R

Install Rtools for Windows users

See http://goo.gl/gYh6C for a step-by-step instruction (based on Rtools30.exe) with screenshot. Note that in the step of 'Select Components', the default is 'Package authoring installation'. But we want 'Full installation to build 32 or 64 bit R'; that is, check all components (including tcl/tk) available. The "extra" files will be stored in subdirectories of the R source home directory. These files are not needed to build packages, only to build R itself. By default, the 32-bit R source home is C:\R and 64-bit source home is C:\R64. After the installation, these two directories will contain a new directory 'Tcl'.

My preferred way is not to check the option of setting PATH environment. But I manually add the followings to the PATH environment (based on Rtools v3.2.2)

c:\Rtools\bin;
c:\Rtools\gcc-4.6.3\bin;
C:\Program Files\R\R-3.2.2\bin\i386;

We can make our life easy by creating a file <Rcommand.bat> with the content (also useful if you have C:\cygwin\bin in your PATH although cygwin setup will not do it automatically for you.)

PS. I put <Rcommand.bat> under C:\Program Files\R folder. I create a shortcut called 'Rcmd' on desktop. I enter C:\Windows\System32\cmd.exe /K "Rcommand.bat" in the Target entry and "C:\Program Files\R" in Start in entry.

@echo off
set PATH=C:\Rtools\bin;c:\Rtools\gcc-4.6.3\bin
set PATH=C:\Program Files\R\R-3.2.2\bin\i386;%PATH%
set PKG_LIBS=`Rscript -e "Rcpp:::LdFlags()"`
set PKG_CPPFLAGS=`Rscript -e "Rcpp:::CxxFlags()"`
echo Setting environment for using R
cmd

So we can open the Command Prompt anywhere and run <Rcommand.bat> to get all environment variables ready! On Windows Vista, 7 and 8, we need to run it as administrator. OR we can change the security of the property so the current user can have an executive right.

Windows Toolset

Note that R on Windows supports Mingw-w64 (not Mingw which is a separate project). See here for the issue of developing a Qt application that links against R using Rcpp. And http://qt-project.org/wiki/MinGW is the wiki for compiling Qt using MinGW and MinGW-w64.

Build R from its source on Windows OS (not cross compile on Linux)

Reference: https://cran.r-project.org/doc/manuals/R-admin.html#Installing-R-under-Windows

First we try to build 32-bit R (tested on R 3.2.2 using Rtools33). At the end I will see how to build a 64-bit R.

Download https://www.stats.ox.ac.uk/pub/Rtools/goodies/multilib/local320.zip (read https://www.stats.ox.ac.uk/pub/Rtools/libs.html). create an empty directory, say c:/R/extsoft, and unpack it in that directory by e.g.

unzip local320.zip -d c:/R/extsoft

Tcl: two methods

1. Download tcl file from http://www.stats.ox.ac.uk/pub/Rtools/R_Tcl_8-5-8.zip. Unzip and put 'Tcl' into R_HOME folder.
2. If you have chosen a full installation when running Rtools, then copy C:/R/Tcl or C:/R64/Tcl (not the same) to R_HOME folder.

Open a command prompt as Administrator"

set PATH=c:\Rtools\bin;c:\Rtools\gcc-4.6.3\bin
set PATH=%PATH%;C:\Users\brb\Downloads\R-3.2.2\bin\i386;c:\windows;c:\windows\system32
set TMPDIR=C:/tmp

tar --no-same-owner -xf R-3.2.2.tar.gz
cp -R c:\R64\Tcl c:\Users\brb\Downloads\R-3.2.2

cd R-3.2.2\src\gnuwin32
cp MkRules.dist MkRules.local
# Modify MkRules.local file; specifically uncomment + change the following 2 flags.
# LOCAL_SOFT = c:/R/extsoft
# EXT_LIBS = $(LOCAL_SOFT)

make

If we see an error of texi2dvi() complaining pdflatex is not available, it means a vanilla R is successfully built.

If we want to build the recommended packages (MASS, lattice, Matrix, ...) as well, run (check all make option in <R_HOME\src\gnuwin32\Makefile>)

make recommended

If we need to rebuild R for whatever reason, run

make clean

If we want to build R with debug information, run

make DEBUG=T

NB: 1. The above works for creating 32-bit R from its source. If we want to build 64-bit R from its source, we need to modify MkRules.local file to turn on the MULTI flag.

MULTI = 64

and reset the PATH variable

set PATH=c:\Rtools\bin;c:\Rtools\gcc-4.6.3\bin
set PATH=%PATH%;C:\Users\brb\Downloads\R-3.2.2\bin\x64;c:\windows;c:\windows\system32

I don't need to mess up with other flags like BINPREF64, M_ARCH, AS_ARCH, RC_ARCH, DT_ARCH or even WIN. The note http://www.stat.yale.edu/~jay/Admin3.3.pdf is kind of old and is not needed. 2. If we have already built 32-bit R and want to continue to build 64-bit R, it is not enough to run 'make clean' before run 'make' again since it will give an error message incompatible ./libR.dll.a when searching for -lR in building Rgraphapp.dll. In fact, libR.dll.a can be cleaned up if we run 'make distclean' but it will also wipe out /bin/i386 folder:(

See also Create_a_standalone_Rmath_library below about how to create and use a standalone Rmath library in your own C/C++/Fortran program. For example, if you want to know the 95-th percentile of a T distribution or generate a bunch of random variables, you don't need to search internet to find a library; you can just use Rmath library.

Compile and install an R package

Command line

cd C:\Documents and Settings\brb
wget http://www.bioconductor.org/packages/2.11/bioc/src/contrib/affxparser_1.30.2.tar.gz
C:\progra~1\r\r-2.15.2\bin\R CMD INSTALL --build affxparser_1.30.2.tar.gz

N.B. the --build is used to create a binary package (i.e. affxparser_1.30.2.zip). In the above example, it will both install the package and create a binary version of the package. If we don't want the binary package, we can ignore the flag.

R console

install.packages("C:/Users/USERNAME/Downloads/DESeq2paper_1.3.tar.gz", repos=NULL, type="source")

See Chapter 6 of R Installation and Administration

Check/Upload to CRAN

http://win-builder.r-project.org/

64 bit toolchain

See January 2010 email https://stat.ethz.ch/pipermail/r-devel/2010-January/056301.html and R-Admin manual.

From R 2.11.0 there is 64 bit Windows binary for R.

Install R using binary package on Linux OS

Ubuntu/Debian

https://cran.rstudio.com/bin/linux/ubuntu/. For more info about GPG stuff, see GPG Authentication_key.

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
# Some people have reported difficulties using this approach. The issue is usually related to a firewall blocking port 11371
# So alternatively (no sudo is needed in front of the gpg command)
# gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
# gpg -a --export E084DAB9 | sudo apt-key add -
sudo nano /etc/apt/sources.list
# For Ubuntu 14.04 (codename is trusty; https://wiki.ubuntu.com/Releases)
# deb https://cran.rstudio.com/bin/linux/ubuntu trusty/
sudo apt-get update
sudo apt-get install r-base

Manually create the public key file if the gpg command failed.

Redhat el6

It should be pretty easy to install via the EPEL: http://fedoraproject.org/wiki/EPEL

Just follow the instructions to enable the EPEL and then from the CLI as root:

yum install R

or via sudo:

sudo yum install R

Install R from source (ix86, x86_64 and arm platforms, Linux system)

Debian system (focus on arm architecture with notes from x86 system)

Simplest configuration

<Method 1 of installing requirements>

On my debian system in Pogoplug (armv5), Raspberry Pi (armv6) OR Beaglebone Black & Udoo(armv7), I can compile R. See R's admin manual. If the OS needs x11, I just need to install 2 required packages.

• install gfortran: apt-get install build-essential gfortran (gfortran is not part of build-essential)
• install readline library: apt-get install libreadline5-dev (pogoplug), apt-get install libreadline6-dev (raspberry pi/BBB), apt-get install libreadline-dev (Ubuntu)

Note: if I need X11, I should install

• libX11 and libX11-devel, libXt, libXt-devel (for fedora)
• libx11-dev (for debian) or xorg-dev (for pogoplug/raspberry pi/BBB/Odroid debian). See here for the difference of x11 and Xorg.

and optional

• texinfo (to fix 'WARNING: you cannot build info or HTML versions of the R manuals')

<Method 2 of installing requirements (recommended)>

Note that it is also safe to install required tools via (please run nano /etc/apt/sources.list to include the repository of your favorite R mirror and also run sudo apt-get update first)

sudo apt-get build-dep r-base

The above command will install R dependence like jdk, tcl, tex, etc. The apt-get build-dep gave a more complete list than apt-get install r-base-dev for some reasons.

[Arm architecture] I also run apt-get install readline-common. I don't know if this is necessary. If x11 is not needed or not available (eg Pogoplug), I can add --with-x=no option in ./configure command. If R will be called from other applications such as Rserve, I can add --enable-R-shlib option in ./configure command. Check out ./configure --help to get a complete list of all options.

After running

wget https://cran.rstudio.com/src/base/R-3/R-3.2.3.tar.gz
tar xzvf R-3.2.3.tar.gz
cd R-3.2.3
./configure --enable-R-shlib

(--enable-R-shlib option will create a shared R library libR.so in $RHOME/lib subdirectory. This allows R to be embedded in other applications. See Embedding R.) I got

R is now configured for armv5tel-unknown-linux-gnueabi

  Source directory:          .
  Installation directory:    /usr/local

  C compiler:                gcc -std=gnu99  -g -O2
  Fortran 77 compiler:       gfortran  -g -O2

  C++ compiler:              g++  -g -O2
  Fortran 90/95 compiler:    gfortran -g -O2
  Obj-C compiler:

  Interfaces supported:
  External libraries:        readline
  Additional capabilities:   NLS
  Options enabled:           shared R library, shared BLAS, R profiling

  Recommended packages:      yes

configure: WARNING: you cannot build info or HTML versions of the R manuals
configure: WARNING: you cannot build PDF versions of the R manuals
configure: WARNING: you cannot build PDF versions of vignettes and help pages
configure: WARNING: I could not determine a browser
configure: WARNING: I could not determine a PDF viewer

After that, we can run make to create R binary. If the computer has multiple cores, we can run make in parallel by using the -j flag (for example, '-j4' means to run 4 jobs simultaneously). We can also add time command in front of make to report the make time (useful for benchmark).

make   
# make -j4
# time make

PS 1. On my raspberry pi machine, it shows R is now configured for armv6l-unknown-linux-gnueabihf and on Beaglebone black it shows R is now configured for armv7l-unknown-linux-gnueabihf.

PS 2. On my Beaglebone black, it took 2 hours to run 'make', Raspberry Pi 2 took 1 hour, Odroid XU4 took 23 minutes and it only took 5 minutes to run 'make -j 12' on my Xeon W3690 @ 3.47Ghz (6 cores with hyperthread) based on R 3.1.2. The timing is obtained by using 'time' command as described above.

PS 3. On my x86 system, it shows

R is now configured for x86_64-unknown-linux-gnu

  Source directory:          .
  Installation directory:    /usr/local

  C compiler:                gcc -std=gnu99  -g -O2
  Fortran 77 compiler:       gfortran  -g -O2

  C++ compiler:              g++  -g -O2
  Fortran 90/95 compiler:    gfortran -g -O2
  Obj-C compiler:

  Interfaces supported:      X11, tcltk
  External libraries:        readline, lzma
  Additional capabilities:   PNG, JPEG, TIFF, NLS, cairo
  Options enabled:           shared R library, shared BLAS, R profiling, Java

  Recommended packages:      yes

[arm] However, make gave errors for recommanded packages like KernSmooth, MASS, boot, class, cluster, codetools, foreign, lattice, mgcv, nlme, nnet, rpart, spatial, and survival. The error stems from gcc: SHLIB_LIBADD: No such file or directory. Note that I can get this error message even I try install.packages("MASS", type="source"). A suggested fix is here; adding perl = TRUE in sub() call for two lines in src/library/tools/R/install.R file. However, I got another error shared object 'MASS.so' not found. See also http://ftp.debian.org/debian/pool/main/r/r-base/. To build R without recommended packages like ./configure --without-recommended.

make[1]: Entering directory `/mnt/usb/R-2.15.2/src/library/Recommended'
make[2]: Entering directory `/mnt/usb/R-2.15.2/src/library/Recommended'
begin installing recommended package MASS
* installing *source* package 'MASS' ...
** libs
make[3]: Entering directory `/tmp/Rtmp4caBfg/R.INSTALL1d1244924c77/MASS/src'
gcc -std=gnu99 -I/mnt/usb/R-2.15.2/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c MASS.c -o MASS.o
gcc -std=gnu99 -I/mnt/usb/R-2.15.2/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c lqs.c -o lqs.o
gcc -std=gnu99 -shared -L/usr/local/lib -o MASSSHLIB_EXT MASS.o lqs.o SHLIB_LIBADD -L/mnt/usb/R-2.15.2/lib -lR
gcc: SHLIB_LIBADD: No such file or directory
make[3]: *** [MASSSHLIB_EXT] Error 1
make[3]: Leaving directory `/tmp/Rtmp4caBfg/R.INSTALL1d1244924c77/MASS/src'
ERROR: compilation failed for package 'MASS'
* removing '/mnt/usb/R-2.15.2/library/MASS'
make[2]: *** [MASS.ts] Error 1
make[2]: Leaving directory `/mnt/usb/R-2.15.2/src/library/Recommended'
make[1]: *** [recommended-packages] Error 2
make[1]: Leaving directory `/mnt/usb/R-2.15.2/src/library/Recommended'
make: *** [stamp-recommended] Error 2
root@debian:/mnt/usb/R-2.15.2#
root@debian:/mnt/usb/R-2.15.2# bin/R

R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: armv5tel-unknown-linux-gnueabi (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(MASS)
Error in library(MASS) : there is no package called 'MASS'
> library()
Packages in library '/mnt/usb/R-2.15.2/library':

base                    The R Base Package
compiler                The R Compiler Package
datasets                The R Datasets Package
grDevices               The R Graphics Devices and Support for Colours
                        and Fonts
graphics                The R Graphics Package
grid                    The Grid Graphics Package
methods                 Formal Methods and Classes
parallel                Support for Parallel computation in R
splines                 Regression Spline Functions and Classes
stats                   The R Stats Package
stats4                  Statistical Functions using S4 Classes
tcltk                   Tcl/Tk Interface
tools                   Tools for Package Development
utils                   The R Utils Package
> Sys.info()["machine"]
   machine
"armv5tel"
> gc()
         used (Mb) gc trigger (Mb) max used (Mb)
Ncells 170369  4.6     350000  9.4   350000  9.4
Vcells 163228  1.3     905753  7.0   784148  6.0

See http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=679180

PS 4. The complete log of building R from source is in here File:Build R log.txt

Full configuration

  Interfaces supported:      X11, tcltk
  External libraries:        readline
  Additional capabilities:   PNG, JPEG, TIFF, NLS, cairo
  Options enabled:           shared R library, shared BLAS, R profiling, Java

Update: R 3.0.1 on Beaglebone Black (armv7a) + Ubuntu 13.04

See the page here.

