) in paragraph at lines 3105--3108
[][][]\T1/pcr/m/n/10 boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 boot.arr
ay[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 boot.ci[][][][]\T1/ptm/m/n/10 ,
[][][]\T1/pcr/m/n/10 control[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 jack
.after.boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 linear.approx[][][][]\
T1/ptm/m/n/10 ,
[2602]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3158--3158
[]\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat))
[2603]
[2604]
[2605]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3378--3378
[]\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling
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[2609]
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[2612]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3838--3838
[] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
= NULL)[]
[2613]
[2614]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3977--3977
[]\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
grav.z0[3])[]
[2615]
[2616]
[2617]
[2618]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4259--4259
[]\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz
e data as in
[2619]
[2620]
Underfull \hbox (badness 10000) in paragraph at lines 4362--4364
[]\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o
f
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\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 t0 []\T1/ptm/m/n/10 is sup-plied but nei-the
r []\T1/pcr/m/n/10 t []\T1/ptm/m/n/10 nor []\T1/pcr/m/n/10 L []\T1/ptm/m/n/10 a
re sup-plied then []\T1/pcr/m/n/10 t0 []\T1/ptm/m/n/10 is set to
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Underfull \hbox (badness 3000) in paragraph at lines 4959--4962
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put
of a call to
[2630]
[2631]
[2632]
[2633]
Underfull \hbox (badness 2293) in paragraph at lines 5238--5241
[]\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the
boot-strap
Underfull \hbox (badness 1668) in paragraph at lines 5238--5241
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2634]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5317--5317
[]\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[]
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[2636]
[2637]
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[2639]
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[2641]
[2642]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5866--5866
[]\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][]
[2643]
Underfull \hbox (badness 1127) in paragraph at lines 5988--6006
[]\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less
than []\T1/pcr/m/n/10 min(alpha)/10[]\T1/ptm/m/n/10 , then
[2644]
Underfull \hbox (badness 2837) in paragraph at lines 6021--6024
[]\T1/ptm/m/n/10 The re-turned value is an ob-ject of class []\T1/pcr/m/n/10 "s
addle.distn"[]\T1/ptm/m/n/10 . See the help file for
[2645]
[2646]
[2647]
[2648]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6306--6306
[]\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and
Wright (1991).
[2649]
[2650]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6495--6495
[]\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6497--6497
[]\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t
ilting was used[]
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[2653]
Underfull \hbox (badness 1596) in paragraph at lines 6742--6746
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m
ent ex-pected by
[2654]
[2655]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6902--6902
[] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
c(0.05, 0.95),[]
[2656]
[2657]
[2658]
[2659]
[2660]
[2661]
[2662]
[2663]) (./class-pkg.tex
[2664]
Chapter 19.
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Overfull \hbox (42.18039pt too wide) in paragraph at lines 1006--1006
[] \T1/pcr/m/n/9 alpha = list(seq(0.05, 0, length.out = 1e4), seq(0.02, 0,
length.out = 1e5)),[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1007--1007
[] \T1/pcr/m/n/9 radii = list(seq(8, 1, length.out = 1e4), seq(4, 1, length
.out = 1e5)))[]
[2679]
[2680]) (./cluster-pkg.tex
Chapter 20.
[2681]
[2682]
[2683]
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[] \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met
hod = 0.5)[iC]) ,[]
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[] \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method=
c(.5,.5,0, -.5))[iC]),[]
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[] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
c(.5,.5,0, +.5))[iC]))[]
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[] \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot
= axes,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 523--523
[] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
...)[]
[2688]
[2689]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 638--638
[] \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c
orrect.d = TRUE)[]
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[2691]
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[][][]\T1/pcr/m/n/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-en
ces; [][][]\T1/pcr/m/n/10 clara.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 pam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 partition.object[][][][]\
T1/ptm/m/n/10 ,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 833--833
[] \T1/pcr/m/n/9 cl[,i] <- clara(xclara, nCl, medoids.x = FALSE, rngR = TRUE
)$clustering[]
[2693]
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[]\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[]
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[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2694]
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[] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code
=3), ...)[]
[2695]
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[]\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is
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[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
2012,
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Underfull \hbox (badness 2503) in paragraph at lines 1092--1096
[]\T1/ptm/m/n/10 Per Broberg (2006). SAGx: Sta-tis-ti-cal Anal-y-sis of the Gen
eChip. R pack-age ver-
[2697]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1118--1118
[] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[]
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[]\T1/pcr/m/n/9 ## You can manually set it before running this : doExtras <
- TRUE # or FALSE[]
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[] \T1/pcr/m/n/9 gskmn <- clusGap(x, FUNcluster = kmeans, nstart = 20, K.max
= 8, B = 60)[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1146--1146
[] \T1/pcr/m/n/9 plot(gskmn, main = "clusGap(., FUNcluster = kmeans, n.start=
20, B= 60)")[]
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[]\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap(<iid_rnorm_p=3>) ==> k = 1 clust
er is optimal")[]
Underfull \hbox (badness 4144) in paragraph at lines 1205--1209
[]\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 does not have a []\T1
/pcr/m/n/10 diss []\T1/ptm/m/n/10 nor a []\T1/pcr/m/n/10 data []\T1/ptm/m/n/10
com-po-nent, e.g., for
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Overfull \hbox (60.78088pt too wide) in paragraph at lines 1281--1281
[] \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1,
cex.txt = cex,[]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 1287--1287
[] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[]
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[][][]\T1/pcr/m/n/10 princomp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cmds
cale[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pam[][][][]\T1/ptm/m/n/10 , [
][][]\T1/pcr/m/n/10 clara[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 daisy[][
][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 par[][][][]\T1/ptm/m/n/10 , [][][]\T
1/pcr/m/n/10 identify[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cov.mve[][][
][]\T1/ptm/m/n/10 ,
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1512--1512
[]\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a
nd label ellipses[]
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[] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[]
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Underfull \hbox (badness 5741) in paragraph at lines 1562--1565
[]\T1/pcr/m/n/10 coefHier() []\T1/ptm/m/n/10 di-rectly in-ter-faces to the un-d
er-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only
[2704]
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[] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa
rnType,[]
[2705]
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[]\T1/ptm/b/n/10 A\T1/ptm/m/n/10 symmetric bi-nary vari-able, aka []\T1/pcr/m/n
/10 "A" []\T1/ptm/m/n/10 in re-sult []\T1/pcr/m/n/10 Types[]\T1/ptm/m/n/10 , se
e
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[]\T1/ptm/b/n/10 I\T1/ptm/m/n/10 nterval scaled -- the \T1/ptm/b/n/10 de-fault
\T1/ptm/m/n/10 for all nu-meric
Underfull \hbox (badness 3746) in paragraph at lines 1694--1698
\T1/ptm/m/n/10 (incl []\T1/pcr/m/n/10 integer[]\T1/ptm/m/n/10 ) columns of []\T
1/pcr/m/n/10 x[]\T1/ptm/m/n/10 , aka []\T1/pcr/m/n/10 "I" []\T1/ptm/m/n/10 in r
e-sult []\T1/pcr/m/n/10 Types[]\T1/ptm/m/n/10 , see
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\T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh
ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1
0 w[]^^N[]$\T1/ptm/m/n/10 , where $\OML/cmm/m/it/10 w[]$[]\T1/pcr/m/n/10 =
[2707]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1856--1856
[]\T1/pcr/m/n/9 ## Example 2 in reference, extended --- different ways of "m
ixed" / "gower":[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1860--1860
[]\T1/pcr/m/n/9 summary(d0 <- daisy(flower)) # -> the first 3 {0,1} treate
d as *N*ominal[]
Overfull \hbox (90.78033pt too wide) in paragraph at lines 1861--1861
[]\T1/pcr/m/n/9 summary(dS123 <- daisy(flower, type = list(symm = 1:3))) # fi
rst 3 treated as *S*ymmetric[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1862--1862
[]\T1/pcr/m/n/9 stopifnot(dS123 == d0) # i.e., *S*ymmetric <==> *N*ominal {fo
r 2-level factor}[]
Overfull \hbox (106.98032pt too wide) in paragraph at lines 1866--1866
[]\T1/pcr/m/n/9 summary(dA123 <- daisy(flowerN)) # .. all 3 logicals treated *
A*symmetric binary (w/ warning)[]
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[]\T1/pcr/m/n/9 summary(dA13 <- daisy(flower, type = list(asymm = c(1, 3), ord
ratio = 7)))[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1875--1875
[]\T1/pcr/m/n/9 Nflow[,1:3] <- lapply(flower[,1:3], function(f) as.integer(as.
character(f)))[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1876--1876
[]\T1/pcr/m/n/9 summary(dN <- daisy(Nflow)) # w/ warning: treated binary .. 1:
3 as interval[]
Overfull \hbox (117.7803pt too wide) in paragraph at lines 1877--1877
[]\T1/pcr/m/n/9 ## Still, using Euclidean/Manhattan distance for {0-1} *is* id
entical to treating them as "N" :[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 1893--1893
[]\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE,
[2708]
[2709]
[2710]
[2711]
[2712]
Underfull \hbox (badness 10000) in paragraph at lines 2212--2215
Underfull \hbox (badness 3179) in paragraph at lines 2223--2229
[][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] []\T1/ptm/m/n/10 which is also the
[][][]\T1/pcr/m/n/10 predict[][][] []\T1/ptm/m/n/10 method for []\T1/pcr/m/n/1
0 ellipsoid []\T1/ptm/m/n/10 ob-jects.
[2713]
[2714]
Underfull \hbox (badness 10000) in paragraph at lines 2380--2383
[][][]\T1/pcr/m/n/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-en
ces; [][][]\T1/pcr/m/n/10 fanny.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 partition.object[][][][]\T1/ptm/m/n/10 ,
[2715]
Underfull \hbox (badness 1292) in paragraph at lines 2448--2451
[]\T1/ptm/m/n/10 named vec-tor with []\T1/pcr/m/n/10 iterations[]\T1/ptm/m/n/10
, the num-ber of it-er-a-tions needed and
[2716]
Underfull \hbox (badness 6675) in paragraph at lines 2457--2459
[]\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl
us-ter-ing, see
Underfull \hbox (badness 10000) in paragraph at lines 2480--2483
[][][]\T1/pcr/m/n/10 fanny[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.f
anny[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 dissimilarity.object[][][][]\
T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 partition.object[][][][]\T1/ptm/m/n/10 ,
[2717]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2555--2555
[] \T1/pcr/m/n/9 "4" = "red", "5" = "blue")[levels(f
lowerN$color)][]
Overfull \hbox (90.78033pt too wide) in paragraph at lines 2556--2556
[]\T1/pcr/m/n/9 levels(flowerN$soil) <- c("1" = "dry", "2" = "normal", "3" =
"wet")[levels(flowerN$soil)][]
[2718]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 2619--2619
[]\T1/pcr/m/n/10 medoids(x, clustering, diss = inherits(x, "dist"), USE.NAMES
= FALSE, ...)