Update: R 3.1.3 & R 3.2.0 on Raspberry Pi 2

It took 134m to run 'make -j 4' on RPi 2 using R 3.1.3.

But I got an error when I ran './configure; make -j 4' using R 3.2.0. The errors start from compiling <main/connections.c> file with 'undefined reference to ....'. The gcc version is 4.6.3.

Install all dependencies for building R

This is a comprehensive list. This list is even larger than r-base-dev.

root@debian:/mnt/usb/R-2.15.2# apt-get build-dep r-base
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages will be REMOVED:
  libreadline5-dev
The following NEW packages will be installed:
  bison ca-certificates ca-certificates-java debhelper defoma ed file fontconfig gettext
  gettext-base html2text intltool-debian java-common libaccess-bridge-java
  libaccess-bridge-java-jni libasound2 libasyncns0 libatk1.0-0 libaudit0 libavahi-client3
  libavahi-common-data libavahi-common3 libblas-dev libblas3gf libbz2-dev libcairo2
  libcairo2-dev libcroco3 libcups2 libdatrie1 libdbus-1-3 libexpat1-dev libflac8
  libfontconfig1-dev libfontenc1 libfreetype6-dev libgif4 libglib2.0-dev libgtk2.0-0
  libgtk2.0-common libice-dev libjpeg62-dev libkpathsea5 liblapack-dev liblapack3gf libnewt0.52
  libnspr4-0d libnss3-1d libogg0 libopenjpeg2 libpango1.0-0 libpango1.0-common libpango1.0-dev
  libpcre3-dev libpcrecpp0 libpixman-1-0 libpixman-1-dev libpng12-dev libpoppler5 libpulse0
  libreadline-dev libreadline6-dev libsm-dev libsndfile1 libthai-data libthai0 libtiff4-dev
  libtiffxx0c2 libunistring0 libvorbis0a libvorbisenc2 libxaw7 libxcb-render-util0
  libxcb-render-util0-dev libxcb-render0 libxcb-render0-dev libxcomposite1 libxcursor1
  libxdamage1 libxext-dev libxfixes3 libxfont1 libxft-dev libxi6 libxinerama1 libxkbfile1
  libxmu6 libxmuu1 libxpm4 libxrandr2 libxrender-dev libxss-dev libxt-dev libxtst6 luatex m4
  openjdk-6-jdk openjdk-6-jre openjdk-6-jre-headless openjdk-6-jre-lib openssl pkg-config
  po-debconf preview-latex-style shared-mime-info tcl8.5-dev tex-common texi2html texinfo
  texlive-base texlive-binaries texlive-common texlive-doc-base texlive-extra-utils
  texlive-fonts-recommended texlive-generic-recommended texlive-latex-base texlive-latex-extra
  texlive-latex-recommended texlive-pictures tk8.5-dev tzdata-java whiptail x11-xkb-utils
  x11proto-render-dev x11proto-scrnsaver-dev x11proto-xext-dev xauth xdg-utils xfonts-base
  xfonts-encodings xfonts-utils xkb-data xserver-common xvfb zlib1g-dev
0 upgraded, 136 newly installed, 1 to remove and 0 not upgraded.
Need to get 139 MB of archives.
After this operation, 410 MB of additional disk space will be used.
Do you want to continue [Y/n]?

Instruction of installing a development version of R under Ubuntu

https://github.com/wch/r-source/wiki (works on Ubuntu 12.04)

Note that texi2dvi has to be installed first to avoid the following error. It is better to follow the Ubuntu instruction (https://github.com/wch/r-source/wiki/Ubuntu-build-instructions) when we work on Ubuntu OS.

$ (cd doc/manual && make front-matter html-non-svn)
creating RESOURCES
/bin/bash: number-sections: command not found
make: [../../doc/RESOURCES] Error 127 (ignored)

To build R, run the following script. To run the built R, type 'bin/R'.

# Get recommended packages if necessary
tools/rsync-recommended

R_PAPERSIZE=letter                              \
R_BATCHSAVE="--no-save --no-restore"            \
R_BROWSER=xdg-open                              \
PAGER=/usr/bin/pager                            \
PERL=/usr/bin/perl                              \
R_UNZIPCMD=/usr/bin/unzip                       \
R_ZIPCMD=/usr/bin/zip                           \
R_PRINTCMD=/usr/bin/lpr                         \
LIBnn=lib                                       \
AWK=/usr/bin/awk                                \
CC="ccache gcc"                                 \
CFLAGS="-ggdb -pipe -std=gnu99 -Wall -pedantic" \
CXX="ccache g++"                                \
CXXFLAGS="-ggdb -pipe -Wall -pedantic"          \
FC="ccache gfortran"                            \
F77="ccache gfortran"                           \
MAKE="make"                                     \
./configure                                     \
    --prefix=/usr/local/lib/R-devel             \
    --enable-R-shlib                            \
    --with-blas                                 \
    --with-lapack                               \
    --with-readline

#CC="clang -O3"                                  \
#CXX="clang++ -03"                               \


# Workaround for explicit SVN check introduced by
# https://github.com/wch/r-source/commit/4f13e5325dfbcb9fc8f55fc6027af9ae9c7750a3

# Need to build FAQ
(cd doc/manual && make front-matter html-non-svn)

rm -f non-tarball

# Get current SVN revsion from git log and save in SVN-REVISION
echo -n 'Revision: ' > SVN-REVISION
git log --format=%B -n 1 \
  | grep "^git-svn-id" \
  | sed -E 's/^git-svn-id: https:\/\/svn.r-project.org\/R\/.*?@([0-9]+).*$/\1/' \
  >> SVN-REVISION
echo -n 'Last Changed Date: ' >>  SVN-REVISION
git log -1 --pretty=format:"%ad" --date=iso | cut -d' ' -f1 >> SVN-REVISION

# End workaround

# Set this to the number of cores on your computer
make --jobs=4

If we DO NOT use -depth option in git clone command, we can use git checkout SHA1 (40 characters) to get a certain version of code.

git checkout f1d91a0b34dbaa6ac807f3852742e3d646fbe95e  # plot(<dendrogram>): Bug 15215 fixed 5/2/2015
git checkout trunk                                     # switch back to trunk

The svn revision number for a certain git revision can be found in the blue box on the github website (git-svn-id). For example, this revision has an svn revision number 68302 even the current trunk is 68319.

Now suppose we have run 'git check trunk', create a devel'R successfully. If we want to build R for a certain svn or git revision, we run 'git checkout SHA1', 'make distclean', code to generate the SVN-REVISION file (it will update this number) and finally './configure' & 'make'.

time (./configure --with-recommended-packages=no && make --jobs=5)

The timing is 4m36s if I skip recommended packages and 7m37s if I don't skip. This is based on Xeon W3690 @ 3.47GHz.

The full bash script is available on Github Gist.

Install multiple versions of R on Ubuntu

• Instruction_of_installing_a_development_version_of_R_under_Ubuntu. You can launch the devel version of R using 'RD' command.
• http://stackoverflow.com/questions/24019503/installing-multiple-versions-of-r
• http://r.789695.n4.nabble.com/Installing-different-versions-of-R-simultaneously-on-Linux-td879536.html
• http://stackoverflow.com/questions/8343686/how-to-install-2-different-r-versions-on-debian

To install the devel version of R alongside the current version of R. See this post. For example you need a script that will build r-devel, but install it in a location different from the stable version of R (eg use --prefix=/usr/local/R-X.Y.Z in the config command). Note that the executable is installed in “/usr/local/lib/R-devel/bin”, but that can be changed to others like "/usr/local/bin".

Another fancy way is to use docker.

Minimal installation of R from source

Assume we have installed g++ (or build-essential) and gfortran (Ubuntu has only gcc pre-installed, but not g++),

sudo apt-get install build-essential gfortran

we can go ahead to build a minimal R.

wget http://cran.rstudio.com/src/base/R-3/R-3.1.1.tar.gz
tar -xzvf R-3.1.1.tar.gz; cd R-3.1.1
./configure --with-x=no --with-recommended-packages=no --with-readline=no

See ./configure --help. This still builds the essential packages like base, compiler, datasets, graphics, grDevices, grid, methods, parallel, splines, stats, stats4, tcltk, tools, and utils.

Note that at the end of 'make', it shows an error of 'cannot find any java interpreter. Please make sure java is on your PATH or set JAVA_HOME correspondingly'. Even with the error message, we can use R by typing bin/R.

To check whether we have Java installed, type 'java -version'.

$ java -version
java version "1.6.0_32"
OpenJDK Runtime Environment (IcedTea6 1.13.4) (6b32-1.13.4-4ubuntu0.12.04.2)
OpenJDK 64-Bit Server VM (build 23.25-b01, mixed mode)

R CMD

• R CMD build someDirectory - create a package
• R CMD check somePackage_1.2-3.tar.gz - check a package
• R CMD INSTALL somePackage_1.2-3.tar.gz - install a package from its source

bin/R (shell script) and bin/exec/R (binary executable) on Linux OS

bin/R is just a shell script to launch bin/exec/R program. So if we try to run the following program

# test.R
cat("-- reading arguments\n", sep = "");
cmd_args = commandArgs();
for (arg in cmd_args) cat("  ", arg, "\n", sep="");

from command line like

$ R --slave --no-save --no-restore --no-environ --silent --args arg1=abc < test.R
# OR using Rscript
-- reading arguments
  /home/brb/R-3.0.1/bin/exec/R
  --slave
  --no-save
  --no-restore
  --no-environ
  --silent
  --args
  arg1=abc

we can see R actually call bin/exec/R program.

Ubuntu/Debian

Since the R packages XML & RCurl are frequently used by other packages (e.g. miniCRAN), it is useful to run the following so the install.packages("RCurl") and install.packages("XML") can work without hiccups.

sudo apt-get update
sudo apt-get install libxml2-dev
sudo apt-get install libcurl4-openssl-dev

CentOS 6.x

Install build-essential (make, gcc, gdb, ...).

su
yum groupinstall "Development Tools"
yum install kernel-devel kernel-headers

Install readline and X11 (probably not necessary if we use ./configure --with-x=no)

yum install readline-devel 
yum install libX11 libX11-devel libXt libXt-devel

Install libpng (already there) and libpng-devel library. This is for web application purpose because png (and possibly svg) is a standard and preferred graphics format. If we want to output different graphics formats, we have to follow the guide in R-admin manual to install extra graphics libraries in Linux.

yum install libpng-devel
rpm -qa | grep "libpng"
# make sure both libpng and libpng-devel exist.

Install Java. One possibility is to download from Oracle. We want to download jdk-7u45-linux-x64.rpm and jre-7u45-linux-x64.rpm (assume 64-bit OS).

rpm -Uvh jdk-7u45-linux-x64.rpm
rpm -Uvh jre-7u45-linux-x64.rpm
# Check
java -version

Now we are ready to build R by using "./configure" and then "make" commands.

We can make R accessible from any directory by either run "make install" command or creating an R_HOME environment variable and export it to PATH environment variable, such as

export R_HOME="path to R"
export PATH=$PATH:$R_HOME/bin 

Web Applications

See also CRAN Task View: Web Technologies and Services

Create HTML5 web and slides using knitr, rmarkdown and pandoc

http://www.gastonsanchez.com/depot/knitr-slides. The HTML5 slides work on my IE 8 too.

HTML5 slides examples

• http://yihui.name/slides/knitr-slides.html
• http://yihui.name/slides/2012-knitr-RStudio.html
• http://yihui.name/slides/2011-r-dev-lessons.html#slide1
• http://inundata.org/R_talks/BARUG/#intro

Software requirement

• Rstudio
• knitr, XML, RCurl (See omegahat or this internal link for installation on Ubuntu)
• pandoc package This is a command line tool. I am testing it on Windows 7.

Slide #22 gives an instruction to create

• regular html file by using RStudio -> Knit HTML button
• HTML5 slides by using pandoc from command line.

Files:

• Rcmd source: 009-slides.Rmd Note that IE 8 was not supported by github. For IE 9, be sure to turn off "Compatibility View".
• markdown output: 009-slides.md
• HTML output: 009-slides.html

We can create Rcmd source in Rstudio by File -> New -> R Markdown.

There are 4 ways to produce slides with pandoc

• S5
• DZSlides
• Slidy
• Slideous

Use the markdown file (md) and convert it with pandoc

pandoc -s -S -i -t dzslides --mathjax html5_slides.md -o html5_slides.html

If we are comfortable with HTML and CSS code, open the html file (generated by pandoc) and modify the CSS style at will.

Built-in examples from rmarkdown

# This is done on my ODroid xu4 running Ubuntu Mate 15.10 (Wily)
# I used sudo apt-get install pandoc in shell
# and install.packages("rmarkdown") in R 3.2.3

library(rmarkdown)
rmarkdown::render("~/R/armv7l-unknown-linux-gnueabihf-library/3.2/rmarkdown/rmarkdown/templates/html_vignette/skeleton/skeleton.Rmd")
# the output <skeleton.html> is located under the same dir as <skeleton.Rmd>

Note that the image files in the html are embedded Base64 images in the html file. See

• http://stackoverflow.com/questions/1207190/embedding-base64-images
• Data URI scheme
• http://www.r-bloggers.com/embed-images-in-rd-documents/
• How to not embed Base64 images in RMarkdown
• Upload plots as PNG file to your wordpress

Examples

Some examples of creating papers (with references) based on knitr can be found on the Papers and reports section of the knitr website.

• https://github.com/EBI-predocs/knitr-example
• https://github.com/timchurches/meta-analyses

Read the docs Sphinx theme and journal article formats

http://blog.rstudio.org/2016/03/21/r-markdown-custom-formats/

• rticles package
• rmdformats package

rmarkdown news

• floating table of contents and tabbed sections

Markdown language

According to wikipedia:

Markdown is a lightweight markup language, originally created by John Gruber with substantial contributions from Aaron Swartz, allowing people “to write using an easy-to-read, easy-to-write plain text format, then convert it to structurally valid XHTML (or HTML)”.

• Markup is a general term for content formatting - such as HTML - but markdown is a library that generates HTML markup.

• Nice summary from stackoverflow.com and more complete list from github.

• An example https://gist.github.com/jeromyanglim/2716336

• basics and syntax

• Convert mediawiki to markdown using online conversion tool from pandoc.

• Cheat sheet.

• Cloud-enabled HTML5 markdown editor

• live demo

• Example from hosted in github

• R markdown file and use it in RStudio. Customizing Chunk Options can be found in knitr page and rpubs.com.

HTTP protocol

• http://en.wikipedia.org/wiki/File:Http_request_telnet_ubuntu.png
• Query string
• How to capture http header? Use curl -i en.wikipedia.org.
• Web Inspector. Build-in in Chrome. Right click on any page and choose 'Inspect Element'.
• Web server
• Simple TCP/IP web server
• HTTP Made Really Easy
• Illustrated Guide to HTTP
• nweb: a tiny, safe Web server with 200 lines
• Tiny HTTPd

An HTTP server is conceptually simple:

1. Open port 80 for listening
2. When contact is made, gather a little information (get mainly - you can ignore the rest for now)
3. Translate the request into a file request
4. Open the file and spit it back at the client

It gets more difficult depending on how much of HTTP you want to support - POST is a little more complicated, scripts, handling multiple requests, etc.

Example in R

> co <- socketConnection(port=8080, server=TRUE, blocking=TRUE) 
> # Now open a web browser and type http://localhost:8080/index.html
> readLines(co,1)
[1] "GET /index.html HTTP/1.1"
> readLines(co,1)
[1] "Host: localhost:8080"
> readLines(co,1)
[1] "User-Agent: Mozilla/5.0 (X11; Ubuntu; Linux i686; rv:23.0) Gecko/20100101 Firefox/23.0"
> readLines(co,1)
[1] "Accept: text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8"
> readLines(co,1)
[1] "Accept-Language: en-US,en;q=0.5"
> readLines(co,1)
[1] "Accept-Encoding: gzip, deflate"
> readLines(co,1)
[1] "Connection: keep-alive"
> readLines(co,1)
[1] ""

Example in C (Very simple http server written in C, 187 lines)

Create a simple hello world html page and save it as <index.html> in the current directory (/home/brb/Downloads/)

Launch the server program (assume we have done gcc http_server.c -o http_server)

$ ./http_server -p 50002
Server started at port no. 50002 with root directory as /home/brb/Downloads

Secondly open a browser and type http://localhost:50002/index.html. The server will respond

GET /index.html HTTP/1.1
Host: localhost:50002
User-Agent: Mozilla/5.0 (X11; Ubuntu; Linux i686; rv:23.0) Gecko/20100101 Firefox/23.0
Accept: text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8
Accept-Language: en-US,en;q=0.5
Accept-Encoding: gzip, deflate
Connection: keep-alive

file: /home/brb/Downloads/index.html
GET /favicon.ico HTTP/1.1
Host: localhost:50002
User-Agent: Mozilla/5.0 (X11; Ubuntu; Linux i686; rv:23.0) Gecko/20100101 Firefox/23.0
Accept: text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8
Accept-Language: en-US,en;q=0.5
Accept-Encoding: gzip, deflate
Connection: keep-alive

file: /home/brb/Downloads/favicon.ico
GET /favicon.ico HTTP/1.1
Host: localhost:50003
User-Agent: Mozilla/5.0 (X11; Ubuntu; Linux i686; rv:23.0) Gecko/20100101 Firefox/23.0
Accept: text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8
Accept-Language: en-US,en;q=0.5
Accept-Encoding: gzip, deflate
Connection: keep-alive

file: /home/brb/Downloads/favicon.ico

The browser will show the page from <index.html> in server.

The only bad thing is the code does not close the port. For example, if I have use Ctrl+C to close the program and try to re-launch with the same port, it will complain socket() or bind(): Address already in use.

Another Example in C (55 lines)

http://mwaidyanatha.blogspot.com/2011/05/writing-simple-web-server-in-c.html

The response is embedded in the C code.

If we test the server program by opening a browser and type "http://localhost:15000/", the server received the follwing 7 lines

GET / HTTP/1.1
Host: localhost:15000
User-Agent: Mozilla/5.0 (X11; Ubuntu; Linux i686; rv:23.0) Gecko/20100101 Firefox/23.0
Accept: text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8
Accept-Language: en-US,en;q=0.5
Accept-Encoding: gzip, deflate
Connection: keep-alive

If we include a non-executable file's name in the url, we will be able to download that file. Try "http://localhost:15000/client.c".

If we use telnet program to test, wee need to type anything we want

$ telnet localhost 15000
Trying 127.0.0.1...
Connected to localhost.
Escape character is '^]'.
ThisCanBeAnything        <=== This is what I typed in the client and it is also shown on server
HTTP/1.1 200 OK          <=== From here is what I got from server
Content-length: 37Content-Type: text/html

HTML_DATA_HERE_AS_YOU_MENTIONED_ABOVE <=== The html tags are not passed from server, interesting!
Connection closed by foreign host.
$ 

See also more examples under C page.

Others

• http://rosettacode.org/wiki/Hello_world/ (Different languages)
• http://kperisetla.blogspot.com/2012/07/simple-http-web-server-in-c.html (Windows web server)
• http://css.dzone.com/articles/web-server-c (handling HTTP GET request, handling content types(txt, html, jpg, zip. rar, pdf, php etc.), sending proper HTTP error codes, serving the files from a web root, change in web root in a config file, zero copy optimization using sendfile method and php file handling.)
• https://github.com/gtungatkar/Simple-HTTP-server
• https://github.com/davidmoreno/onion

shiny

The following is what we see on a browser after we run an example from shiny package. See http://rstudio.github.com/shiny/tutorial/#hello-shiny. Note that the R session needs to be on; i.e. R command prompt will not be returned unless we press Ctrl+C or ESC.

shiny depends on websockets, caTools, bitops, digest packages.

Q & A:

• Q: If we run runExample('01_hello') in Rserve from an R client, we can continue our work in R client without losing the functionality of the GUI from shiny. Question: how do we kill the job?
• If I run the example "01_hello", the browser only shows the control but not graph on Firefox? A: Use Chrome or Opera as the default browser.
• If I run the example "01_hello" on RHEL the first time, it works fine. But if I click 'Ctrl + C' to stop it and run it again, I got a message

Warning in .SOCK_SERVE(port) : R-Websockets(tcpserv): bind() failed. 
Error in createContext(port, webpage, is.binary = is.binary) : 
  Unable to bind socket on port 8100; is it realsy in use?

A simple solution is to close R and open it again.

• Q: Deployment on web. A: Not ready yet. Shiny server platform is still under beta testing. Shiny apps are hosted using the R websockets package which acts more like a tcp server than a web server, and that architecture just doesn't fit with rApache, or even apache for that matter.

• Q: How difficult to put the code in Gist:github? A: Just create an account. Do not even need to create a repository. Just go to http://gist.github.com and create a new gist. The new gist can be secret or public. A secret gist can not be edited again after it is created although it works fine when it was used in runGist() function.

Deploy to run locally

Follow the instruction here, we can do as following (Tested on Windows OS)

1. Create a desktop shortcut with target "C:\Program Files\R\R-3.0.2\bin\R.exe" -e "shiny::runExample('01_hello')" . We can name the shortcut as we like, e.g. R+shiny
2. Double click the shortcut. The Windows Firewall will be popped up and say it block some features of the program. It does not matter if we choose Allow access or Cancel.
3. Look at the command prompt window (black background console window), it will say something like

   Listening on port 7510

   at the last line of the console.
4. Open your browser (Chrome or Firefox works), and type the address http://localhost:7510. You will see something magic happen.
5. If we don't want to play with it, we can close the browser and close the command console (hit 'x')too.

Deploy on cloud

https://www.r-bloggers.com/deploying-r-rstudio-and-shiny-applications-on-unbuntu-server/

Deploy on shinyapps.io

See Getting started with shinyapps.io page.

Shinyapps.io can accept google account to sign up. I create an account and a test application/instance on

https://taichimd.shinyapps.io/testshiny/

Deploy to run remotely -shiny server

If we want to deploy our shiny apps to WWW, we need to install shiny server.

Following the guide on here, shiny-server is up smoothly on my Ubuntu machine. After I run the command sudo gdebi shiny-server-0.4.0.8-amd64.deb, shiny-server is started. Thanks to upstart in Ubuntu, shiny-server is automatically started whenever the machine is started.

Each app directory needs to be copied to /srv/shiny-server/ (which links to /opt/shiny-server/) directory using sudo.

The default port is 3838. That is, the remote computer can access the website using http://xxx.xxx.x.xx:3838/AppName.

Last but not the least, according to its web page, shiny-server is Experimental quality. Use at your own risk!.

Shiny https: Securing Shiny Open Source with SSL

• http://ipub.com/shiny-https/
• ShinyProxy

Deploy your own shiny server

• http://qualityandinnovation.com/2015/12/09/deploying-your-very-own-shiny-server/

Example of embedding shiny in your web page

http://michaeltoth.me/popularity-of-baby-names-since-1880.html

Shiny + Docker

See this post. It uses the gui of Docker called Kitematic.

shinytheme

shinythemes 1.1.1

shinyapps.io

http://www.rstudio.com/products/shinyapps/

websocket

http://illposed.net/jsm2012.pdf

CentOS

http://blog.supstat.com/2014/05/install-rstudio-server-on-centos6-5/

Gallery

• http://www.showmeshiny.com/
• Example of using googleVis: http://shinyeoda.cloudapp.net/
• Integrate with Javascript: https://github.com/wch/shiny-jsdemo and https://github.com/trestletech/ShinyDash-Sample
• interactiveDisplay (Bioconductor package, there is a STOP Application button too): http://www.bioconductor.org/packages/release/bioc/html/interactiveDisplay.html

Persistent data storage in Shiny apps

http://deanattali.com/blog/shiny-persistent-data-storage/

Password protection

• http://ipub.com/shiny-password-protect/

Install all required R packages

http://padamson.github.io/r/shiny/2016/03/13/install-required-r-packages.html

Tips

Shiny tips & tricks for improving your apps and solving common problems by Dean Attali.

Docker

• Using Docker as a Personal Productivity Tool – Running Command Line Apps Bundled in Docker Containers
• RStudio in the cloud with Amazon Lightsail and docker
• Mark McCahill (RStudio + Docker)
  • http://sites.duke.edu/researchcomputing/files/2014/09/mccahill-DockerDays.pdf
  • https://github.com/mccahill/docker-rstudio
  • https://hub.docker.com/r/mccahill/rstudio/~/dockerfile/

httpuv

http and WebSocket library.

gWidgetsWWW

• http://www.jstatsoft.org/v49/i10/paper
• gWidgetsWWW2 gWidgetsWWW based on Rook
• Compare shiny with gWidgetsWWW2.rapache

Rook

Since R 2.13, the internal web server was exposed.

Tutorual from useR2012 and Jeffrey Horner

Here is another one from http://www.rinfinance.com.

Rook is also supported by [rApache too. See http://rapache.net/manual.html.

Google group. https://groups.google.com/forum/?fromgroups#!forum/rrook

Advantage

• the web applications are created on desktop, whether it is Windows, Mac or Linux.
• No Apache is needed.
• create multiple applications at the same time. This complements the limit of rApache.

---

4 lines of code example.

library(Rook)
s <- Rhttpd$new()
s$start(quiet=TRUE)
s$print()
s$browse(1)  # OR s$browse("RookTest")

Notice that after s$browse() command, the cursor will return to R because the command just a shortcut to open the web page http://127.0.0.1:10215/custom/RookTest.