[2719]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 2666--2666
[] \T1/pcr/m/n/9 stopifnot(length(cl.k) == nrow(votes.repub), 1 <= cl.k, cl.k
<= k, table(cl.k) >= 2)[]
[2720]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2771--2771
[]\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to
\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/
9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[]
[2721]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 2850--2850
[] \T1/pcr/m/n/10 variant = c("original", "o_1", "o_2", "f_3", "f_4", "f_5"
, "faster"),[]
[2722]
[2723]
[2724]
[2725]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 3078--3078
[]\T1/pcr/m/n/9 ## use obs. 1 & 16 as starting medoids -- same result (for see
d above, *and* typically) :[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3080--3080
[]\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 3083--3083
[]\T1/pcr/m/n/9 keep_nms <- setdiff(names(pamx), c("call", "objective"))# .$ob
jective["build"] differ[]
[2726]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3187--3187
[]\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[]
[2727]
[2728]
[2729]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3381--3381
[] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3382--3382
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2730]
Underfull \hbox (badness 10000) in paragraph at lines 3449--3452
[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via []\T1/pcr/m
/n/10 pltree() []\T1/ptm/m/n/10 is pro-vided by []\T1/pcr/m/n/10 dg <-
[2731]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3499--3499
[] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
digits = 2)),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 3500--3500
[] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
= TRUE, ...)[]
[2732]
[2733]
[2734]
Underfull \hbox (badness 10000) in paragraph at lines 3685--3688
[]\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 does not have a []\T1
/pcr/m/n/10 diss []\T1/ptm/m/n/10 com-po-nent as for [][][]\T1/pcr/m/n/10 pam[]
[][](*,
Underfull \hbox (badness 1448) in paragraph at lines 3685--3688
\T1/pcr/m/n/10 keep.diss=FALSE)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 dist []\T1/p
tm/m/n/10 must be the dis-sim-i-lar-ity if a clus-plot is
[2735]
Underfull \hbox (badness 10000) in paragraph at lines 3748--3753
[][][]\T1/pcr/m/n/10 partition.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n
/10 clusplot.partition[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 clusplot.de
fault[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pam[][][][]\T1/ptm/m/n/10 ,
[2736]
Underfull \hbox (badness 1748) in paragraph at lines 3810--3815
\T1/ptm/m/n/10 dis-patches to [][][]\T1/pcr/m/n/10 plot.hclust[][][](..)[]\T1/p
tm/m/n/10 . If more flex-i-ble plots are needed, con-sider []\T1/pcr/m/n/10 xx
<-
Underfull \hbox (badness 6268) in paragraph at lines 3822--3825
[][][]\T1/pcr/m/n/10 agnes[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 agnes.o
bject[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 diana[][][][]\T1/ptm/m/n/10
, [][][]\T1/pcr/m/n/10 diana.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/1
0 hclust[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 par[][][][]\T1/ptm/m/n/10
, [][][]\T1/pcr/m/n/10 plot.agnes[][][][]\T1/ptm/m/n/10 ,
[2737]
Underfull \hbox (badness 10000) in paragraph at lines 3883--3885
[]\T1/ptm/m/n/10 Available as `\T1/pcr/m/n/10 pluton.dat\T1/ptm/m/n/10 ' from t
he archive of the Uni-ver-sity of Antwer-pen,
[2738]
[2739]
Underfull \hbox (badness 10000) in paragraph at lines 4002--4005
[][][]\T1/pcr/m/n/10 summary.agnes[][][] []\T1/ptm/m/n/10 pro-duc-ing more out-
put; [][][]\T1/pcr/m/n/10 agnes[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 ag
nes.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/
n/10 ,
[2740]
Underfull \hbox (badness 10000) in paragraph at lines 4033--4036
[][][]\T1/pcr/m/n/10 summary.clara[][][] []\T1/ptm/m/n/10 pro-duc-ing more out-
put; [][][]\T1/pcr/m/n/10 clara[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cl
ara.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/
n/10 ,
[2741]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 4086--4086
[] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
TRUE, ...)[]
Underfull \hbox (badness 2035) in paragraph at lines 4097--4099
[]\T1/ptm/m/n/10 a []\T1/pcr/m/n/10 dissimilarity []\T1/ptm/m/n/10 ob-ject or a
[]\T1/pcr/m/n/10 summary.dissimilarity []\T1/ptm/m/n/10 one for
[2742]
[2743]
[2744]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4290--4290
[] \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w
idth "* s[i]),[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 4292--4292
[] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
= TRUE, ...)[]
[2745]
[2746]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4434--4434
[]\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus
ter-wise coloring[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4443--4443
[] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
do.n.k=FALSE)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4445--4445
[] \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma
in")); frame()[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 4448--4448
[]\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol
denrod4", "gray20")[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4450--4450
[] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
do.n.k=FALSE,[]
[2747]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4457--4457
[]\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro
wnames == indices[]
[2748]
[2749]
[2750]
[2751]
[2752]
[2753]
Underfull \hbox (badness 10000) in paragraph at lines 4828--4834
[]\T1/ptm/m/n/10 Our ver-sion of the []\T1/pcr/m/n/10 xclara []\T1/ptm/m/n/10 i
s slightly more rounded than the one from
Underfull \hbox (badness 10000) in paragraph at lines 4844--4846
[]\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file
`\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side
Overfull \hbox (52.98038pt too wide) in paragraph at lines 4857--4857
[]\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10
01:2000}, {2001:3000}
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4859--4859
[]\T1/pcr/m/n/9 p.ID <- c(78, 1411, 2535) ## PAM\TS1/pcr/m/n/9 '\T1/pcr/m/n/9
s medoid indices == pam(xclara, 3)$id.med[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4869--4869
[] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o
bservations:[]
[2754]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4873--4873
[] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? -
- Robust range:[]
[2755]) (./codetools-pkg.tex
[2756]
Chapter 21.
Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16
[] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
= FALSE,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17
[] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun =
!all,[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18
[] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[]
[2757]
Underfull \hbox (badness 10000) in paragraph at lines 65--70
[]\T1/pcr/m/n/10 checkUsageEnv []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 checkUsage
Package []\T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply
[2758]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 118--118
[]\T1/pcr/m/n/10 makeConstantFolder(..., leaf, handler, call, exit, isLocal, f
oldable,[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 121--121
[]\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[]
[2759]
[2760]
[2761]) (./foreign-pkg.tex
[2762]
Chapter 22.
Underfull \hbox (badness 10000) in paragraph at lines 33--37
[]\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o
ut of a Data
Underfull \hbox (badness 10000) in paragraph at lines 33--37
\T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able as [][]$\T1/p
cr/m/n/10 https : / / support .
Underfull \hbox (badness 10000) in paragraph at lines 33--37
\T1/pcr/m/n/10 sas . com / content / dam / SAS / support / en / technical-[]pap
ers /
Overfull \hbox (74.28088pt too wide) in paragraph at lines 33--37
\T1/pcr/m/n/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[]s
et-[]in-[]sas-[]transport-[]xport-[]format .
[2763]
Underfull \hbox (badness 1231) in paragraph at lines 67--70
[]\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr
om, or a
[2764]
[2765]
Underfull \hbox (badness 3601) in paragraph at lines 234--242
[]\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude []\T1/pcr/m
/n/10 "datalabel"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "time.stamp"[]\T1/ptm/m/n/
10 ,
[2766]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 292--292
[]\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
FALSE,
[2767]
[2768]
[2769]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 458--458
[] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame,[]
[2770]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 459--459
[] \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen
d", "no"),[]
Underfull \hbox (badness 2846) in paragraph at lines 502--511
[]\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif-
fer-ent lev-
Underfull \hbox (badness 3746) in paragraph at lines 502--511
\T1/ptm/m/n/10 els. For []\T1/pcr/m/n/10 "append" []\T1/ptm/m/n/10 (the de-faul
t), the first orig-i-nal value la-bel is
Underfull \hbox (badness 2269) in paragraph at lines 502--511
\T1/ptm/m/n/10 kept while fur-ther du-pli-cated la-bels are re-named to []\T1/p
cr/m/n/10 paste0(label,
Underfull \hbox (badness 10000) in paragraph at lines 512--515
[]\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with
du-
Underfull \hbox (badness 10000) in paragraph at lines 512--515
\T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault []\T1/pcr/m/n/10 "_dup
licated_"[]\T1/ptm/m/n/10 ) if
[2771]
Underfull \hbox (badness 10000) in paragraph at lines 546--554
[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 https : / / learn . microsoft . com /
en-[]us / windows / win32 / intl /
Underfull \hbox (badness 7613) in paragraph at lines 564--570
[]\T1/ptm/m/n/10 There may be at-tributes []\T1/pcr/m/n/10 "label.table" []\T1/
ptm/m/n/10 and []\T1/pcr/m/n/10 "variable.labels"[]\T1/ptm/m/n/10 . At-tribute
[2772]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 619--619
[]\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg
ument settings.[]
Overfull \hbox (112.38031pt too wide) in paragraph at lines 620--620
[]\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to
R factor labels) are uncomplete,[]
[2773]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 653--653
[]\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ
ate variables[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 657--657
[]\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt
h=w), "\n"))[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 664--664
[]\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste,
collapse="")[]
[2774]
[2775]
Underfull \hbox (badness 10000) in paragraph at lines 808--809
Overfull \hbox (4.38043pt too wide) in paragraph at lines 818--818
[]\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[]
[2776]
Underfull \hbox (badness 10000) in paragraph at lines 865--869
[]\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o
ut of a Data
Underfull \hbox (badness 10000) in paragraph at lines 865--869
\T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able at [][]$\T1/p
cr/m/n/10 https : / / support .
Underfull \hbox (badness 10000) in paragraph at lines 865--869
\T1/pcr/m/n/10 sas . com / content / dam / SAS / support / en / technical-[]pap
ers /
Overfull \hbox (74.28088pt too wide) in paragraph at lines 865--869
\T1/pcr/m/n/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[]s
et-[]in-[]sas-[]transport-[]xport-[]format .
[2777]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 896--896
[] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv)
[2778]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 960--960
[]\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x)))
[2779]
[2780]
Underfull \hbox (badness 10000) in paragraph at lines 1072--1073
[][][]$\T1/pcr/m/n/10 https : / / www . clicketyclick . dk / databases / xbase
/ format / data _ types .
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1108--1108
[] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric",
"codes"))[]
[2781]
[2782]
Underfull \hbox (badness 10000) in paragraph at lines 1265--1271
[]\T1/ptm/m/n/10 The work for this func-tion is done by []\T1/pcr/m/n/10 foreig
n:::writeForeignStata[]\T1/ptm/m/n/10 ,
[2783]
Underfull \hbox (badness 2088) in paragraph at lines 1291--1294
[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 package="SPSS"[]\T1/ptm/m/n/10 , as a sid
e ef-fect, the dec-i-mal in-di-ca-tor is al-ways set by []\T1/pcr/m/n/10 SET
[2784]) (./lattice-pkg.tex
Chapter 23.
[2785]
Underfull \hbox (badness 2073) in paragraph at lines 114--118
\T1/ptm/m/n/10 pro-vide a holis-tic in-tro-duc-tion to the Trel-lis paradigm: [
][]$\T1/pcr/m/n/10 http : / / web . archive . org /
Underfull \hbox (badness 10000) in paragraph at lines 114--118
\T1/pcr/m/n/10 web / 20081020164041 / http : / / cm . bell-[]labs . com / cm /
ms / departments / sia /
[2786]
[2787]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 288--288
[] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 292--292
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.xyplot"),[]
[2788]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 303--303
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul
t.dotplot"),[]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 313--313
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.barchart"),[]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 324--324
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.stripplot"),[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 348--348
[] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[]
Underfull \vbox (badness 10000) has occurred while \output is active
[2789]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 352--352
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.bwplot"),[]
[2790]
[2791]
[2792]
Underfull \hbox (badness 1221) in paragraph at lines 655--658
[]\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as
ar-gu-ments to
[2793]
[2794]
[2795]
[2796]
Underfull \hbox (badness 2005) in paragraph at lines 988--1000
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of
fac-tors will be
Underfull \hbox (badness 1199) in paragraph at lines 988--1000
\T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a
use-ful lay-out.
[2797]
[2798]
Underfull \hbox (badness 1661) in paragraph at lines 1101--1107
[]\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 y []\T1/ptm/m/n/10 sho
uld be num-bers be-tween 0 and 1, giv-ing co-or-di-nates
[2799]
Underfull \hbox (badness 1097) in paragraph at lines 1227--1229
[]\T1/ptm/m/n/10 Logical flag, whether leg-end should have a
Underfull \hbox (badness 1917) in paragraph at lines 1241--1242
[]\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to
[2800]
[2801]
[2802]
Underfull \hbox (badness 1540) in paragraph at lines 1476--1482
[]\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][][]\T1/pcr/m/
n/10 plot.trellis[][][][]\T1/ptm/m/n/10 ,
[2803]
Underfull \hbox (badness 10000) in paragraph at lines 1563--1580
[][][]\T1/pcr/m/n/10 panel.dotplot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
panel.stripplot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.superpose[]
[][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.loess[][][][]\T1/ptm/m/n/10 ,
[2804]
Underfull \vbox (badness 10000) has occurred while \output is active
[2805]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 1651--1651
[] \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar
dSprays$rowpos))),[]
[2806]
Underfull \hbox (badness 2012) in paragraph at lines 1705--1707
[]\T1/ptm/m/n/10 additional ar-gu-ments passed to [][][]\T1/pcr/m/n/10 xyplot[]
[][][]\T1/ptm/m/n/10 , which may pass them on to
Underfull \hbox (badness 6808) in paragraph at lines 1735--1739
[]\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p
assed to
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[]\T1/ptm/m/n/10 style set-tings be-yond the stan-dard []\T1/pcr/m/n/10 col[]\T
1/ptm/m/n/10 , []\T1/pcr/m/n/10 lty[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lwd[]\T1
/ptm/m/n/10 , etc; see
[2807]
Underfull \hbox (badness 10000) in paragraph at lines 1804--1806
[]\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix
An-drews
[2808]
[2809]
[2810]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2045--2045
[] \T1/pcr/m/n/10 auto.key = lattice.getOption("default.args")$auto
.key,[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2058--2058
[] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[]
Underfull \vbox (badness 10000) has occurred while \output is active
[2811]
Underfull \hbox (badness 10000) in paragraph at lines 2137--2140
[]\T1/ptm/m/n/10 When []\T1/pcr/m/n/10 breaks []\T1/ptm/m/n/10 is un-spec-i-fie
d, the value of
Underfull \hbox (badness 1320) in paragraph at lines 2137--2140
[]\T1/pcr/m/n/10 lattice.getOption("histogram.breaks") []\T1/ptm/m/n/10 is firs
t checked. If
[2812]
[2813]
[2814]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2342--2342
[] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 2346--2346
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.qqmath"),[]
[2815]
[2816]
[2817]
[2818]
[2819]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 2702--2702
[] \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev
elplot.raster")[]
[2820]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2734--2734
[] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl
ot"),[]
Underfull \vbox (badness 10000) has occurred while \output is active
[2821]
Underfull \hbox (badness 2913) in paragraph at lines 2813--2818
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when []\T1/
pcr/m/n/10 x []\T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 2813--2818
[]\T1/pcr/m/n/10 row.values []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 column.values
[]\T1/ptm/m/n/10 must have the same lengths as
[2822]
[2823]
Underfull \hbox (badness 6758) in paragraph at lines 2941--2945
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be
Underfull \hbox (badness 7576) in paragraph at lines 2941--2945
\T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][][]\T1/pcr/m/n/10 grid.ra
ster[][][][]\T1/ptm/m/n/10 . See also
Underfull \hbox (badness 10000) in paragraph at lines 2947--2949
[]\T1/ptm/m/n/10 Logical flag, passed to [][][]\T1/pcr/m/n/10 rasterGrob[][][]
[]\T1/ptm/m/n/10 when
Underfull \hbox (badness 7256) in paragraph at lines 2984--2984
[]\T1/pcr/m/n/10 allow.multiple[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 outer[]\T1/p
tm/m/n/10 , []\T1/pcr/m/n/10 prepanel[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 scales
[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 strip[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 gr
oups[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1609) in paragraph at lines 2997--3003
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti
ons should be used,
Underfull \hbox (badness 2772) in paragraph at lines 2997--3003
\T1/ptm/m/n/10 both for the false color im-age and the color key (if present).