We can add Rook application to the server; see ?Rhttpd.

s$add(
    app=system.file('exampleApps/helloworld.R',package='Rook'),name='hello'
)
s$add(
    app=system.file('exampleApps/helloworldref.R',package='Rook'),name='helloref'
)
s$add(
    app=system.file('exampleApps/summary.R',package='Rook'),name='summary'
)

s$print()

#Server started on 127.0.0.1:10221
#[1] RookTest http://127.0.0.1:10221/custom/RookTest
#[2] helloref http://127.0.0.1:10221/custom/helloref
#[3] summary  http://127.0.0.1:10221/custom/summary
#[4] hello    http://127.0.0.1:10221/custom/hello

#  Stops the server but doesn't uninstall the app
## Not run: 
s$stop()

## End(Not run)
s$remove(all=TRUE)
rm(s)

For example, the interface and the source code of summary app are given below

app <- function(env) {
    req <- Rook::Request$new(env)
    res <- Rook::Response$new()
    res$write('Choose a CSV file:\n')
    res$write('<form method="POST" enctype="multipart/form-data">\n')
    res$write('<input type="file" name="data">\n')
    res$write('<input type="submit" name="Upload">\n</form>\n<br>')

    if (!is.null(req$POST())){
	data <- req$POST()[['data']]
	res$write("<h3>Summary of Data</h3>");
	res$write("<pre>")
	res$write(paste(capture.output(summary(read.csv(data$tempfile,stringsAsFactors=FALSE)),file=NULL),collapse='\n'))
	res$write("</pre>")
	res$write("<h3>First few lines (head())</h3>");
	res$write("<pre>")
	res$write(paste(capture.output(head(read.csv(data$tempfile,stringsAsFactors=FALSE)),file=NULL),collapse='\n'))
	res$write("</pre>") 
    }
    res$finish()
}

More example:

• http://lamages.blogspot.com/2012/08/rook-rocks-example-with-googlevis.html
• Self-organizing map
• Deploy Rook apps with rApache. First one and two.
• A Simple Prediction Web Service Using the New fiery Package

sumo

Sumo is a fully-functional web application template that exposes an authenticated user's R session within java server pages. See the paper http://journal.r-project.org/archive/2012-1/RJournal_2012-1_Bergsma+Smith.pdf.

FastRWeb

http://cran.r-project.org/web/packages/FastRWeb/index.html

CGHWithR and WebDevelopR

CGHwithR is still working with old version of R although it is removed from CRAN. Its successor is WebDevelopR. Its The vignette (year 2013) provides a review of several available methods.

manipulate from RStudio

This is not a web application. But the manipulate package can be used to create interactive plot within R(Studio) environment easily. Its source is available at here.

Mathematica also has manipulate function for plotting; see here.

RCloud

RCloud is an environment for collaboratively creating and sharing data analysis scripts. RCloud lets you mix analysis code in R, HTML5, Markdown, Python, and others. Much like Sage, iPython notebooks and Mathematica, RCloud provides a notebook interface that lets you easily record a session and annotate it with text, equations, and supporting images.

See also the Talk in UseR 2014.

Dropbox access

rdrop2 package

Web page scraping

rvest package.

Visualizing obesity across United States by using data from Wikipedia

Send email

• mailR package
• send bulk email

GEO (Gene Expression Omnibus)

See this internal link.

Interactive html output

RIGHT

The supported plot types include scatterplot, barplot, box plot, line plot and pie plot.

In addition to tooltip boxes, the package can create a table showing all information about selected nodes.

d3Network

• http://christophergandrud.github.io/d3Network/

library(d3Network)

Source <- c("A", "A", "A", "A", "B", "B", "C", "C", "D") 
Target <- c("B", "C", "D", "J", "E", "F", "G", "H", "I") 
NetworkData <- data.frame(Source, Target) 

d3SimpleNetwork(NetworkData, height = 800, width = 1024, file="tmp.html")

htmlwidgets for R

Embed widgets in R Markdown documents and Shiny web applications.

• Official website http://www.htmlwidgets.org/.
• How to write a useful htmlwidgets in R: tips and walk-through a real example

networkD3

This is a port of Christopher Gandrud's d3Network package to the htmlwidgets framework.

scatterD3

scatterD3 is an HTML R widget for interactive scatter plots visualization. It is based on the htmlwidgets R package and on the d3.js javascript library.

d3heatmap

A package generats interactive heatmaps using d3.js and htmlwidgets. The following screenshots shows 3 features.

• Shows the row/column/value under the mouse cursor
• Zoom in a region (click on the zoom-in image will bring back the original heatmap)
• Highlight a row or a column (click the label of another row will highlight another row. Click the same label again will bring back the original image)

svgPanZoom

This 'htmlwidget' provides pan and zoom interactivity to R graphics, including 'base', 'lattice', and 'ggplot2'. The interactivity is provided through the 'svg-pan-zoom.js' library.

DT: An R interface to the DataTables library

• http://blog.rstudio.org/2015/06/24/dt-an-r-interface-to-the-datatables-library/

plotly

• Power curves and ggplot2.
• TIME SERIES CHARTS BY THE ECONOMIST IN R USING PLOTLY
• Filled chord diagram

Amazon

Download product information and reviews from Amazon.com

sudo apt-get install libxml2-dev
sudo apt-get install libcurl4-openssl-dev

and in R

install.packages("devtools")
install.packages("XML")
install.packages("pbapply")
install.packages("dplyr")
devtools::install_github("56north/Rmazon")
product_info <- Rmazon::get_product_info("1593273843")
reviews <- Rmazon::get_reviews("1593273843")
reviews[1,6] # only show partial characters from the 1st review
nchar(reviews[1,6])
as.character(reviews[1,6]) # show the complete text from the 1st review

OCR

Tesseract package: High Quality OCR in R

Creating local repository for CRAN and Bioconductor (focus on Windows binary packages only)

How to set up a local repository

• CRAN specific: http://cran.r-project.org/mirror-howto.html
• Bioconductor specific: http://www.bioconductor.org/about/mirrors/mirror-how-to/

General guide: http://cran.r-project.org/doc/manuals/R-admin.html#Setting-up-a-package-repository

Utilities such as install.packages can be pointed at any CRAN-style repository, and R users may want to set up their own. The ‘base’ of a repository is a URL such as http://www.omegahat.org/R/: this must be an URL scheme that download.packages supports (which also includes ‘ftp://’ and ‘file://’, but not on most systems ‘https://’). Under that base URL there should be directory trees for one or more of the following types of package distributions:

• "source": located at src/contrib and containing .tar.gz files. Other forms of compression can be used, e.g. .tar.bz2 or .tar.xz files.
• "win.binary": located at bin/windows/contrib/x.y for R versions x.y.z and containing .zip files for Windows.
• "mac.binary.leopard": located at bin/macosx/leopard/contrib/x.y for R versions x.y.z and containing .tgz files.

Each terminal directory must also contain a PACKAGES file. This can be a concatenation of the DESCRIPTION files of the packages separated by blank lines, but only a few of the fields are needed. The simplest way to set up such a file is to use function write_PACKAGES in the tools package, and its help explains which fields are needed. Optionally there can also be a PACKAGES.gz file, a gzip-compressed version of PACKAGES—as this will be downloaded in preference to PACKAGES it should be included for large repositories. (If you have a mis-configured server that does not report correctly non-existent files you will need PACKAGES.gz.)

To add your repository to the list offered by setRepositories(), see the help file for that function.

A repository can contain subdirectories, when the descriptions in the PACKAGES file of packages in subdirectories must include a line of the form

Path: path/to/subdirectory

—once again write_PACKAGES is the simplest way to set this up.

Space requirement if we want to mirror WHOLE repository

• Whole CRAN takes about 92GB (rsync -avn cran.r-project.org::CRAN > ~/Downloads/cran).
• Bioconductor is big (> 64G for BioC 2.11). Please check the size of what will be transferred with e.g. (rsync -avn bioconductor.org::2.11 > ~/Downloads/bioc) and make sure you have enough room on your local disk before you start.

On the other hand, we if only care about Windows binary part, the space requirement is largely reduced.

• CRAN: 2.7GB
• Bioconductor: 28GB.

Misc notes

• If the binary package was built on R 2.15.1, then it cannot be installed on R 2.15.2. But vice is OK.
• Remember to issue "--delete" option in rsync, otherwise old version of package will be installed.
• The repository still need src directory. If it is missing, we will get an error

Warning: unable to access index for repository http://arraytools.no-ip.org/CRAN/src/contrib
Warning message:
package ‘glmnet’ is not available (for R version 2.15.2) 

The error was given by available.packages() function.

To bypass the requirement of src directory, I can use

install.packages("glmnet", contriburl = contrib.url(getOption('repos'), "win.binary"))

but there may be a problem when we use biocLite() command.

I find a workaround. Since the error comes from missing CRAN/src directory, we just need to make sure the directory CRAN/src/contrib exists AND either CRAN/src/contrib/PACKAGES or CRAN/src/contrib/PACKAGES.gz exists.

To create CRAN repository

Before creating a local repository please give a dry run first. You don't want to be surprised how long will it take to mirror a directory.

Dry run (-n option). Pipe out the process to a text file for an examination.

rsync -avn cran.r-project.org::CRAN > crandryrun.txt

To mirror only partial repository, it is necessary to create directories before running rsync command.

cd
mkdir -p ~/Rmirror/CRAN/bin/windows/contrib/2.15
rsync -rtlzv --delete cran.r-project.org::CRAN/bin/windows/contrib/2.15/ ~/Rmirror/CRAN/bin/windows/contrib/2.15
(one line with space before ~/Rmirror)

# src directory is very large (~27GB) since it contains source code for each R version. 
# We just need the files PACKAGES and PACKAGES.gz in CRAN/src/contrib. So I comment out the following line.
# rsync -rtlzv --delete cran.r-project.org::CRAN/src/ ~/Rmirror/CRAN/src/
mkdir -p ~/Rmirror/CRAN/src/contrib
rsync -rtlzv --delete cran.r-project.org::CRAN/src/contrib/PACKAGES ~/Rmirror/CRAN/src/contrib/
rsync -rtlzv --delete cran.r-project.org::CRAN/src/contrib/PACKAGES.gz ~/Rmirror/CRAN/src/contrib/

And optionally

library(tools)
write_PACKAGES("~/Rmirror/CRAN/bin/windows/contrib/2.15", type="win.binary") 

and if we want to get src directory

rsync -rtlzv --delete cran.r-project.org::CRAN/src/contrib/*.tar.gz ~/Rmirror/CRAN/src/contrib/
rsync -rtlzv --delete cran.r-project.org::CRAN/src/contrib/2.15.3 ~/Rmirror/CRAN/src/contrib/

We can use du -h to check the folder size.

For example (as of 1/7/2013),

$ du -k ~/Rmirror --max-depth=1 --exclude ".*" | sort -nr | cut -f2 | xargs -d '\n' du -sh
30G	/home/brb/Rmirror
28G	/home/brb/Rmirror/Bioc
2.7G	/home/brb/Rmirror/CRAN

To create Bioconductor repository

Dry run

rsync -avn bioconductor.org::2.11 > biocdryrun.txt

Then creates directories before running rsync.

cd
mkdir -p ~/Rmirror/Bioc
wget -N http://www.bioconductor.org/biocLite.R -P ~/Rmirror/Bioc

where -N is to overwrite original file if the size or timestamp change and -P in wget means an output directory, not a file name.

Optionally, we can add the following in order to see the Bioconductor front page.

rsync -zrtlv  --delete bioconductor.org::2.11/BiocViews.html ~/Rmirror/Bioc/packages/2.11/
rsync -zrtlv  --delete bioconductor.org::2.11/index.html ~/Rmirror/Bioc/packages/2.11/

The software part (aka bioc directory) installation:

cd
mkdir -p ~/Rmirror/Bioc/packages/2.11/bioc/bin/windows
mkdir -p ~/Rmirror/Bioc/packages/2.11/bioc/src
rsync -zrtlv  --delete bioconductor.org::2.11/bioc/bin/windows/ ~/Rmirror/Bioc/packages/2.11/bioc/bin/windows
# Either rsync whole src directory or just essential files
# rsync -zrtlv  --delete bioconductor.org::2.11/bioc/src/ ~/Rmirror/Bioc/packages/2.11/bioc/src
rsync -zrtlv  --delete bioconductor.org::2.11/bioc/src/contrib/PACKAGES ~/Rmirror/Bioc/packages/2.11/bioc/src/contrib/
rsync -zrtlv  --delete bioconductor.org::2.11/bioc/src/contrib/PACKAGES.gz ~/Rmirror/Bioc/packages/2.11/bioc/src/contrib/
# Optionally the html part
mkdir -p ~/Rmirror/Bioc/packages/2.11/bioc/html
rsync -zrtlv  --delete bioconductor.org::2.11/bioc/html/ ~/Rmirror/Bioc/packages/2.11/bioc/html
mkdir -p ~/Rmirror/Bioc/packages/2.11/bioc/vignettes
rsync -zrtlv  --delete bioconductor.org::2.11/bioc/vignettes/ ~/Rmirror/Bioc/packages/2.11/bioc/vignettes
mkdir -p ~/Rmirror/Bioc/packages/2.11/bioc/news
rsync -zrtlv  --delete bioconductor.org::2.11/bioc/news/ ~/Rmirror/Bioc/packages/2.11/bioc/news
mkdir -p ~/Rmirror/Bioc/packages/2.11/bioc/licenses
rsync -zrtlv  --delete bioconductor.org::2.11/bioc/licenses/ ~/Rmirror/Bioc/packages/2.11/bioc/licenses
mkdir -p ~/Rmirror/Bioc/packages/2.11/bioc/manuals
rsync -zrtlv  --delete bioconductor.org::2.11/bioc/manuals/ ~/Rmirror/Bioc/packages/2.11/bioc/manuals
mkdir -p ~/Rmirror/Bioc/packages/2.11/bioc/readmes
rsync -zrtlv  --delete bioconductor.org::2.11/bioc/readmes/ ~/Rmirror/Bioc/packages/2.11/bioc/readmes

and annotation (aka data directory) part:

mkdir -p ~/Rmirror/Bioc/packages/2.11/data/annotation/bin/windows
mkdir -p ~/Rmirror/Bioc/packages/2.11/data/annotation/src/contrib
# one line for each of the following
rsync -zrtlv --delete bioconductor.org::2.11/data/annotation/bin/windows/ ~/Rmirror/Bioc/packages/2.11/data/annotation/bin/windows
rsync -zrtlv --delete bioconductor.org::2.11/data/annotation/src/contrib/PACKAGES ~/Rmirror/Bioc/packages/2.11/data/annotation/src/contrib/
rsync -zrtlv --delete bioconductor.org::2.11/data/annotation/src/contrib/PACKAGES.gz ~/Rmirror/Bioc/packages/2.11/data/annotation/src/contrib/

and experiment directory:

mkdir -p ~/Rmirror/Bioc/packages/2.11/data/experiment/bin/windows/contrib/2.15
mkdir -p ~/Rmirror/Bioc/packages/2.11/data/experiment/src/contrib
# one line for each of the following
# Note that we are cheating by only downloading PACKAGES and PACKAGES.gz files
rsync -zrtlv --delete bioconductor.org::2.11/data/experiment/bin/windows/contrib/2.15/PACKAGES ~/Rmirror/Bioc/packages/2.11/data/experiment/bin/windows/contrib/2.15/
rsync -zrtlv --delete bioconductor.org::2.11/data/experiment/bin/windows/contrib/2.15/PACKAGES.gz ~/Rmirror/Bioc/packages/2.11/data/experiment/bin/windows/contrib/2.15/
rsync -zrtlv --delete bioconductor.org::2.11/data/experiment/src/contrib/PACKAGES ~/Rmirror/Bioc/packages/2.11/data/experiment/src/contrib/
rsync -zrtlv --delete bioconductor.org::2.11/data/experiment/src/contrib/PACKAGES.gz ~/Rmirror/Bioc/packages/2.11/data/experiment/src/contrib/

and extra directory:

mkdir -p ~/Rmirror/Bioc/packages/2.11/extra/bin/windows/contrib/2.15
mkdir -p ~/Rmirror/Bioc/packages/2.11/extra/src/contrib
# one line for each of the following
# Note that we are cheating by only downloading PACKAGES and PACKAGES.gz files
rsync -zrtlv --delete bioconductor.org::2.11/extra/bin/windows/contrib/2.15/PACKAGES ~/Rmirror/Bioc/packages/2.11/extra/bin/windows/contrib/2.15/
rsync -zrtlv --delete bioconductor.org::2.11/extra/bin/windows/contrib/2.15/PACKAGES.gz ~/Rmirror/Bioc/packages/2.11/extra/bin/windows/contrib/2.15/
rsync -zrtlv --delete bioconductor.org::2.11/extra/src/contrib/PACKAGES ~/Rmirror/Bioc/packages/2.11/extra/src/contrib/
rsync -zrtlv --delete bioconductor.org::2.11/extra/src/contrib/PACKAGES.gz ~/Rmirror/Bioc/packages/2.11/extra/src/contrib/

To test local repository

Create soft links in Apache server

su
ln -s /home/brb/Rmirror/CRAN /var/www/html/CRAN
ln -s /home/brb/Rmirror/Bioc /var/www/html/Bioc
ls -l /var/www/html

The soft link mode should be 777.

To test CRAN

Replace the host name arraytools.no-ip.org by IP address 10.133.2.111 if necessary.

r <- getOption("repos"); r["CRAN"] <- "http://arraytools.no-ip.org/CRAN"
options(repos=r)
install.packages("glmnet")

We can test if the backup server is working or not by installing a package which was removed from the CRAN. For example, 'ForImp' was removed from CRAN in 11/8/2012, but I still a local copy built on R 2.15.2 (run rsync on 11/6/2012).

r <- getOption("repos"); r["CRAN"] <- "http://cran.r-project.org"
r <- c(r, BRB='http://arraytools.no-ip.org/CRAN')
#                        CRAN                            CRANextra                                  BRB 
# "http://cran.r-project.org" "http://www.stats.ox.ac.uk/pub/RWin"   "http://arraytools.no-ip.org/CRAN"
options(repos=r)
install.packages('ForImp')

Note by default, CRAN mirror is selected interactively.

> getOption("repos")
                                CRAN                            CRANextra 
                            "@CRAN@" "http://www.stats.ox.ac.uk/pub/RWin" 

To test Bioconductor

# CRAN part:
r <- getOption("repos"); r["CRAN"] <- "http://arraytools.no-ip.org/CRAN"
options(repos=r)
# Bioconductor part:
options("BioC_mirror" = "http://arraytools.no-ip.org/Bioc")
source("http://bioconductor.org/biocLite.R")
# This source biocLite.R line can be placed either before or after the previous 2 lines
biocLite("aCGH")

If there is a connection problem, check folder attributes.

chmod -R 755 ~/CRAN/bin

• Note that if a binary package was created for R 2.15.1, then it can be installed under R 2.15.1 but not R 2.15.2. The R console will show package xxx is not available (for R version 2.15.2).

• For binary installs, the function also checks for the availability of a source package on the same repository, and reports if the source package has a later version, or is available but no binary version is.

So for example, if the mirror does not have contents under src directory, we need to run the following line in order to successfully run install.packages() function.

options(install.packages.check.source = "no")

• If we only mirror the essential directories, we can run biocLite() successfully. However, the R console will give some warning

> biocLite("aCGH")
BioC_mirror: http://arraytools.no-ip.org/Bioc
Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
Installing package(s) 'aCGH'
Warning: unable to access index for repository http://arraytools.no-ip.org/Bioc/packages/2.11/data/experiment/src/contrib
Warning: unable to access index for repository http://arraytools.no-ip.org/Bioc/packages/2.11/extra/src/contrib
Warning: unable to access index for repository http://arraytools.no-ip.org/Bioc/packages/2.11/data/experiment/bin/windows/contrib/2.15
Warning: unable to access index for repository http://arraytools.no-ip.org/Bioc/packages/2.11/extra/bin/windows/contrib/2.15
trying URL 'http://arraytools.no-ip.org/Bioc/packages/2.11/bioc/bin/windows/contrib/2.15/aCGH_1.36.0.zip'
Content type 'application/zip' length 2431158 bytes (2.3 Mb)
opened URL
downloaded 2.3 Mb

package ‘aCGH’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\limingc\AppData\Local\Temp\Rtmp8IGGyG\downloaded_packages
Warning: unable to access index for repository http://arraytools.no-ip.org/Bioc/packages/2.11/data/experiment/bin/windows/contrib/2.15
Warning: unable to access index for repository http://arraytools.no-ip.org/Bioc/packages/2.11/extra/bin/windows/contrib/2.15
> library()

CRAN repository directory structure

The information below is specific to R 2.15.2. There are linux and macosx subdirecotries whenever there are windows subdirectory.

bin/winows/contrib/2.15
src/contrib
   /contrib/2.15.2
   /contrib/Archive
web/checks
   /dcmeta
   /packages
   /views

A clickable map [1]

Bioconductor package download statistics

http://bioconductor.org/packages/stats/

Bioconductor repository directory structure

The information below is specific to Bioc 2.11 (R 2.15). There are linux and macosx subdirecotries whenever there are windows subdirectory.

bioc/bin/windows/contrib/2.15
    /html
    /install
    /license
    /manuals 
    /news
    /src
    /vignettes
data/annotation/bin/windows/contrib/2.15
               /html
               /licenses
               /manuals
               /src
               /vignettes
     /experiment/bin/windows/contrib/2.15
                /html
                /manuals
                /src/contrib
                /vignettes
extra/bin/windows/contrib
     /html
     /src
     /vignettes

List all R packages from CRAN/Bioconductor

Check my daily result based on R 2.15 and Bioc 2.11 in [2]

1. CRAN
2. Bioc software
3. Bioc annotation
4. Bioc experiment

See METACRAN for packages hosted on CRAN. The 'https://github.com/metacran/PACKAGES' file contains the latest update.

r-hub: the everything-builder the R community needs

https://github.com/r-hub/proposal

Introducing R-hub, the R package builder service

http://blog.revolutionanalytics.com/2016/10/r-hub-public-beta.html

Parallel Computing

1. Example code for the book Parallel R by McCallum and Weston.
2. A gentle introduction to parallel computing in R
3. An introduction to distributed memory parallelism in R and C
4. Processing: When does it worth?

Windows Security Warning

It seems it is safe to choose 'Cancel' when Windows Firewall tried to block R program when we use makeCluster() to create a socket cluster.

library(parallel)
cl <- makeCluster(2)
clusterApply(cl, 1:2, get("+"), 3)
stopCluster(cl)

If we like to see current firewall settings, just click Windows Start button, search 'Firewall' and choose 'Windows Firewall with Advanced Security'. In the 'Inbound Rules', we can see what programs (like, R for Windows GUI front-end, or Rserve) are among the rules. These rules are called 'private' in the 'Profile' column. Note that each of them may appear twice because one is 'TCP' protocol and the other one has a 'UDP' protocol.

parallel package

Parallel package was included in R 2.14.0. It is derived from the snow and multicore packages and provides many of the same functions as those packages.

The parallel package provides several *apply functions for R users to quickly modify their code using parallel computing.

• makeCluster(makePSOCKcluster, makeForkCluster), stopCluster. Other cluster types are passed to package snow.
• clusterCall, clusterEvalQ, clusterSplit
• clusterApply, clusterApplyLB
• clusterExport
• clusterMap
• parLapply, parSapply, parApply, parRapply, parCapply
• parLapplyLB, parSapplyLB (load balance version)
• clusterSetRNGStream, nextRNGStream, nextRNGSubStream

Examples (See ?clusterApply)

library(parallel)
cl <- makeCluster(2, type = "SOCK")
clusterApply(cl, 1:2, function(x) x*3)    # OR clusterApply(cl, 1:2, get("*"), 3)
# [[1]]
# [1] 3
#
# [[2]]
# [1] 6
parSapply(cl, 1:20, get("+"), 3)
#  [1]  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
stopCluster(cl)

snow package

Supported cluster types are "SOCK", "PVM", "MPI", and "NWS".

multicore package

This package is removed from CRAN.

Consider using package ‘parallel’ instead.

foreach package

This package depends on one of the following

• doParallel - Foreach parallel adaptor for the parallel package
• doSNOW - Foreach parallel adaptor for the snow package
• doMC - Foreach parallel adaptor for the multicore package
• doMPI - Foreach parallel adaptor for the Rmpi package
• doRedis - Foreach parallel adapter for the rredis package

as a backend.

library(foreach)
library(doParallel)

m <- matrix(rnorm(9), 3, 3)

cl <- makeCluster(2, type = "SOCK")
registerDoParallel(cl)
foreach(i=1:nrow(m), .combine=rbind) %dopar%
  (m[i,] / mean(m[i,]))

stopCluster(cl)

See also this post Updates to the foreach package and its friends on Oct 2015.

• Cross validation in prediction for glm

snowfall package

http://www.imbi.uni-freiburg.de/parallel/docs/Reisensburg2009_TutParallelComputing_Knaus_Porzelius.pdf

Rmpi package

Some examples/tutorials

• http://trac.nchc.org.tw/grid/wiki/R-MPI_Install
• http://www.arc.vt.edu/resources/software/r/index.php
• https://www.sharcnet.ca/help/index.php/Using_R_and_MPI
• http://math.acadiau.ca/ACMMaC/Rmpi/examples.html
• http://www.umbc.edu/hpcf/resources-tara/how-to-run-R.html
• Ryan Rosario
• http://pj.freefaculty.org/guides/Rcourse/parallel-1/parallel-1.pdf
• * http://biowulf.nih.gov/apps/R.html

OpenMP

• R and openMP: boosting compiled code on multi-core cpu-s from parallelr.com.

BiocParallel

• Orchestrating a small, parallel, RNA-seq pre-processing workflow using R

Apache Spark

• Introduction to Apache Spark

Microsoft R Server

• Microsoft R Server (not Microsoft R Open)

GPU

• GPU Programming for All with ‘gpuR from parallelr.com. The gpuR is available on CRAN.
• gputools

Future

1. Asynchronous and Distributed Programming in R with the Future Package

Cloud Computing

Install R on Amazon EC2

http://randyzwitch.com/r-amazon-ec2/

Bioconductor on Amazon EC2

http://www.bioconductor.org/help/bioconductor-cloud-ami/

Big Data Analysis

http://blog.comsysto.com/2013/02/14/my-favorite-community-links/

Useful R packages

• awesome-R

RInside

• http://dirk.eddelbuettel.com/code/rinside.html
• http://dirk.eddelbuettel.com/papers/rfinance2010_rcpp_rinside_tutorial_handout.pdf

Ubuntu

With RInside, R can be embedded in a graphical application. For example, $HOME/R/x86_64-pc-linux-gnu-library/3.0/RInside/examples/qt directory includes source code of a Qt application to show a kernel density plot with various options like kernel functions, bandwidth and an R command text box to generate the random data. See my demo on Youtube. I have tested this qtdensity example successfully using Qt 4.8.5.

1. Follow the instruction cairoDevice to install required libraries for cairoDevice package and then cairoDevice itself.
2. Install Qt. Check 'qmake' command becomes available by typing 'whereis qmake' or 'which qmake' in terminal.
3. Open Qt Creator from Ubuntu start menu/Launcher. Open the project file $HOME/R/x86_64-pc-linux-gnu-library/3.0/RInside/examples/qt/qtdensity.pro in Qt Creator.
4. Under Qt Creator, hit 'Ctrl + R' or the big green triangle button on the lower-left corner to build/run the project. If everything works well, you shall see the interactive program qtdensity appears on your desktop.

.

With RInside + Wt web toolkit installed, we can also create a web application. To demonstrate the example in examples/wt directory, we can do

cd ~/R/x86_64-pc-linux-gnu-library/3.0/RInside/examples/wt
make
sudo ./wtdensity --docroot . --http-address localhost --http-port 8080

Then we can go to the browser's address bar and type http://localhost:8080 to see how it works (a screenshot is in here).