Ef-
Underfull \hbox (badness 1400) in paragraph at lines 2997--3003
\T1/ptm/m/n/10 fec-tively, set-ting this to []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n
/10 changes the de-fault panel func-tion from
Underfull \hbox (badness 2486) in paragraph at lines 3021--3025
[]\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for
the de-fault panel func-tion
[2824]
[2825]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3126--3126
[] \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite
= TRUE),[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3127--3127
[] \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite
= TRUE),[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3128--3128
[] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
= TRUE),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3139--3139
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[]
[2826]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 3154--3154
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[]
[2827]
Underfull \hbox (badness 2913) in paragraph at lines 3219--3224
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when []\T1/
pcr/m/n/10 x []\T1/ptm/m/n/10 is a ma-trix.
Underfull \hbox (badness 3058) in paragraph at lines 3219--3224
[]\T1/pcr/m/n/10 row.values []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 column.values
[]\T1/ptm/m/n/10 must have the same lengths as
Underfull \hbox (badness 2418) in paragraph at lines 3225--3225
[]\T1/pcr/m/n/10 allow.multiple[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 outer[]\T1/p
tm/m/n/10 , []\T1/pcr/m/n/10 auto.key[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 prepan
el[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 strip[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10
groups[]\T1/ptm/m/n/10 ,
[2828]
[2829]
[2830]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.parallel}
) has been already used, duplicate ignored
<to be read again>
\relax
l.3506 \aliasA{parallel}{B\_08\_splom}{parallel}
[2831]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3548--3548
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3571--3571
[] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[]
Underfull \vbox (badness 10000) has occurred while \output is active
[2832]
[2833]
[2834]
[2835]
[2836]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3906--3906
[]\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x)))
[2837]
[2838]
Underfull \hbox (badness 2277) in paragraph at lines 3992--3996
[]\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault
set-tings by
Underfull \hbox (badness 2435) in paragraph at lines 3992--3996
\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2839]
Overfull \hbox (120.78088pt too wide) in paragraph at lines 4089--4089
[] \T1/pcr/m/n/10 symbol = palette.colors(palette = "Okabe-Ito")
[c(6, 2, 4, 7, 3, 5, 8)],[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 4091--4091
[] \T1/pcr/m/n/10 region = hcl.colors(14, palette = "YlGnBu", re
v = TRUE),[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 4098--4098
[] \T1/pcr/m/n/10 reference = "gray90", bg = "transparent", fg = "
black",[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 4099--4099
[] \T1/pcr/m/n/10 strip.bg = rep("gray95", 7), strip.fg = rep("gra
y70", 7),[]
[2840]
[2841]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4242--4242
[]\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict
= FALSE)
Underfull \hbox (badness 1173) in paragraph at lines 4251--4255
[]\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un-
spec-i-fied in
[2842]
Underfull \hbox (badness 3219) in paragraph at lines 4278--4280
[]\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i
s-sued when
Underfull \hbox (badness 1728) in paragraph at lines 4295--4299
[]\T1/pcr/m/n/10 theme[]\T1/ptm/m/n/10 ). These are used to mod-ify the cur-ren
t set-tings (ob-tained by
[2843]
Underfull \hbox (badness 5161) in paragraph at lines 4360--4364
[]\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in []\T1/pcr/m/n/10 trell
is.settings []\T1/ptm/m/n/10 has not been fi-nal-ized,
Underfull \hbox (badness 4913) in paragraph at lines 4360--4364
\T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca
n be ob-tained by
[2844]
Underfull \hbox (badness 1067) in paragraph at lines 4478--4488
[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. []\T1/pcr/m/n/10 col []\T1/ptm/m/n/
10 is used for com-po-nents []\T1/pcr/m/n/10 "plot.symbol"[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4478--4488
[]\T1/pcr/m/n/10 "plot.line"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "plot.polygon"[
]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "superpose.symbol"[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1735) in paragraph at lines 4478--4488
[]\T1/pcr/m/n/10 "superpose.line"[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 "super
pose.polygon"[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 col.points
Underfull \hbox (badness 10000) in paragraph at lines 4478--4488
[]\T1/ptm/m/n/10 over-rides []\T1/pcr/m/n/10 col[]\T1/ptm/m/n/10 , but is used
only for []\T1/pcr/m/n/10 "plot.symbol" []\T1/ptm/m/n/10 and
Underfull \hbox (badness 5231) in paragraph at lines 4478--4488
[]\T1/pcr/m/n/10 "superpose.symbol"[]\T1/ptm/m/n/10 . Sim-i-larly, []\T1/pcr/m/
n/10 col.line []\T1/ptm/m/n/10 over-rides []\T1/pcr/m/n/10 col []\T1/ptm/m/n/10
for
[2845]
Underfull \hbox (badness 1701) in paragraph at lines 4503--4506
[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents []\T1/pcr/m/n/10 pl
ot.symbol[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 plot.polygon[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 4506--4508
[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents []\T1/pcr/m/n/10
plot.polygon []\T1/ptm/m/n/10 and
[2846]
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[]\T1/pcr/m/n/10 auto.key[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 aspect[]\T1/ptm/m/
n/10 , []\T1/pcr/m/n/10 between[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 grid[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 skip[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 strip[]\T1/
ptm/m/n/10 , []\T1/pcr/m/n/10 xscale.components[]\T1/ptm/m/n/10 ,
[2847]
[2848]
[2849]
[2850]
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[]\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
= "Height")[]
[2851]
[2852]
Underfull \hbox (badness 1558) in paragraph at lines 5048--5048
[]\T1/pcr/m/n/10 main[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 page[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 par.strip.text[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 prepanel[]\
T1/ptm/m/n/10 , []\T1/pcr/m/n/10 scales[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 skip
[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 strip[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 1270) in paragraph at lines 5048--5048
[]\T1/pcr/m/n/10 xscale.components[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 yscale.co
mponents[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 axis[]\T1/ptm/m/n/10 , []\T1/pcr/m/
n/10 par.settings[]\T1/ptm/m/n/10 ,
Underfull \vbox (badness 1092) has occurred while \output is active
[2853]
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[]\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 trellis[]\T1/ptm/m/n/10 ,
by de-fault plot-ted by []\T1/pcr/m/n/10 print.trellis[]\T1/ptm/m/n/10 .
[2854]
[2855]
Underfull \hbox (badness 1442) in paragraph at lines 5232--5235
[]\T1/pcr/m/n/10 plot.shingle []\T1/ptm/m/n/10 dis-plays the ranges of shin-gle
s via rect-an-gles. []\T1/pcr/m/n/10 print.shingle []\T1/ptm/m/n/10 and
[2856]
[2857]
[2858]
[2859]
[2860]
Underfull \hbox (badness 3646) in paragraph at lines 5571--5574
[][][]\T1/pcr/m/n/10 Lattice[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 draw.
key[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 trellis.par.get[][][][]\T1/ptm
/m/n/10 , and [][][]\T1/pcr/m/n/10 xyplot[][][][]\T1/ptm/m/n/10 , specif-i-call
y the en-try for
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[] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5602--5602
[] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[]
[2861]
Underfull \hbox (badness 10000) in paragraph at lines 5684--5687
[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.
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[]\T1/pcr/m/n/10 horizontal=FALSE []\T1/ptm/m/n/10 is use-ful for strips on the
left of pan-els us-ing
[2862]
Underfull \hbox (badness 1635) in paragraph at lines 5710--5715
[]\T1/pcr/m/n/10 strip.default []\T1/ptm/m/n/10 is called for its side-effect,
which is to draw a strip ap-pro-pri-ate for
[2863]
[2864]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5861--5861
[]\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5875--5875
[]\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[]
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[]\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5879--5879
[]\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5882--5882
[] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[]
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[] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5890--5890
[] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5891--5891
[] \T1/pcr/m/n/10 prefix = pre
fix),[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 5892--5892
[] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[]
[2865]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5893--5893
[] \T1/pcr/m/n/10 prefix = pre
fix),[]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5894--5894
[] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[]
Underfull \hbox (badness 10000) in paragraph at lines 5910--5912
[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of
Underfull \hbox (badness 2376) in paragraph at lines 5921--5923
[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
De-faults to
[2866]
Underfull \hbox (badness 2538) in paragraph at lines 6045--6049
\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 trellis.focus[]\T1/ptm/m/n/10 , the de-faul
t is []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 in in-ter-ac-tive mode, and
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[]\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 panel.identify.qqmath[]\T1/ptm/m/n/10 , e
x-tra pa-ram-e-ters are passed on to
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[]\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 trellis.switchFocus[]\T1/ptm/m/n/10 , the
se are used (in com-bi-na-tion with
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[][][]\T1/pcr/m/n/10 identify[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Latt
ice[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.trellis[][][][]\T1/ptm/m
/n/10 , [][][]\T1/pcr/m/n/10 trellis.currentLayout[][][][]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
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[2873]
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[]\T1/ptm/m/n/10 Creates Box and Whisker plot of []\T1/pcr/m/n/10 x []\T1/ptm/m
/n/10 for ev-ery level of []\T1/pcr/m/n/10 y []\T1/ptm/m/n/10 (or the other way
round
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\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 horizontal=FALSE[]\T1/ptm/m/n/10 ). By de-fa
ult, the ac-tual box-plot statis-tics are cal-cu-lated us-ing
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[] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[]
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[]\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The
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[]\T1/ptm/m/n/10 numeric, be-tween 0 and 1, giv-ing a min-i-mum sat-u-ra-tion i
n
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[] \T1/pcr/m/n/9 shade.colors.palette = makeShadePalette(hcl.colors(1
0, "Inferno"),[]
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[] \T1/pcr/m/n/9 shade.colors.palette = makeShadePalette(hcl.colors(1
0, "Dark Mint"),[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6864--6864
[] \T1/pcr/m/n/9 shade.colors.palette = makeShadePalette(hcl.colors(1
0, "Harmonic"),[]
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[]\T1/pcr/m/n/10 panel.levelplot.raster []\T1/ptm/m/n/10 is an al-ter-na-tive p
anel func-tion that uses the raster draw-
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\T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more
ef-fi-cient. When us-ing
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[2885]
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[] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels =
NULL,[]
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[]\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments
to
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[]\T1/pcr/m/n/10 diag.panel.splom []\T1/ptm/m/n/10 to know what ar-gu-ments thi
s func-tion is passed
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\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 diag.panel []\T1/ptm/m/n/10 from []\T1/pcr/
m/n/10 panel.pairs[]\T1/ptm/m/n/10 . Cur-rently ig-nored by
Overfull \hbox (101.58032pt too wide) in paragraph at lines 7460--7460
[] \T1/pcr/m/n/9 function(i,j) hcl.colors(11)[i+j-1]) ## rainbow(
11, start=.12, end=.5)[i+j-1])[]
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[2889]
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[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
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[] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[]
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[]\T1/pcr/m/n/10 "lm" []\T1/ptm/m/n/10 adds a lin-ear re-gres-sion line (same a
s [][][]\T1/pcr/m/n/10 panel.lmline[][][][]\T1/ptm/m/n/10 , ex-cept
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\T1/ptm/m/n/10 for de-fault graph-i-cal pa-ram-e-ters). []\T1/pcr/m/n/10 "loess
" []\T1/ptm/m/n/10 adds a loess fit (same as
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[]\T1/ptm/m/n/10 Most gen-er-ally, []\T1/pcr/m/n/10 grid []\T1/ptm/m/n/10 can b
e a list of ar-gu-ments to be sup-plied to
[2894]
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[] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
= c(1/6, 4/6)),[]
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[] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[]
[2895]
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[] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[]
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[] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ide
ntifier, name.type)[]
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[]\T1/pcr/m/n/10 col[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 alpha[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 lty[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lwd[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 fill[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pch[]\T1/ptm/m/n/10 ,
[]\T1/pcr/m/n/10 cex[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lineheight[]\T1/ptm/m/n
/10 , []\T1/pcr/m/n/10 font[]\T1/ptm/m/n/10 ,
[2897]
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[]\T1/pcr/m/n/9 xyplot(y ~ x, d, panel = panel.rect, col = 4, alpha = 0.5, wid
th = 0.1, height = 0.1)[]
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[]\T1/pcr/m/n/9 xyplot(y ~ x, d, panel = panel.polygon, col = 4, alpha = 0.5,
rule = "evenodd")[]
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[]\T1/pcr/m/n/9 ## Example adapted from https://journal.r-project.org/articles
/RJ-2012-017/[]
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[]\T1/pcr/m/n/9 xyplot(y ~ x, data = d, panel = panel.polygon, rule = "none",
col = "grey")[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8194--8194
[]\T1/pcr/m/n/9 xyplot(y ~ x, data = d, panel = panel.polypath, rule = "windin
g", col = "grey")[]
[2898]
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[]\T1/pcr/m/n/9 xyplot(y ~ x, data = d, panel = panel.polypath, rule = "evenod
d", col = "grey")[]
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[]\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[]
[2899]
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[]\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c
al pa-ram-e-ters for
[2900]
[2901]
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[] \T1/pcr/m/n/9 panel.superpose(x, y, ..., panel.groups = panel.ave
rage, grid = FALSE,[]
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[] \T1/pcr/m/n/9 args = list(mean = mean(x), sd
= sd(x)), ...)[]
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[2903]
[2904]
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[2906]
[2907]
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[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to []\T1/pcr/m/n/10 panel.super
pose
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[]\T1/ptm/m/n/10 from []\T1/pcr/m/n/10 panel.superpose.2[]\T1/ptm/m/n/10 , and
to []\T1/pcr/m/n/10 panel.groups []\T1/ptm/m/n/10 from
[2908]
[2909]
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[]\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[]
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[]\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[]
[2910]
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[]\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[]
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[]\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. []\T1/pcr/m/n/10 type [
]\T1/ptm/m/n/10 has a dif-fer-ent mean-ing in
[2911]
Underfull \hbox (badness 1515) in paragraph at lines 9160--9164
[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
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[2913]
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[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2914]
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[] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[]
[2915]
[2916]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9515--9515
[]\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[]
[2917]
Underfull \hbox (badness 1028) in paragraph at lines 9574--9578
\T1/pcr/m/n/10 condition []\T1/ptm/m/n/10 for 2-D, and []\T1/pcr/m/n/10 left, r
ight.x, right.y, left.name, right.x.name,
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[2921]
[2922]
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[2924]
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[]\T1/ptm/m/n/10 Factor with lev-els []\T1/pcr/m/n/10 "Svansota"[]\T1/ptm/m/n/1
0 , []\T1/pcr/m/n/10 "No. 462"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Manchuria"[]
\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "No. 475"[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 10018--10022
[]\T1/pcr/m/n/10 "Velvet"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Peatland"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "Glabron"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "No. 4
57"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Wisconsin No. 38"[]\T1/ptm/m/n/10 ,
[2925]
[2926]
[2927]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma}
) has been already used, duplicate ignored
<to be read again>
\relax
l.10249 \aliasA{melanoma}{H\_melanoma}{melanoma}
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[2929]
[2930]
Underfull \hbox (badness 10000) in paragraph at lines 10411--10416
\T1/pcr/m/n/10 diseases[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Diabetes[]\T1/ptm/m/
n/10 , []\T1/pcr/m/n/10 Flu and pneumonia[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 He
art disease[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Lower
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10484--10484
[] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list(
columns = 2),[]
[2931]
[2932]) (./mgcv-pkg.tex
Chapter 24.
[2933]
[2934]
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[]\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,
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[] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret
e=FALSE,[]
[2935]
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[] \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in
tercept=NULL,[]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known
scale.
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[2937]
[2938]
[2939]
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[][][]\T1/pcr/m/n/10 mgcv.parallel[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gamObject[][][][]\T1
/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/ptm/m/n/10 , [][][]\T1
/pcr/m/n/10 smooth.terms[][][][]\T1/ptm/m/n/10 ,
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[][][]\T1/pcr/m/n/10 linear.functional.terms[][][][]\T1/ptm/m/n/10 , [][][]\T1/
pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][] [][]predict.
gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10
,
Underfull \hbox (badness 10000) in paragraph at lines 382--389
[][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 g
am.side[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.selection[][][][]\T1/p
tm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][][]\T1/ptm
/m/n/10 ,
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[]\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2
,bs=bs,k=k)+[]
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[2942]
[2943]
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[]\T1/ptm/m/n/10 The link func-tion: one of []\T1/pcr/m/n/10 "logit"[]\T1/ptm/m
/n/10 , []\T1/pcr/m/n/10 "probit"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cloglog"
[]\T1/ptm/m/n/10 and
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[2945]
Underfull \hbox (badness 1406) in paragraph at lines 707--708
[]\T1/ptm/m/n/10 The MKL BLAS is mut-lithreaded by de-fault. Un-der linux set-t
ing en-vi-ron-ment vari-able
[2946]
[2947]
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[]\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe
n us-ing pe-nal-ized re-gres-sion
[2948]
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[]\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro
-duc-tion with R (2nd edi-tion).
[2949]
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[]\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$
q^.5),col=2)[]
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[]\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[]
[2959]
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[] \T1/pcr/m/n/9 plot(b$y[oy],rs[oy,ii[1]],ylim=c(-3,3),type="l",ylab="scor
e residuals",[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1453--1453
[]\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor
+rx+obstruct[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1462--1462
[]\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in
d]),type="l",[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1464--1464
[] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind])
,lwd=2,col=i)[]
Underfull \vbox (badness 10000) has occurred while \output is active
[2960]
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[]\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights=
d,data=surv)[]
[2961]
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[] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid),
initial = 0,[]
[2962]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1589--1589
[] \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][
nrow(um)] <- 1[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1628--1628
[]\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter
polate to te[]
[2963]
[2964]
[2965]
[2966]
[2967]
[2968]
[2969]
[2970]
[2971]
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[]\T1/pcr/m/n/9 bd <- bam(y~s(x0)+ s(x1) + s(x1,fac,bs="sz",k=5)+s(x2,k=20),di
screte=TRUE)[]
[2972]
[2973]
[2974]
[2975]
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[]\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE)
[2976]
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[]\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,[]
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[]\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][][]\T1/pcr/m/n
/10 formula.gam[][][] []\T1/ptm/m/n/10 and also
[2982]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known
scale.
[2983]
[2984]
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[]\T1/ptm/m/n/10 A list spec-i-fy-ing the neigh-bour-hood struc-ture for [][][]
\T1/pcr/m/n/10 NCV[][][][]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 a []\T1/ptm/m/n/10
is the vec-tor
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[]\T1/ptm/m/n/10 gives the points dropped for the neigh-bour-hood []\T1/pcr/m/n
/10 j[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 d []\T1/ptm/m/n/10 is the vec-tor
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\T1/ptm/m/n/10 of in-dices of points to pre-dict, with cor-re-spond-ing end-poi
nts []\T1/pcr/m/n/10 md[]\T1/ptm/m/n/10 . So
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\T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v
en-tion mech-a-nism de-scribed in
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[][][]\T1/pcr/m/n/10 mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
gamObject[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/pt
m/m/n/10 , [][][]\T1/pcr/m/n/10 smooth.terms[][][][]\T1/ptm/m/n/10 ,
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[][][]\T1/pcr/m/n/10 linear.functional.terms[][][][]\T1/ptm/m/n/10 , [][][]\T1/
pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][] [][]predict.
gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10
,
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[][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 g
am.side[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.selection[][][][]\T1/p
tm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][][]\T1/ptm
/m/n/10 ,
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[]\T1/pcr/m/n/10 gam.control(nthreads=1,ncv.threads=1,irls.reg=0.0,epsilon = 1
e-07,
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[] \T1/pcr/m/n/10 maxit = 200,mgcv.tol=1e-7,mgcv.half=15, trace = F
ALSE,[]
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[] \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco
l(x)),[]
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[] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol
(x)),[]
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[] \T1/pcr/m/n/10 pearson.extra=0,dev.extra=0,n.true=-1,Sl=NULL,nei=NU
LL,...)[]
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[]\T1/ptm/m/n/10 Random ef-fects can be added to []\T1/pcr/m/n/10 gam []\T1/ptm
/m/n/10 mod-els us-ing []\T1/pcr/m/n/10 s(...,bs="re") []\T1/ptm/m/n/10 terms (
see
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[]\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[]
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[]\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix
ed penalty, if
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[] \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i
d=1)+s(x1,id=1)+[]
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[]\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0,
d1b = 0,
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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[]\T1/ptm/m/n/10 In the event of []\T1/pcr/m/n/10 lme []\T1/ptm/m/n/10 con-ver-
gence fail-ures, con-sider mod-i-fy-ing
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[][][]\T1/pcr/m/n/10 magic[][][] []\T1/ptm/m/n/10 for an al-ter-na-tive for cor
-re-lated data, [][][]\T1/pcr/m/n/10 te[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m
/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.gam[][][][]\T1/ptm
/m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10 ,
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[][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 n
egbin[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 vis.gam[][][][]\T1/ptm/m/n/1
0 ,[][][]\T1/pcr/m/n/10 pdTens[][][][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 gamm4 [
]\T1/ptm/m/n/10 ( [][]$\T1/pcr/m/n/10 https : / / cran . r-[]project .
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[]\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see []
[][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 ar-gu-ment
Underfull \hbox (badness 2181) in paragraph at lines 5804--5805
[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
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[]\T1/pcr/m/n/10 ginla(G,A=NULL,nk=16,nb=100,J=1,interactive=FALSE,integ=0,app
rox=0)
Underfull \hbox (badness 6708) in paragraph at lines 6313--6314
[]\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by []\T1/pcr/m/n/10 gam(..
.,fit=FALSE) []\T1/ptm/m/n/10 or
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[] \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d
ata. A simple[]
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[] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j]
,lty=lty[j])[]
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[] \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo
r comparison[]
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Overfull \hbox (4.38043pt too wide) in paragraph at lines 6538--6538
[] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r
norm(100)*.4[]
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[]\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n
a.action,
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[]\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona
lize=FALSE)[]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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[]\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999,
all.derivs=FALSE)
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[]\T1/pcr/m/n/10 lp(c,A,b,C=NULL,d=NULL,Bi=NULL,maxit=max(1000, nrow(A) * 10),
phase1 = FALSE)
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[]\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
to rule the world.",[]
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[] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[]
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[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
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[]\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt
ion with bam...[]
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[]\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate
d covariates[]
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[] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]]
,na.rm=TRUE)[]
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[]\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: []\T1/pcr/m/n/10 Dim
.pdIndot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 coef.pdIdnot[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 corMatrix.pdIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 logDet.pd
Idnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdConstruct.pdIdnot[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3118) in paragraph at lines 9877--9880
[]\T1/pcr/m/n/10 pdFactor.pdIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdMatrix.p
dIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 solve.pdIdnot[]\T1/ptm/m/n/10 , []\T1
/pcr/m/n/10 summary.pdIdnot[]\T1/ptm/m/n/10 .
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[]\T1/ptm/m/n/10 These func-tions ([]\T1/pcr/m/n/10 pdTens[]\T1/ptm/m/n/10 , []
\T1/pcr/m/n/10 pdConstruct.pdTens[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdFactor.p
dTens[]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 3108) in paragraph at lines 9933--9936
[]\T1/pcr/m/n/10 pdMatrix.pdTens[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 coef.pdTens
[]\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 summary.pdTens[]\T1/ptm/m/n/10 ) would n
ot nor-mally be
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[]\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s
cale=-1,[]
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[] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi
ds=FALSE,[]
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[]\T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion
is some-times to clone the
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[] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,gc.level=0,...)[]
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[]\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 type=="terms" []\T1/ptm/m/n/10 or []\T1/pc
r/m/n/10 type="iterms" []\T1/ptm/m/n/10 then terms (smooth or para-
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[] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL
L,...)[]
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[]\T1/pcr/m/n/9 x1 <- seq(.2,.8,length=m1);x2 <- seq(.2,.8,length=m2) ## margi
nal grid points[]
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[]\T1/pcr/m/n/9 df <- data.frame(x0=rep(.5,n),x1=rep(x1,m2),x2=rep(x2,each=m1)
,x3=rep(0,n))[]
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[] \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s
mooth deriv i[]
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are
as for
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[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which
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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are
as for
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[]\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from
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[][][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][][]\T1/ptm/m/n/10 , al
-though el-e-ments []\T1/pcr/m/n/10 X []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 S [
]\T1/ptm/m/n/10 are not needed,
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[]\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion
cri-te-rion re-ported is one of GCV,
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[]\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef-
fects in a GAM in the same
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\T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre
s-sion terms. This method
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\T1/ptm/m/n/10 can be used with [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10
by mak-ing use of []\T1/pcr/m/n/10 s(...,bs="re") []\T1/ptm/m/n/10 terms in a
model: see
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[]\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the []\T1/pcr/m/n
/10 paraPen []\T1/ptm/m/n/10 ar-gu-ment to [][][]\T1/pcr/m/n/10 gam[][][] []\T1
/ptm/m/n/10 can be used:
Underfull \hbox (badness 5862) in paragraph at lines 11584--11587
\T1/ptm/m/n/10 see [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/ptm/m/n/10 . If s
mooth-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g.