Windows 7

To make RInside works on Windows OS, try the following

1. Make sure R is installed under C:\ instead of C:\Program Files if we don't want to get an error like g++.exe: error: Files/R/R-3.0.1/library/RInside/include: No such file or directory.
2. Install RTools
3. Instal RInside package from source (the binary version will give an error )
4. Create a DOS batch file containing necessary paths in PATH environment variable

@echo off
set PATH=C:\Rtools\bin;c:\Rtools\gcc-4.6.3\bin;%PATH%
set PATH=C:\R\R-3.0.1\bin\i386;%PATH%
set PKG_LIBS=`Rscript -e "Rcpp:::LdFlags()"`
set PKG_CPPFLAGS=`Rscript -e "Rcpp:::CxxFlags()"`
set R_HOME=C:\R\R-3.0.1
echo Setting environment for using R
cmd

In the Windows command prompt, run

cd C:\R\R-3.0.1\library\RInside\examples\standard
make -f Makefile.win

Now we can test by running any of executable files that make generates. For example, rinside_sample0.

rinside_sample0

As for the Qt application qdensity program, we need to make sure the same version of MinGW was used in building RInside/Rcpp and Qt. See some discussions in

• http://stackoverflow.com/questions/12280707/using-rinside-with-qt-in-windows
• http://www.mail-archive.com/[email protected]/msg04377.html

So the Qt and Wt web tool applications on Windows may or may not be possible.

GUI

Qt and R

• http://cran.r-project.org/web/packages/qtbase/index.html QtDesigner is such a tool, and its output is compatible with the qtbase R package
• http://qtinterfaces.r-forge.r-project.org

tkrplot

On Ubuntu, we need to install tk packages, such as by

sudo apt-get install tk-dev

Hadoop (eg ~100 terabytes)

See also HighPerformanceComputing

• RHadoop
• Hive
• MapReduce. Introduction by Linux Journal.
• http://www.techspritz.com/category/tutorials/hadoopmapredcue/ Single node or multinode cluster setup using Ubuntu with VirtualBox (Excellent)
• Running Hadoop on Ubuntu Linux (Single-Node Cluster)
• Ubuntu 12.04 http://www.youtube.com/watch?v=WN2tJk_oL6E and instruction
• Linux Mint http://blog.hackedexistence.com/installing-hadoop-single-node-on-linux-mint
• http://www.r-bloggers.com/search/hadoop

RHadoop

• RDataMining.com based on Mac.
• Ubuntu 12.04 - Crishantha.com, nikhilshah123sh.blogspot.com.Bighadoop.wordpress contains an example.
• RapReduce in R by RevolutionAnalytics with a few examples.
• https://twitter.com/hashtag/rhadoop
• Bigd8ta.com based on Ubuntu 14.04.

Snowdoop: an alternative to MapReduce algorithm

• http://matloff.wordpress.com/2014/11/26/how-about-a-snowdoop-package/
• http://matloff.wordpress.com/2014/12/26/snowdooppartools-update/comment-page-1/#comment-665

XML

On Ubuntu, we need to install libxml2-dev before we can install XML package.

sudo apt-get update
sudo apt-get install libxml2-dev

On CentOS,

yum -y install libxml2 libxml2-devel

xmlview

• http://rud.is/b/2016/01/13/cobble-xpath-interactively-with-the-xmlview-package/

RCurl

On Ubuntu, we need to install the packages (the first one is for XML package that RCurl suggests)

# Test on Ubuntu 14.04
sudo apt-get install libxml2-dev
sudo apt-get install libcurl4-openssl-dev

devtools

devtools package depends on Curl.

# Test on Ubuntu 14.04
sudo apt-get install libcurl4-openssl-dev

httr

httr imports curl, jsonlite, mime, openssl and R6 packages.

When I tried to install httr package, I got an error and some message:

Configuration failed because openssl was not found. Try installing:
 * deb: libssl-dev (Debian, Ubuntu, etc)
 * rpm: openssl-devel (Fedora, CentOS, RHEL)
 * csw: libssl_dev (Solaris)
 * brew: openssl (Mac OSX)
If openssl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘openssl’

It turns out after I run sudo apt-get install libssl-dev in the terminal (Debian), it would go smoothly with installing httr package. Nice httr!

Real example: see this post. Unfortunately I did not get a table result; I only get an html file (R 3.2.5, httr 1.1.0 on Ubuntu and Debian).

Since httr package was used in many other packages, take a look at how others use it. For example, aRxiv package.

curl

curl is independent of RCurl package.

• http://cran.r-project.org/web/packages/curl/vignettes/intro.html
• https://www.opencpu.org/posts/curl-release-0-8/

library(curl)
h <- new_handle()
handle_setform(h,
  name="aaa", email="bbb"
)
req <- curl_fetch_memory("http://localhost/d/phpmyql3_scripts/ch02/form2.html", handle = h)
rawToChar(req$content)

rOpenSci packages

rOpenSci contains packages that allow access to data repositories through the R statistical programming environment

DirichletMultinomial

On Ubuntu, we do

sudo apt-get install libgsl0-dev

GenOrd: Generate ordinal and discrete variables with given correlation matrix and marginal distributions

here

rjson

http://heuristically.wordpress.com/2013/05/20/geolocate-ip-addresses-in-r/

RJSONIO

Accessing Bitcoin Data with R

http://blog.revolutionanalytics.com/2015/11/accessing-bitcoin-data-with-r.html

Plot IP on google map

• http://thebiobucket.blogspot.com/2011/12/some-fun-with-googlevis-plotting-blog.html#more (RCurl, RJONIO, plyr, googleVis)
• http://devblog.icans-gmbh.com/using-the-maxmind-geoip-api-with-r/ (RCurl, RJONIO, maps)
• http://cran.r-project.org/web/packages/geoPlot/index.html (geoPlot package (deprecated as 8/12/2013))
• http://archive09.linux.com/feature/135384 (Not R) ApacheMap
• http://batchgeo.com/features/geolocation-ip-lookup/ (Not R) (Enter a spreadsheet of adress, city, zip or a column of IPs and it will show the location on google map)
• http://code.google.com/p/apachegeomap/

The following example is modified from the first of above list.

require(RJSONIO) # fromJSON
require(RCurl)   # getURL

temp = getURL("https://gist.github.com/arraytools/6743826/raw/23c8b0bc4b8f0d1bfe1c2fad985ca2e091aeb916/ip.txt", 
                           ssl.verifypeer = FALSE)
ip <- read.table(textConnection(temp), as.is=TRUE)
names(ip) <- "IP"
nr = nrow(ip)
 
Lon <- as.numeric(rep(NA, nr))
Lat <- Lon
Coords <- data.frame(Lon, Lat)
 
ip2coordinates <- function(ip) {
  api <- "http://freegeoip.net/json/"
  get.ips <- getURL(paste(api, URLencode(ip), sep=""))
  # result <- ldply(fromJSON(get.ips), data.frame)
  result <- data.frame(fromJSON(get.ips))
  names(result)[1] <- "ip.address"
  return(result)
}

for (i in 1:nr){
  cat(i, "\n")
  try(
  Coords[i, 1:2] <- ip2coordinates(ip$IP[i])[c("longitude", "latitude")]
  )
}
 
# append to log-file:
logfile <- data.frame(ip, Lat = Coords$Lat, Long = Coords$Lon,
                                       LatLong = paste(round(Coords$Lat, 1), round(Coords$Lon, 1), sep = ":")) 
log_gmap <- logfile[!is.na(logfile$Lat), ]

require(googleVis) # gvisMap
gmap <- gvisMap(log_gmap, "LatLong",
                options = list(showTip = TRUE, enableScrollWheel = TRUE,
                               mapType = 'hybrid', useMapTypeControl = TRUE,
                               width = 1024, height = 800))
plot(gmap)

The plot.gvis() method in googleVis packages also teaches the startDynamicHelp() function in the tools package, which was used to launch a http server. See Jeffrey Horner's note about deploying Rook App.

Map

leaflet

• rstudio.github.io/leaflet/#installation-and-use
• https://metvurst.wordpress.com/2015/07/24/mapview-basic-interactive-viewing-of-spatial-data-in-r-6/

choroplethr

• http://blog.revolutionanalytics.com/2014/01/easy-data-maps-with-r-the-choroplethr-package-.html
• http://www.arilamstein.com/blog/2015/06/25/learn-to-map-census-data-in-r/
• http://www.arilamstein.com/blog/2015/09/10/user-question-how-to-add-a-state-border-to-a-zip-code-map/

googleVis

See an example from RJSONIO above.

googleAuthR

Create R functions that interact with OAuth2 Google APIs easily, with auto-refresh and Shiny compatibility.

gtrendsR

Download and plot Google Trends data with R

quantmod

Maintaining a database of price files in R. It consists of 3 steps.

1. Initial data downloading
2. Update existing data
3. Create a batch file

Rcpp

Discussion archive

Speed Comparison

• A comparison of high-performance computing techniques in R. It compares Rcpp to an R looping operator (like mapply), a parallelized version of a looping operator (like mcmapply), explicit parallelization, via the parallel package or the ParallelR suite.
• In the following example, C++ avoids the overhead of creating an intermediate object (eg vector of the same length as the original vector). The c++ uses an intermediate scalar. So C++ wins R over memory management in this case.

# http://blog.mckuhn.de/2016/03/avoiding-unnecessary-memory-allocations.html 
library(Rcpp)

`%count<%` <- cppFunction('
size_t count_less(NumericVector x, NumericVector y) {
  const size_t nx = x.size();
  const size_t ny = y.size();
  if (nx > 1 & ny > 1) stop("Only one parameter can be a vector!");
  size_t count = 0;
  if (nx == 1) {
    double c = x[0];
    for (int i = 0; i < ny; i++) count += c < y[i];
  } else {
    double c = y[0];
    for (int i = 0; i < nx; i++) count += x[i] < c;
  }
  return count;
}
')

set.seed(42)

N <- 10^7
v <- runif(N, 0, 10000)

# Testing on my ODroid xu4 running ubuntu 15.10
system.time(sum(v < 5000))
#   user  system elapsed
#  1.135   0.305   1.453
system.time(v %count<% 5000)
#   user  system elapsed
#  0.535   0.000   0.540

Use Rcpp in RStudio

RStudio makes it easy to use Rcpp package.

Open RStudio, click New File -> C++ File. It will create a C++ template on the RStudio editor

#include <Rcpp.h>
using namespace Rcpp;

// Below is a simple example of exporting a C++ function to R. You can
// source this function into an R session using the Rcpp::sourceCpp 
// function (or via the Source button on the editor toolbar)

// For more on using Rcpp click the Help button on the editor toolbar

// [[Rcpp::export]]
int timesTwo(int x) {
   return x * 2;
}

Now in R console, type

library(Rcpp)
sourceCpp("~/Downloads/timesTwo.cpp")
timesTwo(9)
# [1] 18

See more examples on http://adv-r.had.co.nz/Rcpp.html.

If we wan to test Boost library, we can try it in RStudio. Consider the following example in stackoverflow.com.

// [[Rcpp::depends(BH)]]
#include <Rcpp.h>
#include <boost/foreach.hpp>
#include <boost/math/special_functions/gamma.hpp>

#define foreach BOOST_FOREACH

using namespace boost::math;

//[[Rcpp::export]]
Rcpp::NumericVector boost_gamma( Rcpp::NumericVector x ) {
  foreach( double& elem, x ) {
    elem = boost::math::tgamma(elem);
  };

  return x;
}

Then the R console

boost_gamma(0:10 + 1)
#  [1]       1       1       2       6      24     120     720    5040   40320
# [10]  362880 3628800

identical( boost_gamma(0:10 + 1), factorial(0:10) )
# [1] TRUE

Example 1. convolution example

First, Rcpp package should be installed (I am working on Linux system). Next we try one example shipped in Rcpp package.

PS. If R was not available in global environment (such as built by ourselves), we need to modify 'Makefile' file by replacing 'R' command with its complete path (4 places).

cd ~/R/x86_64-pc-linux-gnu-library/3.0/Rcpp/examples/ConvolveBenchmarks/
make
R

Then type the following in an R session to see how it works. Note that we don't need to issue library(Rcpp) in R.

dyn.load("convolve3_cpp.so")
x <- .Call("convolve3cpp", 1:3, 4:6)
x # 4 13 28 27 18

If we have our own cpp file, we need to use the following way to create dynamic loaded library file. Note that the character (grave accent) ` is not (single quote)'. If you mistakenly use ', it won't work.

export PKG_CXXFLAGS=`Rscript -e "Rcpp:::CxxFlags()"`
export PKG_LIBS=`Rscript -e "Rcpp:::LdFlags()"`
R CMD SHLIB xxxx.cpp

Example 2. Use together with inline package

• http://adv-r.had.co.nz/C-interface.html#calling-c-functions-from-r

library(inline)
src <-'
 Rcpp::NumericVector xa(a);
 Rcpp::NumericVector xb(b);
 int n_xa = xa.size(), n_xb = xb.size();

 Rcpp::NumericVector xab(n_xa + n_xb - 1);
 for (int i = 0; i < n_xa; i++)
 for (int j = 0; j < n_xb; j++)
 xab[i + j] += xa[i] * xb[j];
 return xab;
'
fun <- cxxfunction(signature(a = "numeric", b = "numeric"),
 src, plugin = "Rcpp")
fun(1:3, 1:4) 
# [1]  1  4 10 16 17 12

Read/Write Excel files package

• xlsx: depends on Java
• openxlsx: not depend on Java. Depend on zip application. On Windows, it seems to be OK without installing Rtools. But it can not read xls file; it works on xlsx file.
• readxl: it does not depend on anything although it can only read but not write Excel files. Tested it on Ubuntu machine with R 3.1.3 using <BRCA.xls> file. Usage:

read_excel(path, sheet = 1, col_names = TRUE, col_types = NULL, na = "", skip = 0)

For the Chromosome column, integer values becomes strings (but converted to double, so 5 becomes 5.000000) or NA (empty on sheets).