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[]\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[]
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[]\T1/pcr/m/n/9 ## The effect of the new factor levels (or any interaction inv
olving them)[]
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[]\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of []\T1/pcr/m/n/
10 "deviance"[]\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 s(..., k=-1,fx=FALSE,bs="tp",m=NA,by=NA,xt=NULL,id=NULL,sp=NU
LL,pc=NULL)
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[] \T1/pcr/m/n/9 true <- mu + (del * sigma) * sinh((1/del) * asinh(qnorm(qq))
+ (eps/del))[]
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[]\T1/pcr/m/n/9 b <- gam(list(accel~s(times, k=20, bs = "ad"), ~s(times, k = 1
0), ~1, ~1),[]
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[]\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to
model ma-trix X, or, if
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[]\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE,
cov = TRUE,[]
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[]\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 inverse==TRUE []\T1/ptm/m/n/10 and []\T1/p
cr/m/n/10 both.sides==FALSE []\T1/ptm/m/n/10 then the re-
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[]\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 inverse==TRUE []\T1/ptm/m/n/10 and []\T1/p
cr/m/n/10 both.sides==FALSE []\T1/ptm/m/n/10 then the re-
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[]\T1/pcr/m/n/10 Sl.setup(G,cholesky=FALSE,no.repara=FALSE,sparse=FALSE,keepS=
FALSE)
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Overfull \hbox (20.58041pt too wide) in paragraph at lines 12695--12695
[] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$
vectors[,ind]))[]
Underfull \hbox (badness 1975) in paragraph at lines 12706--12711
[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[3153]
Underfull \hbox (badness 1803) in paragraph at lines 12783--12787
\T1/ptm/m/n/10 The last en-try will be the []\T1/pcr/m/n/10 by []\T1/ptm/m/n/10
vari-able, if []\T1/pcr/m/n/10 object$by []\T1/ptm/m/n/10 is not []\T1/pcr/m/n
/10 "NA"[]\T1/ptm/m/n/10 .
Underfull \hbox (badness 1502) in paragraph at lines 12795--12807
[]\T1/pcr/m/n/10 cs.smooth.spec []\T1/ptm/m/n/10 (cu-bic re-gres-sion splines w
ith shrinkage-to-zero); []\T1/pcr/m/n/10 cc.smooth.spec
[3154]
Underfull \hbox (badness 2401) in paragraph at lines 12812--12816
[]\T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able
. Plot meth-ods can be
Underfull \hbox (badness 2970) in paragraph at lines 12812--12816
\T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for []\T1/pc
r/m/n/10 mgcv:::plot.sos.smooth[]\T1/ptm/m/n/10 ,
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Underfull \hbox (badness 6876) in paragraph at lines 13007--13013
[][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use adap-tive smooths of on
e or two vari-ables, spec-i-fied via terms like
[3158]
Underfull \hbox (badness 10000) in paragraph at lines 13048--13049
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
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Underfull \hbox (badness 10000) in paragraph at lines 13166--13167
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
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[] \T1/pcr/m/n/9 b <- gam(y~s(x0,bs=bs,m=c(4,2))+s(x1,bs=bs)+s(x2,k=15,bs=bs,
m=c(4,3,0))+[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13232--13232
[] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5,
1.5) (black)[]
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[] \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions
and intervals[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13249--13249
[] \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i
ntervals away[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13255--13255
[] \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w
ild and wide[]
Overfull \hbox (3.70428pt too wide) in paragraph at lines 13256--13256
[] \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/cmtt/m/n/9 `\T1
/pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
Underfull \hbox (badness 10000) in paragraph at lines 13325--13327
\T1/ptm/m/n/10 term []\T1/pcr/m/n/10 s(...,bs="cr",...)[]\T1/ptm/m/n/10 , []\T1
/pcr/m/n/10 s(...,bs="cs",...) []\T1/ptm/m/n/10 or
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Underfull \hbox (badness 10000) in paragraph at lines 13455--13456
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
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Overfull \hbox (9.78043pt too wide) in paragraph at lines 13536--13536
[]\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data) ## first
deriv penalty[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13537--13537
[]\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi
ed 2nd deriv[]
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Underfull \hbox (badness 10000) in paragraph at lines 13690--13691
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
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[]\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[]
[3175]
Underfull \hbox (badness 10000) in paragraph at lines 14001--14003
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
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Underfull \hbox (badness 10000) in paragraph at lines 14160--14163
[]\T1/ptm/m/n/10 For the []\T1/pcr/m/n/10 smooth.construct []\T1/ptm/m/n/10 met
hod a smooth spec-i-fi-ca-tion ob-
Underfull \hbox (badness 3312) in paragraph at lines 14160--14163
\T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term []\T1/pcr/m/n/10 s(x,...,bs
="re",)[]\T1/ptm/m/n/10 . For the
Underfull \hbox (badness 7099) in paragraph at lines 14160--14163
[]\T1/pcr/m/n/10 predict.Matrix []\T1/ptm/m/n/10 method an ob-ject of class []\
T1/pcr/m/n/10 "random.effect"
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[3179]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 14246--14246
[]\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with
2 variances[]
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Underfull \hbox (badness 10000) in paragraph at lines 14291--14297
[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a
Underfull \hbox (badness 7832) in paragraph at lines 14291--14297
[]\T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) []\T1/ptm/m/n/10 term in a
[]\T1/pcr/m/n/10 gam []\T1/ptm/m/n/10 for-
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[3182]
[3183]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 14506--14506
[]\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[]
Underfull \vbox (badness 10000) has occurred while \output is active
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Underfull \hbox (badness 10000) in paragraph at lines 14609--14617
[][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths on th
e sphere, via terms like
Underfull \hbox (badness 10000) in paragraph at lines 14635--14636
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
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[]\T1/ptm/m/n/10 method an ob-ject of class []\T1/pcr/m/n/10 "sz.interaction" [
]\T1/ptm/m/n/10 pro-duced by the
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[]\T1/ptm/m/n/10 The terms can have a smooth-ing pa-ram-e-ter per smooth, or a
sin-gle smooth-ing pa-ram-e-
Overfull \hbox (128.58029pt too wide) in paragraph at lines 14847--14847
[]\T1/pcr/m/n/9 b <- gam(y ~ s(x)+s(f1,x,bs="sz")+s(f2,x,bs="sz")+s(f1,f2,x,bs
="sz",id=1),data=dat,method="REML")[]
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[3192]
Underfull \hbox (badness 3396) in paragraph at lines 14993--14996
[][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths of an
y num-ber of vari-ables, spec-i-fied via terms like
Underfull \hbox (badness 10000) in paragraph at lines 15038--15040
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a
term
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Underfull \hbox (badness 10000) in paragraph at lines 15329--15331
[]\T1/pcr/m/n/10 bs="fs" []\T1/ptm/m/n/10 A spe-cial smoother class (see
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Underfull \hbox (badness 10000) in paragraph at lines 15363--15367
[][][]\T1/pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][][]\
T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 t2[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m
/n/10 tprs[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Duchon.spline[][][][]\T
1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cubic.regression.spline[][][][]\T1/ptm/m/n/
10 ,
Underfull \hbox (badness 10000) in paragraph at lines 15363--15367
[][][]\T1/pcr/m/n/10 p.spline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 d.sp
line[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 mrf[][][][]\T1/ptm/m/n/10 , [
][][]\T1/pcr/m/n/10 soap[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Spherical
.Spline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 adaptive.smooth[][][][]\T1
/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 15363--15367
[][][]\T1/pcr/m/n/10 user.defined.smooth[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/
m/n/10 smooth.construct.re.smooth.spec[][][][]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[3205]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 15731--15731
[]\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[]
[3206]
[3207]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 15865--15865
[] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[]
[3208]
[3209]
Underfull \hbox (badness 4846) in paragraph at lines 15996--15999
[]\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or
es-ti-ma-tors if
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[]\T1/pcr/m/n/10 vcov(object, sandwich=FALSE, freq = FALSE, dispersion = NULL,
unconditional=FALSE, ...)[]
[3230]
Underfull \hbox (badness 1715) in paragraph at lines 17242--17243
[]\T1/ptm/m/n/10 Basically, just ex-tracts []\T1/pcr/m/n/10 object$Ve[]\T1/ptm/
m/n/10 , []\T1/pcr/m/n/10 object$Vp []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 object
$Vc []\T1/ptm/m/n/10 (if avail-able) from a
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Overfull \hbox (54.78088pt too wide) in paragraph at lines 17433--17433
[]\T1/pcr/m/n/10 XWXd(X,w,k,ks,ts,dt,v,qc,nthreads=1,drop=NULL,ar.stop=-1,ar.r
ow=-1,ar.w=-1,
Overfull \hbox (48.78088pt too wide) in paragraph at lines 17435--17435
[]\T1/pcr/m/n/10 XWyd(X,w,y,k,ks,ts,dt,v,qc,drop=NULL,ar.stop=-1,ar.row=-1,ar.
w=-1,lt=NULL)[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17437--17437
[]\T1/pcr/m/n/10 diagXVXd(X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,rt=
NULL)[]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 17438--17438
[]\T1/pcr/m/n/10 ijXVXd(i,j,X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,r
t=NULL)[]
[3234]
Underfull \hbox (badness 10000) in paragraph at lines 17458--17459
[]\T1/ptm/m/n/10 Negative to ig-nore. Oth-er-wise sum rows
Underfull \hbox (badness 1668) in paragraph at lines 17458--17459
[]\T1/pcr/m/n/10 (ar.stop[i-1]+1):ar.stop[i] []\T1/ptm/m/n/10 of the rows se-le
cted by []\T1/pcr/m/n/10 ar.row
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[3236]
[3237]
[3238]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 17656--17656
[]\T1/pcr/m/n/9 ## 1. If the zero inflation rate becomes decoupled from the li
near predictor,[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 17657--17657
[]\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun
ded in regions[]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17669--17669
[]\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[]
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[3241]) (./nlme-pkg.tex
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Chapter 25.
[3243]
Underfull \hbox (badness 1009) in paragraph at lines 78--87
[]\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served
- fit-ted) are used; else, if
[3244]
Underfull \hbox (badness 1009) in paragraph at lines 168--177
[]\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served
- fit-ted) are used; else, if
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[3247]
[3248]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 448--448
[] \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[]
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[3251]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 589--589
[]\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 251-254 ---------------------------
---------------[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 605--605
[]\T1/pcr/m/n/9 # Compare an "lme" object with a "gls" object (test would be n
on-sensical!)[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 608--608
[]\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 222-225 ---------------------------
---------------[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 615--615
[]\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 352-365 ---------------------------
---------------[]
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[3256]
[3257]
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[] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil
lary fissure"),[]
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[3260]
Underfull \hbox (badness 5446) in paragraph at lines 1140--1142
[]\T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel
.htm[]\T1/ptm/m/n/10 ', the first edi-tion of
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[3265]
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Underfull \hbox (badness 10000) in paragraph at lines 1617--1620
[][][]\T1/pcr/m/n/10 lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fixed.