> head(read_excel("~/Downloads/BRCA.xls", 4)[ , -9], 3)
  UniqueID (Double-click) CloneID UGCluster
1                   HK1A1   21652 Hs.445981
2                   HK1A2   22012 Hs.119177
3                   HK1A4   22293 Hs.501376
                                                    Name Symbol EntrezID
1 Catenin (cadherin-associated protein), alpha 1, 102kDa CTNNA1     1495
2                              ADP-ribosylation factor 3   ARF3      377
3                          Uroporphyrinogen III synthase   UROS     7390
  Chromosome      Cytoband ChimericClusterIDs Filter
1   5.000000        5q31.2               <NA>      1
2  12.000000         12q13               <NA>      1
3       <NA> 10q25.2-q26.3               <NA>      1

The hidden worksheets become visible (Not sure what are those first rows mean in the output).

> excel_sheets("~/Downloads/BRCA.xls")
DEFINEDNAME: 21 00 00 01 0b 00 00 00 02 00 00 00 00 00 00 0d 3b 01 00 00 00 9a 0c 00 00 1a 00 
DEFINEDNAME: 21 00 00 01 0b 00 00 00 04 00 00 00 00 00 00 0d 3b 03 00 00 00 9b 0c 00 00 0a 00 
DEFINEDNAME: 21 00 00 01 0b 00 00 00 03 00 00 00 00 00 00 0d 3b 02 00 00 00 9a 0c 00 00 06 00 
[1] "Experiment descriptors" "Filtered log ratio"     "Gene identifiers"      
[4] "Gene annotations"       "CollateInfo"            "GeneSubsets"           
[7] "GeneSubsetsTemp"

The Chinese character works too.

> read_excel("~/Downloads/testChinese.xlsx", 1)
   中文 B C
1     a b c
2     1 2 3

readr

Compared to base equivalents like read.csv(), readr is much faster and gives more convenient output: it never converts strings to factors, can parse date/times, and it doesn’t munge the column names.

1.0.0 released.

ggplot2

Books

• R Graphics Cookbook by Winston Chang.
• ggplot2 and its source code. Before I build the (pdf version) of the book, I need to follow this suggestion by running the following in R before calling make.

devtools::install_github("hadley/oldbookdown")

• R Graph Essentials Essentials by David Lillis. Chapters 3 and 4.

Some examples:

• http://blog.diegovalle.net/2015/01/the-74-most-violent-cities-in-mexico.html
• R Graph Catalog

Introduction

• https://www.youtube.com/watch?v=SaJCKpYX5Lo&t=2742

ggthemr: Themes for ggplot2

• http://www.shanelynn.ie/themes-and-colours-for-r-ggplots-with-ggthemr/

ggedit – interactive ggplot aesthetic and theme editor

https://www.r-statistics.com/2016/11/ggedit-interactive-ggplot-aesthetic-and-theme-editor/

Plotting individual observations and group means

https://drsimonj.svbtle.com/plotting-individual-observations-and-group-means-with-ggplot2

Colors

• How to expand color palette with ggplot and RColorBrewer
• Cookbook for R

Data Manipulation

• Best packages for data manipulation in R. It demonstrates to perform the same tasks using data.table and dplyr packages. data.table is faster and it may be a go-to package when performance and memory are the constraints.

5 most useful data manipulation functions

• subset() for making subsets of data (natch)
• merge() for combining data sets in a smart and easy way
• melt()-reshape2 package for converting from wide to long data formats
• dcast()-reshape2 package for converting from long to wide data formats, and for making summary tables
• ddply()-plyr package for doing split-apply-combine operations, which covers a huge swath of the most tricky data operations

data.table

Fast aggregation of large data (e.g. 100GB in RAM or just several GB size file), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns and a fast file reader (fread).

Question: how to make use multicore with data.table package?

• Reading large data tables in R

library(data.table)
x <- fread("mylargefile.txt")

• Note that 'x[, 2] always return 2. If you want to do the thing you want, use x[, 2, with=FALSE] or x[, V2] where V2 is the header name. See the FAQ #1 in data.table.
• Understanding data.table Rolling Joins
• Intro to The data.table Package
• In the Introduction to data.table vignette, the data.table::order() function is SLOWER than base::order() from my Odroid xu4 (running Ubuntu 14.04.4 trusty on uSD)

odt = data.table(col=sample(1e7))
(t1 <- system.time(ans1 <- odt[base::order(col)]))  ## uses order from base R
#   user  system elapsed 
#  2.730   0.210   2.947 
(t2 <- system.time(ans2 <- odt[order(col)]))        ## uses data.table's order
#   user  system elapsed 
#  2.830   0.215   3.052
(identical(ans1, ans2))
# [1] TRUE

• Boost Your Data Munging with R

stringr, plyr, dplyr packages

http://martinsbioblogg.wordpress.com/2013/03/24/using-r-reading-tables-that-need-a-little-cleaning/

A data.frame is pretty much a list of vectors, so we use plyr to apply over the list and stringr to search and replace in the vectors.

Intro to dplyr by rollingyours.

reshape

Data Shape Transformation With Reshape()

reshape2

Use acast() function in reshape2 package. It will convert data.frame used for analysis to a table-like data.frame good for display.

• http://lamages.blogspot.com/2013/10/creating-matrix-from-long-dataframe.html

tidyr

An evolution of reshape2. It's designed specifically for data tidying (not general reshaping or aggregating) and works well with dplyr data pipelines.

• http://blog.rstudio.org/2014/07/22/introducing-tidyr/
• http://rpubs.com/seandavi/GEOMetadbSurvey2014
• http://timelyportfolio.github.io/rCharts_factor_analytics/factors_with_new_R.html
• tidyr vs reshape2
• Google: R tidyr

magrittr

Instead of nested statements, it is using pipe operator %>%. So the code is easier to read. Impressive!

• http://rud.is/b/2015/02/04/a-step-to-the-right-in-r-assignments/
• http://rpubs.com/tjmahr/pipelines_2015
• http://danielmarcelino.com/i-loved-this-crosstable/
• http://moderndata.plot.ly/using-the-pipe-operator-in-r-with-plotly/

jpeg

If we want to create the image on this wiki left hand side panel, we can use the jpeg package to read an existing plot and then edit and save it.

We can also use the jpeg package to import and manipulate a jpg image. See Fun with Heatmaps and Plotly.

cairoDevice

PS. Not sure the advantage of functions in this package compared to R's functions (eg. Cairo_svg() vs svg()) or even Cairo package.

For ubuntu OS, we need to install 2 libraries and 1 R package RGtk2.

sudo apt-get install libgtk2.0-dev libcairo2-dev

On Windows OS, we may got the error: unable to load shared object 'C:/Program Files/R/R-3.0.2/library/cairoDevice/libs/x64/cairoDevice.dll' . We need to follow the instruction in here.

iterators

Iterator is useful over for-loop if the data is already a collection. It can be used to iterate over a vector, data frame, matrix, file

Iterator can be combined to use with foreach package http://www.exegetic.biz/blog/2013/11/iterators-in-r/ has more elaboration.

Colors

• http://www.bauer.uh.edu/parks/truecolor.htm Interactive RGB, Alpha and Color Picker
• http://deanattali.com/blog/colourpicker-package/ Not sure what it is doing
• How to Choose the Best Colors For Your Data Charts
• How to expand color palette with ggplot and RColorBrewer
• Colors in ggplot2
• Color names in R

colortools

Tools that allow users generate color schemes and palettes

rex

Friendly Regular Expressions

formatR

The best strategy to avoid failure is to put comments in complete lines or after complete R expressions.

See also this discussion on stackoverflow talks about R code reformatting.

library(formatR)
tidy_source("Input.R", file = "output.R", width.cutoff=70)
tidy_source("clipboard") 
# default width is getOption("width") which is 127 in my case.

Some issues

• Comments appearing at the beginning of a line within a long complete statement. This will break tidy_source().

cat("abcd",
    # This is my comment
    "defg")

will result in

> tidy_source("clipboard")
Error in base::parse(text = code, srcfile = NULL) : 
  3:1: unexpected string constant
2: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# This is my comment.HaHaHa_EnD_TiDy_IdEnTiFiEr")
3: "defg"
   ^

• Comments appearing at the end of a line within a long complete statement won't break tidy_source() but tidy_source() cannot re-locate/tidy the comma sign.

cat("abcd"
    ,"defg"   # This is my comment
  ,"ghij")

will become

cat("abcd", "defg"  # This is my comment
, "ghij") 

Still bad!!

• Comments appearing at the end of a line within a long complete statement breaks tidy_source() function. For example,

cat("</p>",
	"<HR SIZE=5 WIDTH=\"100%\" NOSHADE>",
	ifelse(codeSurv == 0,"<h3><a name='Genes'><b><u>Genes which are differentially expressed among classes:</u></b></a></h3>", #4/9/09
	                     "<h3><a name='Genes'><b><u>Genes significantly associated with survival:</u></b></a></h3>"), 
	file=ExternalFileName, sep="\n", append=T)

will result in

> tidy_source("clipboard", width.cutoff=70)
Error in base::parse(text = code, srcfile = NULL) : 
  3:129: unexpected SPECIAL
2: "<HR SIZE=5 WIDTH=\"100%\" NOSHADE>" ,
3: ifelse ( codeSurv == 0 , "<h3><a name='Genes'><b><u>Genes which are differentially expressed among classes:</u></b></a></h3>" , %InLiNe_IdEnTiFiEr%

• width.cutoff parameter is not always working. For example, there is no any change for the following snippet though I hope it will move the cat() to the next line.

if (codePF & !GlobalTest & !DoExactPermTest) cat(paste("Multivariate Permutations test was computed based on", 
    NumPermutations, "random permutations"), "<BR>", " ", file = ExternalFileName, 
    sep = "\n", append = T)

• It merges lines though I don't always want to do that. For example

cat("abcd"
    ,"defg"  
  ,"ghij")

will become

cat("abcd", "defg", "ghij") 

Download papers

biorxivr

Search and Download Papers from the bioRxiv Preprint Server

aRxiv

Interface to the arXiv API

pdftools

http://ropensci.org/blog/2016/03/01/pdftools-and-jeroen

Different ways of using R

R call C/C++

Mainly talks about .C() and .Call().

• R-Extension manual of course.
• http://faculty.washington.edu/kenrice/sisg-adv/sisg-07.pdf
• http://www.stat.berkeley.edu/scf/paciorek-cppWorkshop.pdf (Very useful)
• http://www.stat.harvard.edu/ccr2005/
• http://mazamascience.com/WorkingWithData/?p=1099

R call Fortran 90

• https://stat.ethz.ch/pipermail/r-devel/2015-March/070851.html

Embedding R

• See Writing for R Extensions Manual Chapter 8.
• Talk by Simon Urbanek in UseR 2004.
• Technical report by Friedrich Leisch in 2007.
• https://stat.ethz.ch/pipermail/r-help/attachments/20110729/b7d86ed7/attachment.pl

An very simple example (do not return from shell) from Writing R Extensions manual

The command-line R front-end, R_HOME/bin/exec/R, is one such example. Its source code is in file <src/main/Rmain.c>.

This example can be run by

R_HOME/bin/R CMD R_HOME/bin/exec/R

Note:

1. R_HOME/bin/exec/R is the R binary. However, it couldn't be launched directly unless R_HOME and LD_LIBRARY_PATH are set up. Again, this is explained in Writing R Extension manual.
2. R_HOME/bin/R is a shell-script front-end where users can invoke it. It sets up the environment for the executable. It can be copied to /usr/local/bin/R. When we run R_HOME/bin/R, it actually runs R_HOME/bin/R CMD R_HOME/bin/exec/R (see line 259 of R_HOME/bin/R as in R 3.0.2) so we know the important role of R_HOME/bin/exec/R.

More examples of embedding can be found in tests/Embedding directory. Read <index.html> for more information about these test examples.

An example from Bioconductor workshop

• What is covered in this section is different from Create and use a standalone Rmath library.
• Use eval() function. See R-Ext 8.1 and 8.2 and 5.11.
• http://stackoverflow.com/questions/2463437/r-from-c-simplest-possible-helloworld (obtained from searching R_tryEval on google)
• http://stackoverflow.com/questions/7457635/calling-r-function-from-c

Example: Create <embed.c> file

#include <Rembedded.h>
#include <Rdefines.h>

static void doSplinesExample();
int
main(int argc, char *argv[])
{
    Rf_initEmbeddedR(argc, argv);
    doSplinesExample();
    Rf_endEmbeddedR(0);
    return 0;
}
static void
doSplinesExample()
{
    SEXP e, result;
    int errorOccurred;

    // create and evaluate 'library(splines)'
    PROTECT(e = lang2(install("library"), mkString("splines")));
    R_tryEval(e, R_GlobalEnv, &errorOccurred);
    if (errorOccurred) {
        // handle error
    }
    UNPROTECT(1);

    // 'options(FALSE)' ...
    PROTECT(e = lang2(install("options"), ScalarLogical(0)));
    // ... modified to 'options(example.ask=FALSE)' (this is obscure)
    SET_TAG(CDR(e), install("example.ask"));
    R_tryEval(e, R_GlobalEnv, NULL);
    UNPROTECT(1);

    // 'example("ns")'
    PROTECT(e = lang2(install("example"), mkString("ns")));
    R_tryEval(e, R_GlobalEnv, &errorOccurred);
    UNPROTECT(1);
}

Then build the executable. Note that I don't need to create R_HOME variable.

cd 
tar xzvf 
cd R-3.0.1
./configure --enable-R-shlib
make
cd tests/Embedding
make
~/R-3.0.1/bin/R CMD ./Rtest

nano embed.c
# Using a single line will give an error and cannot not show the real problem.
# ../../bin/R CMD gcc -I../../include -L../../lib -lR embed.c
# A better way is to run compile and link separately
gcc -I../../include -c embed.c
gcc -o embed embed.o -L../../lib -lR -lRblas
../../bin/R CMD ./embed

Note that if we want to call the executable file ./embed directly, we shall set up R environment by specifying R_HOME variable and including the directories used in linking R in LD_LIBRARY_PATH. This is based on the inform provided by Writing R Extensions.

export R_HOME=/home/brb/Downloads/R-3.0.2
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/brb/Downloads/R-3.0.2/lib
./embed # No need to include R CMD in front.