effects.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 ranef.lmList[][][][
]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.ranef.lmList[][][][]\T1/ptm/m/n/10
,
Underfull \hbox (badness 3780) in paragraph at lines 1634--1636
[]\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a
ted with each com-po-nent of the
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[3272]
Underfull \hbox (badness 2042) in paragraph at lines 1975--1981
\T1/ptm/m/n/10 is in-ner to the []\T1/pcr/m/n/10 displayLevel []\T1/ptm/m/n/10
group-ing fac-tor. If equal to []\T1/pcr/m/n/10 TRUE[]\T1/ptm/m/n/10 ,
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[3274]
Underfull \hbox (badness 1132) in paragraph at lines 2127--2129
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
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[3276]
Underfull \hbox (badness 4168) in paragraph at lines 2238--2244
[][][]\T1/pcr/m/n/10 ACF.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corAR
MA[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/1
0 , [][][]\T1/pcr/m/n/10 Dim.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m
/n/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 ,
[3277]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2263--2263
[] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[]
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Underfull \hbox (badness 10000) in paragraph at lines 2816--2820
[][][]\T1/pcr/m/n/10 corFactor[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cor
Matrix.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 recalc.corStruct[
][][][]\T1/ptm/m/n/10 ,
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Underfull \hbox (badness 6493) in paragraph at lines 3548--3556
[][][]\T1/pcr/m/n/10 corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corGau
s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corLin[][][][]\T1/ptm/m/n/10 , [
][][]\T1/pcr/m/n/10 corRatio[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corSp
her[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][][]\T
1/ptm/m/n/10 ,
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Underfull \hbox (badness 10000) in paragraph at lines 5116--5120
[][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/p
cr/m/n/10 getCovariate.data.frame[][][][]\T1/ptm/m/n/10 ,
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Underfull \hbox (badness 10000) in paragraph at lines 5540--5543
[][][]\T1/pcr/m/n/10 getGroups.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/
m/n/10 getGroups.data.frame[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 getGro
ups.gls[][][][]\T1/ptm/m/n/10 ,
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Underfull \hbox (badness 2799) in paragraph at lines 6044--6050
\T1/ptm/m/n/10 covariance ma-trix, ei-ther []\T1/pcr/m/n/10 "random.effects" []
\T1/ptm/m/n/10 for the random-effects
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[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in [
]\T1/pcr/m/n/10 model[]\T1/ptm/m/n/10 ,
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[][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gl
sControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 glsObject[][][][]\T1/ptm/
m/n/10 , [][][]\T1/pcr/m/n/10 glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m
/n/10 plot.gls[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.gls[][][][]
\T1/ptm/m/n/10 ,
[3339]
Underfull \hbox (badness 10000) in paragraph at lines 6258--6260
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
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Underfull \hbox (badness 7133) in paragraph at lines 6505--6509
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in [
]\T1/pcr/m/n/10 model[]\T1/ptm/m/n/10 ,
[3344]
Underfull \hbox (badness 10000) in paragraph at lines 6602--6608
[][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gn
lsControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gnlsObject[][][][]\T1/pt
m/m/n/10 , [][][]\T1/pcr/m/n/10 gnlsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc
r/m/n/10 predict.gnls[][][][]\T1/ptm/m/n/10 ,
Overfull \hbox (54.78088pt too wide) in paragraph at lines 6629--6629
[]\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min
Scale = 0.001,
[3345]
Underfull \hbox (badness 10000) in paragraph at lines 6667--6669
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
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[3349]
Underfull \hbox (badness 10000) in paragraph at lines 6936--6943
[][][]\T1/pcr/m/n/10 formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gappl
y[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gsummary[][][][]\T1/ptm/m/n/10 ,
[][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.nff
GroupedData[][][][]\T1/ptm/m/n/10 ,
[3350]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6954--6954
[] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6959--6959
[]\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted
from object[]
Underfull \hbox (badness 2875) in paragraph at lines 6981--6983
[]\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a []\T1/pcr/m/n/10 gr
oupedData []\T1/ptm/m/n/10 ob-ject or a
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Underfull \hbox (badness 10000) in paragraph at lines 7196--7202
[][][]\T1/pcr/m/n/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr
/m/n/10 Initialize.glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initi
alize.lmeStruct[][][][]\T1/ptm/m/n/10 ,
[3354]
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Underfull \hbox (badness 1997) in paragraph at lines 7341--7349
[]\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial
-iza-tion and op-ti-
Underfull \hbox (badness 2205) in paragraph at lines 7341--7349
\T1/ptm/m/n/10 miza-tion al-go-rithms used in []\T1/pcr/m/n/10 lme[]\T1/ptm/m/n
/10 . De-faults to []\T1/pcr/m/n/10 list(niterEM=20,
Underfull \hbox (badness 3118) in paragraph at lines 7364--7367
[][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initializ
e.reStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.corStruct[][
][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.varFunc[][][][]\T1/ptm/m/
n/10 ,
[3357]
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[3359]
Underfull \hbox (badness 3354) in paragraph at lines 7574--7576
[]\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when []\T1/pcr/m/n/
10 which []\T1/ptm/m/n/10 is not equal to
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Underfull \hbox (badness 10000) in paragraph at lines 8101--8118
[][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lm
e.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lme.groupedData[][][][]\T
1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lmeControl[][][][]\T1/ptm/m/n/10 , [][][]\T
1/pcr/m/n/10 lmeObject[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 8101--8118
[][][]\T1/pcr/m/n/10 lmeStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lmL
ist[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/1
0 , [][][]\T1/pcr/m/n/10 plot.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
predict.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 qqnorm.lme[][][][]\T1/
ptm/m/n/10 ,
[3368]
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[] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data
= TRUE)[]
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[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
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Overfull \hbox (36.78088pt too wide) in paragraph at lines 8418--8418
[]\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni
terEM = 25,
Underfull \hbox (badness 1189) in paragraph at lines 8443--8445
[]\T1/ptm/m/n/10 maximum num-ber of eval-u-a-tions of the ob-jec-tive func-tion
per-mit-ted for
[3373]
Underfull \hbox (badness 10000) in paragraph at lines 8466--8468
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
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[]\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[]
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Underfull \hbox (badness 10000) in paragraph at lines 9266--9273
[][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 ,[][][]\T1/pcr/m/n/10 gls[][][][
]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logLik.corStruct[][][][]\T1/ptm/m/n/10 ,
[][][]\T1/pcr/m/n/10 logLik.glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 logLik.lmeStruct[][][][]\T1/ptm/m/n/10 ,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9277--9277
[]\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML")
[3386]
[3387]
[3388]
[3389]
[3390]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Matrix})
has been already used, duplicate ignored
<to be read again>
\relax
l.9628 ...rA{Matrix}{Assign Matrix Values}{Matrix}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Matrix.1}
) has been already used, duplicate ignored
<to be read again>
\relax
l.9628 ...rA{Matrix}{Assign Matrix Values}{Matrix}
[3391]
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[]\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a
s
Underfull \hbox (badness 3108) in paragraph at lines 9692--9695
[]\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive
-definite
Underfull \hbox (badness 2521) in paragraph at lines 9692--9695
\T1/ptm/m/n/10 ma-trix rep-re-sented by []\T1/pcr/m/n/10 object[]\T1/ptm/m/n/10
. Must have the same di-men-sions as
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[3402]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10362--10362
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,
[3403]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10366--10366
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,[]
Underfull \hbox (badness 1596) in paragraph at lines 10395--10421
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3404]
[3405]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10549--10549
[]\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation,
weights,[]
[3406]
[3407]
[3408]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10700--10700
[] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
NULL, ...)[]
Underfull \hbox (badness 2213) in paragraph at lines 10711--10716
[]\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][][]\T1/pcr/m/n/10 nlmi
nb[][][] []\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 iter.max[]\T1/ptm/m/n/10 ) or the [
][][]\T1/pcr/m/n/10 nlm[][][]
Underfull \hbox (badness 6961) in paragraph at lines 10733--10737
[]\T1/ptm/m/n/10 a log-i-cal value passed as the []\T1/pcr/m/n/10 trace []\T1/p
tm/m/n/10 to [][][]\T1/pcr/m/n/10 nlminb[][][](.., control=
[3409]
Underfull \hbox (badness 10000) in paragraph at lines 10752--10754
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
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[3411]
[3412]
[3413]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 11048--11048
[]\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one*
message instead of one *each*[]
Overfull \hbox (90.78033pt too wide) in paragraph at lines 11049--11049
[]\T1/pcr/m/n/9 mat.class <- class(matrix(1)) # ("matrix", "array") for R >= 4
.0.0; ("matrix" in older R)[]
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[3415]
[3416]
[3417]
[3418]
[3419]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11439--11439
[]\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*))
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[3422]
[3423]
[3424]
[3425]
Underfull \hbox (badness 6268) in paragraph at lines 11826--11836
[][][]\T1/pcr/m/n/10 pdBlocked[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdC
ompSymm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdDiag[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 pdFactor[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
pdIdent[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 pdMatrix[][][][]\T1/ptm/m/n/10 ,
[3426]
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Underfull \hbox (badness 10000) in paragraph at lines 12087--12093
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 coef.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdBlocked[][][][]\T1
/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/
pcr/m/n/10 pdConstruct[][][][]\T1/ptm/m/n/10 ,
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Underfull \hbox (badness 6876) in paragraph at lines 12409--12411
[]\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 value []\T1/ptm/m/n/10 is an \T1/ptm/m/it/
10 ini-tial-ized []\T1/pcr/m/n/10 pdMat []\T1/ptm/m/n/10 ob-ject, []\T1/pcr/m/n
/10 object []\T1/ptm/m/n/10 will be con-structed from
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[3436]
Underfull \hbox (badness 2452) in paragraph at lines 12565--12572
[][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdC
ompSymm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdDiag[][][][]\T1/ptm/m/n/
10 , [][][]\T1/pcr/m/n/10 pdIdent[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
pdNatural[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdSymm[][][][]\T1/ptm/m/
n/10 , [][][]\T1/pcr/m/n/10 reStruct[][][][]\T1/ptm/m/n/10 ,
[3437]
Underfull \hbox (badness 10000) in paragraph at lines 12631--12637
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdFactor[][][][]\T1/p
tm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 pdMatrix.reStruct[][][][]\T1/ptm/m/n/10 ,
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[3445]
[3446]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 13220--13220
[]\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*))
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[3448]
[3449]
[3450]
[3451]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13585--13585
[]\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline =
0, id = 0.05)[]
[3452]
Underfull \hbox (badness 10000) in paragraph at lines 13612--13615
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nffGroupe
dData[]\T1/ptm/m/n/10 , rep-re-sent-ing a
[3453]
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[]\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If []\T1/pcr/m/
n/10 TRUE []\T1/ptm/m/n/10 and ei-ther []\T1/pcr/m/n/10 inner
Underfull \hbox (badness 3713) in paragraph at lines 13655--13662
[]\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 innerGroups []\T1/ptm/m/n/10 are non-[]\T1
/pcr/m/n/10 NULL[]\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent []\T1/pcr/m/n/
10 inner
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13712--13712
[]\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
panel,[]
[3454]
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[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nfnGroupe
dData[]\T1/ptm/m/n/10 , rep-re-sent-ing a
Underfull \hbox (badness 2469) in paragraph at lines 13719--13722
[]\T1/pcr/m/n/10 groupedData []\T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary
co-vari-ate and a sin-gle
[3455]
Underfull \hbox (badness 10000) in paragraph at lines 13827--13830
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nmGrouped
Data[]\T1/ptm/m/n/10 , rep-re-sent-ing a
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[3457]
Underfull \hbox (badness 10000) in paragraph at lines 13921--13923
[][][]\T1/pcr/m/n/10 groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 c
ollapse.groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.nfnGroupe
dData[][][][]\T1/ptm/m/n/10 ,
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[3463]
[3464]
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Overfull \hbox (20.58041pt too wide) in paragraph at lines 14445--14445
[]\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[]
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fects}) has been already used, duplicate ignored
<to be read again>
\relax
l.15098 ...Extract Random Effects}{random.effects}
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fects.1}) has been already used, duplicate ignored
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l.15098 ...Extract Random Effects}{random.effects}
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Overfull \hbox (25.98041pt too wide) in paragraph at lines 15734--15734
[]\T1/pcr/m/n/9 plot(Remifentanil, type = "l", lwd = 2) # shows the 65 patient
s\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 remi profiles
[3486]
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[]\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served
- fit-ted) are used; else, if
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[3488]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 15933--15933
[] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[]
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Underfull \hbox (badness 10000) in paragraph at lines 16268--16274
[][][]\T1/pcr/m/n/10 groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 l
me[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/10 , [
][][]\T1/pcr/m/n/10 solve.reStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
summary.reStruct[][][][]\T1/ptm/m/n/10 ,
[3494]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 16300--16300
[] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[]
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[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
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\T1/pcr/m/n/10 of an Identity" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pdIdent[]\
T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "General Positive-Definite,
Underfull \hbox (badness 10000) in paragraph at lines 17120--17129
\T1/pcr/m/n/10 Natural Parametrization" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 p
dNatural[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "General
Underfull \hbox (badness 7888) in paragraph at lines 17120--17129
\T1/pcr/m/n/10 Positive-Definite" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pdSymm[
]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 data.class(object)
[3507]
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[]\T1/pcr/m/n/10 "Constant plus power of variance
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[]\T1/pcr/m/n/10 "Constant plus proportion of variance
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[3509]
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[3511]
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[][][]\T1/pcr/m/n/10 varComb[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varCo
nstPower[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varConstProp[][][][]\T1/p
tm/m/n/10 , [][][]\T1/pcr/m/n/10 varExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m
/n/10 varFixed[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varIdent[][][][]\T1
/ptm/m/n/10 ,
[3512]
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[]\T1/pcr/m/n/9 # Generate some synthetic data using the two-component error m
odel and use
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[]\T1/pcr/m/n/9 # overparameterisation in the case of a constant term in the v
ariance function[]
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[3521]
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[][][]\T1/pcr/m/n/10 Variogram.corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n
/10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.co
rLin[][][][]\T1/ptm/m/n/10 ,
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[][][]\T1/pcr/m/n/10 Variogram.corRatio[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m
/n/10 Variogram.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogr
am.corSpher[][][][]\T1/ptm/m/n/10 ,
[3522]
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
[3523]
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
[3524]
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
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[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 "[][]corR
atio[][][]"[]\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
[3526]
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
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[][][]\T1/pcr/m/n/10 corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Va
riogram[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.default[][][][]\
T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.corExp[][][][]\T1/ptm/m/n/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 18471--18480
[][][]\T1/pcr/m/n/10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/
n/10 Variogram.corLin[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.co
rRatio[][][][]\T1/ptm/m/n/10 ,
[3527]
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\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p
tm/m/n/10 , in which case a se-quence
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[3529]
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[]\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served
- fit-ted) are used; else, if
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[3531]
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[]\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served
- fit-ted) are used; else, if
[3532]
[3533]
[3534]
[3535]
[3536]
[3537]
[3538]
[3539]
[3540]) (./nnet-pkg.tex
Chapter 26.
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom}
) has been already used, duplicate ignored
<to be read again>
\relax
l.47 ...t Multinomial Log-linear Models}{multinom}
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom.
1}) has been already used, duplicate ignored
<to be read again>
\relax
l.47 ...t Multinomial Log-linear Models}{multinom}
[3541]
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[] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
FALSE,[]
[3542]
[3543]
[3544]
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[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3545]
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[]\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c(
0,0,1),50)),[]
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[]\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[]
[3546]
[3547]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 511--511
[]\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size =
2, rang = 0.1,[]
[3548]) (./rpart-pkg.tex
Chapter 27.
[3549]
[3550]
[3551]
[3552]
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[]\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse =
TRUE, ...)[]
[3553]
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\T1/ptm/m/n/10 age: []\T1/pcr/m/n/10 pretty = 0 []\T1/ptm/m/n/10 im-plies []\T1
/pcr/m/n/10 minlength = 0L[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pretty = NULL []\
T1/ptm/m/n/10 im-plies
[3554]
[3555]
[3556]
Underfull \hbox (badness 1442) in paragraph at lines 592--598
[]\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 FALSE[]\T1/ptm/m/n/10 , the leaf nodes wil
l be at the hor-i-zon-tal plot co-or-di-nates of
[3557]
[3558]
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[] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
""),[]
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[]\T1/ptm/m/n/10 Logical. If []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 (de-fault),
adds to the la-bel
Underfull \hbox (badness 1142) in paragraph at lines 771--775
\T1/pcr/m/n/10 #events level1/ #events level2/ \T1/ptm/m/n/10 etc. for method [
]\T1/pcr/m/n/10 class[]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 n
[3559]
[3560]
[3561]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 915--915
[]\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 934--934
[]\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"),[]
[3562]
[3563]
[3564]
[3565]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1180--1180
[]\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m
ethod,
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[] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[]
Underfull \hbox (badness 2846) in paragraph at lines 1243--1245
[]\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the []\T1/pcr/m/n
/10 rpart []\T1/ptm/m/n/10 al-go-rithm. See
[3566]
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[]\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the
text is clipped[]
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[]\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c
p = 0.01,
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[] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate
= 2, xval = 10,[]
[3567]
[3568]
[3569]
[3570]
[3571]
[3572]
[3573]
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[]\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val-
ues are `[]\T1/pcr/m/n/10 diploid[]\T1/ptm/m/n/10 ',
[3574]
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[] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
FALSE,[]
[3575]
[3576]
[3577]) (./spatial-pkg.tex
[3578]
Chapter 28.
[3579]
[3580]
[3581]
[3582]
[3583]
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[3585]
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[3593]
[3594]
[3595]
[3596]
[3597]) (./survival-pkg.tex
[3598]
Chapter 29.
[3599]
[3600]
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[]\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data
= lung, nmin = 1[]
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[]\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2) # Nearly the same, until t
he last point[]
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[]\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a
nd Grambsch.[]
[3601]
[3602]
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[]\T1/ptm/m/n/10 an op-tional list or vec-tor of group-ing el-e-ments, each as
long as
[3603]
[3604]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has
been already used, duplicate ignored
<to be read again>
\relax
l.384 ... Myelogenous Leukemia survival data}{aml}
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as been already used, duplicate ignored
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\relax
l.384 ... Myelogenous Leukemia survival data}{aml}
[3605]
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[]\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da
ta = ovarian)
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[]\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[]
[3606]
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[] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
lung)[]
[3607]
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[]\T1/ptm/m/n/10 If H(t; z) is the pre-dicted cu-mu-la-tive haz-ard for an ob-s
er-va-tion with co-vari-ate vec-tor z,
[3608]
[3609]
[3610]
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[]\T1/pcr/m/n/9 py <- pseudo(survfit(Surv(time, status) ~1, lung), time=730) #
2 year survival
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[]\T1/pcr/m/n/10 brier(fit, times, newdata, ties = TRUE, detail = FALSE, timef
ix = TRUE,
[3611]
[3612]
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[] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[]
[3613]
[3614]
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[] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[]
[3615]
[3616]
Underfull \hbox (badness 1097) in paragraph at lines 1205--1207
[]\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi
al and negative-binomial data.
[3617]
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[]\T1/pcr/m/n/9 ppois(4, 10.24153) #chance of seeing 4 or fewer events wit
h large rate[]
[3618]
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[]\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert)
[3619]
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[]\T1/pcr/m/n/9 marginal.model <- coxph(Surv(time, status) ~ rx, data= rats, c
luster=litter,
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colon}) h
as been already used, duplicate ignored
<to be read again>
\relax
l.1407 ...erapy for Stage B/C colon cancer}{colon}
[3620]
[3621]
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[] \T1/pcr/m/n/10 influence=0, ranks = FALSE, reverse=FALSE, timefix=TRUE, ke
epstrata=10, ...)[]
[3622]
[3623]
[3624]
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[]\T1/pcr/m/n/9 options(na.action = na.exclude) # predict all 1384 obs, incl
uding missing[]
[3625]
[3626]
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[]\T1/pcr/m/n/10 cox.zph(fit, transform="km", terms=TRUE, singledf=FALSE, glob
al=TRUE)
[3627]
[3628]
[3629]
[3630]
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[]\T1/ptm/m/n/10 One user mis-take that has re-cently arisen is to slav-ishly f
ol-low the ad-vice of
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\T1/ptm/m/n/10 some cod-ing guides and prepend []\T1/pcr/m/n/10 survival:: []\T
1/ptm/m/n/10 onto ev-er-thing, in-clud-ing the spe-
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\T1/ptm/m/n/10 cial terms, e.g., []\T1/pcr/m/n/10 survival::coxph(survival:Surv
(time, status) ~ age +
[3631]
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[][][]\T1/pcr/m/n/10 coxph.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10
coxphms.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 coxph.control[][][]
[]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cluster[][][][]\T1/ptm/m/n/10 , [][][]\
T1/pcr/m/n/10 strata[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Surv[][][][]\
T1/ptm/m/n/10 ,
[3632]
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[]\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix
=TRUE)[]
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[3640]
[3641]
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[] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" "
exponential"[]
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[]\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass,
etype,
[3642]
[3643]
[3644]
[3645]
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[]\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[]
[3646]
[3647]
[3648]
[3649]
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[]\T1/ptm/m/n/10 outcome: []\T1/pcr/m/n/10 censor[]\T1/ptm/m/n/10 , []\T1/pcr/m
/n/10 thymic lymphoma[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 reticulum cell sarcoma
other
[3650]
[3651]
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[]\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney)
[3652]
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[] \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre
ssion", "death")))[]
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[]\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan
-Meier plot gen-er-ated with
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[] \T1/pcr/m/n/10 conf.type = c("log", "log-log", "plain", "logit", "ar
csin"),[]
[3653]
[3654]
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[] \T1/pcr/m/n/9 rmap=list(sex=sex, age=age*365.35, year=as.Da
te(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/01/01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[]
[3655]
[3656]
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[] []
[3657]
[3658]
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[]\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[]
[3659]
[3660]
[3661]
[3662]
[3663]
[3664]
[3665]
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[] \T1/pcr/m/n/9 entry.dt = as.Date(paste("2011", 1:10, "5"
, sep=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 -\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[]
[3666]
[3667]
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[]\T1/pcr/m/n/9 tdata <- data.frame(x= lung$age, y = 10*log(lung$age-35) + rno
rm(228, 0, 2))[]
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[]\T1/pcr/m/n/9 knots <- unlist(attributes(fit1$model[[2]])[c(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 Boundary.knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , \TS1/pcr/m/n/9 '\T1
/pcr/m/n/9 knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )])[]
[3668]
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[]\T1/pcr/m/n/9 unname(coef(fit1)[-1] - coef(fit1)[1]) # differences: yhat[2:
4] - yhat[1][]
[3669]
[3670]
[3671] [3672]
[3673]
[3674]
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[] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca
le=1,[]
[3675]
[3676]
[3677]
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[]\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign),
collapse,[]
[3678]
[3679]
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[]\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[]
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[] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means
, na.rm=TRUE)[]
[3680]
[3681]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5616--5616
[]\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival
is at +infinity[]
[3682]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5694--5694
[] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars"), expand=FALSE
, ...)[]
[3683]
Underfull \hbox (badness 1852) in paragraph at lines 5766--5768
[]\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.survfit"[]\T1/pt
m/m/n/10 , which is the re-sult of the
[3684]
[3685]
[3686]
[3687]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6020--6020
[]\T1/pcr/m/n/9 rhat <- predict(rfit, newdata=expand.grid(ph.ecog=0:3, sex=1:2
), se.fit=TRUE)[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6032--6032
[]\T1/pcr/m/n/9 # the estimate for ph.ecog=3 is very unstable (n=1), pseudoval
ues smooth it.[]
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[]\T1/pcr/m/n/9 # In all the above we should be using the robust variance, e.g
., svyglm, but[]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6058--6058
[]\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me
thod,
Overfull \hbox (36.78088pt too wide) in paragraph at lines 6059--6059
[] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co
mbine, ...)[]
[3688]
[3689]
[3690]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 6222--6222
[] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[]
[3691]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6324--6324
[]\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age
+ sex, mgus,[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6345--6345
[]\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50
,60,70,100)) +[]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6347--6347
[]\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[]
[3692]
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[3698]
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[]\T1/pcr/m/n/9 gfit <- survfit(Surv(day1, day2, status) ~ batch, braking, id=
locomotive)[]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 6803--6803
[] \T1/pcr/m/n/9 xlab="Locomotive Age in Months", ylab="Mean cumulative nu
mber replacements")[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6806--6806
[]\T1/pcr/m/n/9 # natural target, an estimate of the number of replacements b
y a given time[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6808--6808
[]\T1/pcr/m/n/9 # When two valve seats failed at the same inspection, we need
to jitter one[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6810--6810
[]\T1/pcr/m/n/9 ties <- which(with(valveSeat, diff(id)==0 & diff(time)==0)) #
first of a tie[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6814--6814
[]\T1/pcr/m/n/9 vdata$time1 <- ifelse(!duplicated(vdata$id), 0, c(0, temp[-len
gth(temp)]))[]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 6841--6841
[] \T1/pcr/m/n/10 collapse=FALSE, weighted= (type %in% c("dfbeta", "dfbe
tas")), ...)[]
[3699]
[3700]
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[] \T1/pcr/m/n/10 type="pstate", collapse=FALSE, weighted= collapse, data.f
rame=FALSE,[]
[3701]
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[]\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[]
Underfull \hbox (badness 1043) in paragraph at lines 7046--7049
[]\T1/pcr/m/n/10 "dfbetas"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "working"[]\T1/pt
m/m/n/10 , []\T1/pcr/m/n/10 "ldcase"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lsresp
"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ldshape"[]\T1/ptm/m/n/10 , and
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[3704]
[3705]
[3706]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7353--7353
[]\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), lung)[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 7354--7354
[]\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), lung)[]
[3707]
[3708]
[3709]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 7544--7544
[]\T1/pcr/m/n/10 rttright(formula, data, weights, subset, na.action, times, id
, timefix = TRUE,
[3710]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 7627--7627
[]\T1/pcr/m/n/9 cdf <- cdf[!duplicated(aml$time[index], fromLast=TRUE)] # rem
ove duplicate times[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7631--7631
[]\T1/pcr/m/n/9 wt2 <- rttright(Surv(dtime, death) ~ hormon, rotterdam, times=
365*c(3, 5))[]
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder})
has been already used, duplicate ignored
<to be read again>
\relax
l.7635 ...ata from a soldering experiment}{solder}
[3711]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7690--7690
[]\T1/pcr/m/n/9 dummy <- expand.grid(Opening= c("S", "M", "L"), Solder=c("Thin
", "Thick"))[]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 7692--7692
[] \T1/pcr/m/n/9 dimnames=list(Opening= c("S", "M", "L"), Solder=c(
"Thin", "Thick")))[]
[3712]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 7752--7752
[]\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1,
col = 1,
[3713]
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[3716]
[3717]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8118--8118
[]\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r
r =expected,[]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8119--8119
[]\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli
ne = FALSE,[]
[3718]
[3719]
[3720]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 8277--8277
[] \T1/pcr/m/n/10 extend=FALSE, rmean=getOption(\TS1/pcr/m/n/10 '\T1/pcr/m/n/
10 survfit.rmean\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ), data.frame=FALSE, dosum, ...
)[]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8280--8280
[] \T1/pcr/m/n/10 extend=FALSE, rmean=getOption(\TS1/pcr/m/n/10 '\T1/pcr/m/n/
10 survfit.rmean\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ), data.frame=FALSE, ...)[]
[3721]
[3722]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 8471--8471
[] \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/
10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p
cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/
n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10
, \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T
S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[]
[3723]
[3724]
[3725]
Underfull \hbox (badness 1253) in paragraph at lines 8750--8753
[]\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 median[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10
quantile []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 plot []\T1/ptm/m/n/10 meth-ods
first con-struct a sur-vival curve us-ing
[3726]
[3727]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 8889--8889
[]\T1/pcr/m/n/10 survcheck(formula, data, subset, na.action, id, istate, istat
e0="(s0)",
[3728]
[3729]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9021--9021
[]\T1/pcr/m/n/10 survcondense(formula, data, subset, weights, na.action= na.pa
ss, id,
[3730]
[3731]
[3732]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9221--9221
[]\T1/pcr/m/n/9 check <- coxph(Surv(time, status) ~ factor(pat.karno) + strata
(inst), lung)[]
[3733]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 9227--9227
[] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1
, year=accept.dt),[]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 9252--9252
[] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[]
Underfull \hbox (badness 1038) in paragraph at lines 9294--9300
[]\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre
-dicted sur-vival
[3734]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 9346--9346
[] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[]
[3735]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9432--9432
[]\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival
by 1/2 years[]
[3736]
[3737]
[3738]
Underfull \hbox (badness 10000) in paragraph at lines 9652--9657
[][][]\T1/pcr/m/n/10 survfit.formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/
10 survfit.coxph[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 survfit.object[][
][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.survfit[][][][]\T1/ptm/m/n/10
,
[3739]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9672--9672
[] \T1/pcr/m/n/10 se.fit=TRUE, conf.int=.95, individual=FALSE, stype=2,
ctype,[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 9673--9673
[] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit",
"arcsin"),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 9678--9678
[] \T1/pcr/m/n/10 se.fit=FALSE, conf.int=.95, individual=FALSE, stype=2
, ctype,[]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 9679--9679
[] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit",
"arcsin"),[]
[3740]
[3741]
[3742]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9901--9901
[] \T1/pcr/m/n/10 stype=1, ctype=1, id, cluster, robust, istate, timefi
x=TRUE,[]
[3743]
Underfull \hbox (badness 4441) in paragraph at lines 10042--10052
[]\T1/ptm/m/n/10 by de-fault, the surv-fit rou-tines only re-turn in-for-ma-tio
n at the
[3744]
Underfull \hbox (badness 2653) in paragraph at lines 10054--10059
\T1/pcr/m/n/10 ctype=1[]\T1/ptm/m/n/10 , "fleming-harrington" which is equiv-a-
lent to []\T1/pcr/m/n/10 stype=2,
[3745]
[3746]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10242--10242
[]\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored
(status=3),[]
[3747]
[3748]
[3749]
[3750]
[3751]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 10674--10674
[]\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
survtype,
[3752]
Underfull \hbox (badness 1354) in paragraph at lines 10715--10719
[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
e time range
[3753]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 10761--10761
[]\T1/pcr/m/n/10 survConcordance(formula, data, weights, subset, na.action) #
use concordance
[3754]
[3755]
Underfull \hbox (badness 2035) in paragraph at lines 10925--10932
\T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][][]\T1/pcr/m/n/10 su
rvreg.distributions[][][][]\T1/ptm/m/n/10 .
Underfull \hbox (badness 10000) in paragraph at lines 10925--10932
\T1/ptm/m/n/10 These in-clude []\T1/pcr/m/n/10 "weibull"[]\T1/ptm/m/n/10 , []\T
1/pcr/m/n/10 "exponential"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "gaussian"[]\T1/p
tm/m/n/10 ,
Underfull \hbox (badness 1297) in paragraph at lines 10925--10932
[]\T1/pcr/m/n/10 "logistic"[]\T1/ptm/m/n/10 ,[]\T1/pcr/m/n/10 "lognormal" []\T1
/ptm/m/n/10 and []\T1/pcr/m/n/10 "loglogistic"[]\T1/ptm/m/n/10 . Oth-er-wise, i
t is
[3756]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11015--11015
[]\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[]
[3757]
[3758]
[3759]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 11172--11172
[] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[]
[3760]
[3761]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11304--11304
[] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x
^2*temp -1))[]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 11307--11307
[] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[]
[3762]
[3763]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11483--11483
[]\T1/pcr/m/n/9 pfit2 <- pyears(Surv(years, death) ~ fgrp + agegrp, scale =100
0, data=test)[]
[3764]
[3765]
[3766]
[3767]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11712--11712
[]\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic
al trial plus[]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11713--11713
[]\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data
set has data[]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11719--11719
[] \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day
, alk.phos))[]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 11721--11721
[]\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil
i), data=pbc2)[]
[3768]
[3769]
[3770]
[3771]
[3772]
[3773]
[3774]
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[]\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l
inear",[]
[3775]
[3776]
[3777])
[3778] (./fullrefman.ind
[3779]
[3780]
[3781]
[3782]
[3783]
[3784]
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[3802]
[3803]
[3804]
[3805]
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[]| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.bs.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.gp.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 ,
[3806]
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[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.sz.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 ,
[3807]
[3808]
[3809]
[3810]
[3811]
[3812]
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[]| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.bs.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.gp.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 ,
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[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 ,
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[]\T1/pcr/m/n/10 %&%,diagonalMatrix,denseMatrix-method
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[]\T1/pcr/m/n/10 %&%,diagonalMatrix,diagonalMatrix-method
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[]\T1/pcr/m/n/10 %&%,diagonalMatrix,matrix-method
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[]\T1/pcr/m/n/10 %&%,diagonalMatrix,vector-method
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[]\T1/pcr/m/n/10 %&%,matrix,diagonalMatrix-method
[3829]
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[]\T1/pcr/m/n/10 %&%,sparseVector,sparseVector-method
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[]\T1/pcr/m/n/10 %&%,vector,diagonalMatrix-method
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[]\T1/pcr/m/n/10 all.equal,abIndex,numLike-method
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[]\T1/pcr/m/n/10 all.equal,sparseVector,vector-method
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[]\T1/pcr/m/n/10 all.equal,vector,sparseVector-method
[3832]
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[]\T1/pcr/m/n/10 Arith,CsparseMatrix,CsparseMatrix-method
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[]\T1/pcr/m/n/10 Arith,CsparseMatrix,numeric-method
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[]\T1/pcr/m/n/10 Arith,ddenseMatrix,logical-method
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[]\T1/pcr/m/n/10 Arith,ddenseMatrix,numeric-method
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[]\T1/pcr/m/n/10 Arith,ddenseMatrix,sparseVector-method
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[]\T1/pcr/m/n/10 Arith,dgCMatrix,dgCMatrix-method
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[]\T1/pcr/m/n/10 Arith,dgeMatrix,dgeMatrix-method
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[]\T1/pcr/m/n/10 Arith,dgeMatrix,sparseVector-method
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[]\T1/pcr/m/n/10 Arith,dsCMatrix,dsCMatrix-method
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[]\T1/pcr/m/n/10 Arith,dsparseMatrix,logical-method
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[]\T1/pcr/m/n/10 Arith,dsparseMatrix,nsparseMatrix-method
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[]\T1/pcr/m/n/10 Arith,dsparseMatrix,numeric-method
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[]\T1/pcr/m/n/10 Arith,dsparseVector,dsparseVector-method
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[]\T1/pcr/m/n/10 Arith,dtCMatrix,dtCMatrix-method
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[]\T1/pcr/m/n/10 Arith,lgCMatrix,lgCMatrix-method
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[]\T1/pcr/m/n/10 Arith,lgeMatrix,lgeMatrix-method
[3833]
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[]\T1/pcr/m/n/10 Arith,lgTMatrix,lgTMatrix-method
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[]\T1/pcr/m/n/10 Arith,logical,ddenseMatrix-method
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[]\T1/pcr/m/n/10 Arith,logical,dsparseMatrix-method
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[]\T1/pcr/m/n/10 Arith,lsparseMatrix,Matrix-method
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[]\T1/pcr/m/n/10 Arith,lsparseMatrix,nsparseMatrix-method
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[]\T1/pcr/m/n/10 Arith,Matrix,lsparseMatrix-method
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[]\T1/pcr/m/n/10 Arith,Matrix,nsparseMatrix-method
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[]\T1/pcr/m/n/10 Arith,ngeMatrix,ngeMatrix-method
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[]\T1/pcr/m/n/10 Arith,nsparseMatrix,dsparseMatrix-method
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[]\T1/pcr/m/n/10 Arith,nsparseMatrix,lsparseMatrix-method
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[]\T1/pcr/m/n/10 Arith,nsparseMatrix,Matrix-method
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[]\T1/pcr/m/n/10 Arith,numeric,CsparseMatrix-method
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[]\T1/pcr/m/n/10 Arith,numeric,ddenseMatrix-method
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[]\T1/pcr/m/n/10 Arith,numeric,dsparseMatrix-method
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[]\T1/pcr/m/n/10 Arith,sparseVector,ddenseMatrix-method
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[]\T1/pcr/m/n/10 Arith,sparseVector,dgeMatrix-method
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[]\T1/pcr/m/n/10 Arith,sparseVector,sparseVector-method
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[]\T1/pcr/m/n/10 Arith,triangularMatrix,diagonalMatrix-method
[3834]
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[]\T1/pcr/m/n/10 aspell_write_personal_dictionary_file
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)\T1/ptm/m/n/10 ,
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ptm/m/n/10 ,
[3840]
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[]\T1/pcr/m/n/10 chol2inv,triangularMatrix-method
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[]\T1/pcr/m/n/10 Cholesky,triangularMatrix-method
[3842]
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[3843]
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[]\T1/pcr/m/n/10 coerce,BunchKaufman,dtrMatrix-method
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[]\T1/pcr/m/n/10 coerce,CHMsimpl,dtCMatrix-method
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[]\T1/pcr/m/n/10 coerce,CHMsuper,dgCMatrix-method
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[]\T1/pcr/m/n/10 coerce,Cholesky,dtrMatrix-method
[3845]
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[]\T1/pcr/m/n/10 coerce,copMatrix,corMatrix-method
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[]\T1/pcr/m/n/10 coerce,corMatrix,copMatrix-method
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[]\T1/pcr/m/n/10 coerce,dgCMatrix,matrix.csc-method
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[]\T1/pcr/m/n/10 coerce,dgRMatrix,matrix.csr-method
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[]\T1/pcr/m/n/10 coerce,dgTMatrix,matrix.coo-method
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[]\T1/pcr/m/n/10 coerce,diagonalMatrix,symmetricMatrix-method
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[]\T1/pcr/m/n/10 coerce,dsyMatrix,corMatrix-method
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[]\T1/pcr/m/n/10 coerce,factor,sparseMatrix-method
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[]\T1/pcr/m/n/10 coerce,generalMatrix,packedMatrix-method
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[]\T1/pcr/m/n/10 coerce,graph,CsparseMatrix-method
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[]\T1/pcr/m/n/10 coerce,Matrix,CsparseMatrix-method
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[]\T1/pcr/m/n/10 coerce,matrix,CsparseMatrix-method
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[]\T1/pcr/m/n/10 coerce,Matrix,ddenseMatrix-method
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[]\T1/pcr/m/n/10 coerce,Matrix,denseMatrix-method
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[]\T1/pcr/m/n/10 coerce,Matrix,diagonalMatrix-method
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[3846]
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[]\T1/pcr/m/n/10 coerce,Matrix,generalMatrix-method
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[]\T1/pcr/m/n/10 coerce,Matrix,triangularMatrix-method
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[]\T1/pcr/m/n/10 coerce,Matrix,unpackedMatrix-method
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[]\T1/pcr/m/n/10 coerce,matrix.coo,dgCMatrix-method
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[3847]
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[3848]
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replaced by a fixed one
pdfTeX warning (dest): name{Rfn.xfig} has been referenced but does not exist, r
eplaced by a fixed one
pdfTeX warning (dest): name{Rfn.roundX} has been referenced but does not exist,
replaced by a fixed one
pdfTeX warning (dest): name{Rfn.getNamespace} has been referenced but does not
exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.asNamespace} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.formalArgs} has been referenced but does not ex
ist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.base.Rdash.deprecated} has been referenced but
does not exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.base.Rdash.defunct} has been referenced but doe
s not exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.isRematched} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist,
replaced by a fixed one
</usr/share/texmf-dist/fonts/type1/public/amsfonts/cmextra/cmbsy7.pfb></usr/sha
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usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmmib10.pfb></usr/share/tex
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texmf-dist/fonts/type1/public/amsfonts/cm/cmsy5.pfb></usr/share/texmf-dist/font
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amsfonts/cm/cmtt10.pfb></usr/share/texmf-dist/fonts/type1/public/amsfonts/symbo
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are/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texmf-dist/fonts/ty
pe1/urw/times/utmri8a.pfb>
Output written on fullrefman.pdf (3990 pages, 10332771 bytes).
Transcript written on fullrefman.log.
make[1]: Leaving directory '/build/r/src/R-4.5.1/doc/manual'
make: [Makefile:297: install-pdf] Error 2 (ignored)
make[1]: Entering directory '/build/r/src/R-4.5.1/src/include'
make[1]: 'Rmath.h' is up to date.
make[1]: Leaving directory '/build/r/src/R-4.5.1/src/include'
==> Tidying install...
-> Removing empty directories...
-> Removing libtool files...
-> Purging unwanted files...
-> Removing static library files...
-> Stripping unneeded symbols from binaries and libraries...
-> Compressing man and info pages...
==> Checking for packaging issues...
==> WARNING: Package contains reference to $srcdir
usr/share/doc/R/NEWS.pdf
==> Creating package "r"...
-> Generating .PKGINFO file...
-> Generating .BUILDINFO file...
-> Generating .MTREE file...
-> Compressing package...
==> Leaving fakeroot environment.
==> Finished making: r 4.5.1-1 (Fri Jun 13 10:00:14 2025)
==> Cleaning up...