Question: Create a data frame in C? Answer: Use data.frame() via an eval() call from C. Or see the code is stats/src/model.c, as part of model.frame.default. Or using Rcpp as here.

Reference http://bioconductor.org/help/course-materials/2012/Seattle-Oct-2012/AdvancedR.pdf

Create a Simple Socket Server in R

This example is coming from this paper.

Create an R function

simpleServer <- function(port=6543)
{
  sock <- socketConnection ( port=port , server=TRUE)
  on.exit(close( sock ))
  cat("\nWelcome to R!\nR>" ,file=sock )
  while(( line <- readLines ( sock , n=1)) != "quit")
  {
    cat(paste("socket >" , line , "\n"))
    out<- capture.output (try(eval(parse(text=line ))))
    writeLines ( out , con=sock )
    cat("\nR> " ,file =sock )
  }
}

Then run simpleServer(). Open another terminal and try to communicate with the server

$ telnet localhost 6543
Trying 127.0.0.1...
Connected to localhost.
Escape character is '^]'.

Welcome to R!
R> summary(iris[, 3:5])
  Petal.Length    Petal.Width          Species  
 Min.   :1.000   Min.   :0.100   setosa    :50  
 1st Qu.:1.600   1st Qu.:0.300   versicolor:50  
 Median :4.350   Median :1.300   virginica :50  
 Mean   :3.758   Mean   :1.199                  
 3rd Qu.:5.100   3rd Qu.:1.800                  
 Max.   :6.900   Max.   :2.500                  

R> quit
Connection closed by foreign host.

Rserve

Note the way of launching Rserve is like the way we launch C program when R was embedded in C. See Call R from C/C++ or Example from Bioconductor workshop.

See my Rserve page.

RApache

• http://www.stat.ucla.edu/~jeroen/files/seminar.pdf

littler

http://dirk.eddelbuettel.com/code/littler.html

Difference between Rscript and littler

RInside: Embed R in C++

See RInside

(From RInside documentation) The RInside package makes it easier to embed R in your C++ applications. There is no code you would execute directly from the R environment. Rather, you write C++ programs that embed R which is illustrated by some the included examples.

The included examples are armadillo, eigen, mpi, qt, standard, threads and wt.

To run 'make' when we don't have a global R, we should modify the file <Makefile>. Also if we just want to create one executable file, we can do, for example, 'make rinside_sample1'.

To run any executable program, we need to specify LD_LIBRARY_PATH variable, something like

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/brb/Downloads/R-3.0.2/lib 

The real build process looks like (check <Makefile> for completeness)

g++ -I/home/brb/Downloads/R-3.0.2/include \
    -I/home/brb/Downloads/R-3.0.2/library/Rcpp/include \
    -I/home/brb/Downloads/R-3.0.2/library/RInside/include -g -O2 -Wall \
    -I/usr/local/include   \
    rinside_sample0.cpp  \
    -L/home/brb/Downloads/R-3.0.2/lib -lR  -lRblas -lRlapack \
    -L/home/brb/Downloads/R-3.0.2/library/Rcpp/lib -lRcpp \
    -Wl,-rpath,/home/brb/Downloads/R-3.0.2/library/Rcpp/lib \
    -L/home/brb/Downloads/R-3.0.2/library/RInside/lib -lRInside \
    -Wl,-rpath,/home/brb/Downloads/R-3.0.2/library/RInside/lib \
    -o rinside_sample0

Hello World example of embedding R in C++.

#include <RInside.h>                    // for the embedded R via RInside

int main(int argc, char *argv[]) {

    RInside R(argc, argv);              // create an embedded R instance 

    R["txt"] = "Hello, world!\n";	// assign a char* (string) to 'txt'

    R.parseEvalQ("cat(txt)");           // eval the init string, ignoring any returns

    exit(0);
}

The above can be compared to the Hello world example in Qt.

#include <QApplication.h>
#include <QPushButton.h>

int main( int argc, char **argv )
{
    QApplication app( argc, argv );

    QPushButton hello( "Hello world!", 0 );
    hello.resize( 100, 30 );

    app.setMainWidget( &hello );
    hello.show();

    return app.exec();
}

RFortran

RFortran is an open source project with the following aim:

To provide an easy to use Fortran software library that enables Fortran programs to transfer data and commands to and from R.

It works only on Windows platform with Microsoft Visual Studio installed:(

Call R from other languages

JRI

http://www.rforge.net/JRI/

ryp2

http://rpy.sourceforge.net/rpy2.html

Create a standalone Rmath library

R has many math and statistical functions. We can easily use these functions in our C/C++/Fortran. The definite guide of doing this is on Chapter 9 "The standalone Rmath library" of R-admin manual.

Here is my experience based on R 3.0.2 on Windows OS.

Create a static library <libRmath.a> and a dynamic library <Rmath.dll>

Suppose we have downloaded R source code and build R from its source. See Build_R_from_its_source. Then the following 2 lines will generate files <libRmath.a> and <Rmath.dll> under C:\R\R-3.0.2\src\nmath\standalone directory.

cd C:\R\R-3.0.2\src\nmath\standalone
make -f Makefile.win

Use Rmath library in our code

set CPLUS_INCLUDE_PATH=C:\R\R-3.0.2\src\include
set LIBRARY_PATH=C:\R\R-3.0.2\src\nmath\standalone
# It is not LD_LIBRARY_PATH in above.

# Created <RmathEx1.cpp> from the book "Statistical Computing in C++ and R" web site
# http://math.la.asu.edu/~eubank/CandR/ch4Code.cpp
# It is OK to save the cpp file under any directory.

# Force to link against the static library <libRmath.a>
g++ RmathEx1.cpp -lRmath -lm -o RmathEx1.exe
# OR
g++ RmathEx1.cpp -Wl,-Bstatic -lRmath -lm -o RmathEx1.exe

# Force to link against dynamic library <Rmath.dll>
g++ RmathEx1.cpp Rmath.dll -lm -o RmathEx1Dll.exe

Test the executable program. Note that the executable program RmathEx1.exe can be transferred to and run in another computer without R installed. Isn't it cool!

c:\R>RmathEx1
Enter a argument for the normal cdf:
1
Enter a argument for the chi-squared cdf:
1
Prob(Z <= 1) = 0.841345
Prob(Chi^2 <= 1)= 0.682689

Below is the cpp program <RmathEx1.cpp>.

//RmathEx1.cpp
#define MATHLIB_STANDALONE 
#include <iostream>
#include "Rmath.h"

using std::cout; using std::cin; using std::endl;

int main()
{
  double x1, x2;
  cout << "Enter a argument for the normal cdf:" << endl;
  cin >> x1;
  cout << "Enter a argument for the chi-squared cdf:" << endl;
  cin >> x2;

  cout << "Prob(Z <= " << x1 << ") = " << 
    pnorm(x1, 0, 1, 1, 0)  << endl;
  cout << "Prob(Chi^2 <= " << x2 << ")= " << 
    pchisq(x2, 1, 1, 0) << endl;
  return 0;
}

Calling R.dll directly

See Chapter 8.2.2 of R Extensions. This is related to embedding R under Windows. The file <R.dll> on Windows is like <libR.so> on Linux.

Create HTML 5 web and slides

See here

Scheduling R Markdown Reports via Email

http://www.analyticsforfun.com/2016/01/scheduling-r-markdown-reports-via-email.html

Create presentation file (beamer)

• http://rmarkdown.rstudio.com/beamer_presentation_format.html
• http://www.theresearchkitchen.com/archives/1017 (markdown and presentation files)
• http://rmarkdown.rstudio.com/

1. Create Rmd file first in Rstudio by File -> R markdown. Select Presentation > choose pdf (beamer) as output format.
2. Edit the template created by RStudio.
3. Click 'Knit pdf' button (Ctrl+Shift+k) to create/display the pdf file.

An example of Rmd is

---
title: "My Example"
author: You Know Me
date: Dec 32, 2014
output: beamer_presentation
---

## R Markdown

This is an R Markdown presentation. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. 
For more details on using R Markdown see <http://rmarkdown.rstudio.com>.

When you click the **Knit** button a document will be generated that includes both content as well as the output of any 
embedded R code chunks within the document.

## Slide with Bullets

- Bullet 1
- Bullet 2
- Bullet 3. Mean is $\frac{1}{n} \sum_{i=1}^n x_i$.
$$ 
\mu = \frac{1}{n} \sum_{i=1}^n x_i
$$

## New slide

![picture of BDGE](/home/brb/Pictures/BDGEFinished.png)

## Slide with R Code and Output

```{r}
summary(cars)
```

## Slide with Plot

```{r, echo=FALSE}
plot(cars)
```

Create HTML report

ReportingTools (Jason Hackney) from Bioconductor.

htmlTable package

The htmlTable package is intended for generating tables using HTML formatting. This format is compatible with Markdown when used for HTML-output. The most basic table can easily be created by just passing a matrix or a data.frame to the htmlTable-function.

• http://cran.r-project.org/web/packages/htmlTable/vignettes/general.html
• http://gforge.se/2014/01/fast-track-publishing-using-knitr-part-iv/

formattable

http://www.magesblog.com/2016/01/formatting-table-output-in-r.html

htmltab package

This package is NOT used to CREATE html report but EXTRACT html table.

ztable package

Makes zebra-striped tables (tables with alternating row colors) in LaTeX and HTML formats easily from a data.frame, matrix, lm, aov, anova, glm or coxph objects.

Create academic report

reports package in CRAN and in github repository. The youtube video gives an overview of the package.

Create pdf and epub files

# Idea:
#        knitr        pdflatex
#   rnw -------> tex ----------> pdf
library(knitr)
knit("example.rnw") # create example.tex file

• A very simple example <002-minimal.Rnw> from yihui.name works fine on linux.

git clone https://github.com/yihui/knitr-examples.git

• <knitr-minimal.Rnw>. I have no problem to create pdf file on Windows but still cannot generate pdf on Linux from tex file. Some people suggested to run sudo apt-get install texlive-fonts-recommended to install missing fonts. It works!

To see a real example, check out DESeq2 package (inst/doc subdirectory). In addition to DESeq2, I also need to install DESeq, BiocStyle, airway, vsn, gplots, and pasilla packages from Bioconductor. Note that, it is best to use sudo/admin account to install packages.

Or starts with markdown file. Download the example <001-minimal.Rmd> and remove the last line of getting png file from internet.

# Idea:
#        knitr        pandoc
#   rmd -------> md ----------> pdf

git clone https://github.com/yihui/knitr-examples.git
cd knitr-examples
R -e "library(knitr); knit('001-minimal.Rmd')"
pandoc 001-minimal.md -o 001-minimal.pdf # require pdflatex to be installed !!

To create an epub file (not success yet on Windows OS, missing figures on Linux OS)

# Idea:
#        knitr        pandoc
#   rnw -------> tex ----------> markdown or epub

library(knitr)
knit("DESeq2.Rnw") # create DESeq2.tex
system("pandoc  -f latex -t markdown -o DESeq2.md DESeq2.tex")

## Windows OS, epub cannot be built
pandoc:
Error:
"source" (line 41, column 7):
unexpected "k"
expecting "{document}"

## Linux OS, epub missing figures and R codes.
## First install texlive base and extra packages
## sudo apt-get install texlive-latex-base texlive-latex-extra
pandoc: Could not find media `figure/SchwederSpjotvoll-1', skipping...
pandoc: Could not find media `figure/sortedP-1', skipping...
pandoc: Could not find media `figure/figHeatmap2c-1', skipping...
pandoc: Could not find media `figure/figHeatmap2b-1', skipping...
pandoc: Could not find media `figure/figHeatmap2a-1', skipping...
pandoc: Could not find media `figure/plotCountsAdv-1', skipping...
pandoc: Could not find media `figure/plotCounts-1', skipping...
pandoc: Could not find media `figure/MA-1', skipping...
pandoc: Could not find media `figure/MANoPrior-1', skipping...

The problems are at least

• figures need to be generated under the same directory as the source code
• figures cannot be in the format of pdf (DESeq2 generates both pdf and png files format)
• missing R codes

Convert tex to epub

• http://tex.stackexchange.com/questions/156668/tex-to-epub-conversion

Create Word report

knitr + pandoc

• http://www.r-statistics.com/2013/03/write-ms-word-document-using-r-with-as-little-overhead-as-possible/
• http://www.carlboettiger.info/2012/04/07/writing-reproducibly-in-the-open-with-knitr.html
• http://rmarkdown.rstudio.com/articles_docx.html

It is better to create rmd file in RStudio. Rstudio provides a template for rmd file and it also provides a quick reference to R markdown language.

# Idea:
#        knitr       pandoc
#   rmd -------> md --------> docx
library(knitr)
knit2html("example.rmd") #Create md and html files

and then

FILE <- "example"
system(paste0("pandoc -o ", FILE, ".docx ", FILE, ".md"))

Note. For example reason, if I play around the above 2 commands for several times, the knit2html() does not work well. However, if I click 'Knit HTML' button on the RStudio, it then works again.

Another way is

library(pander)
name = "demo"
knit(paste0(name, ".Rmd"), encoding = "utf-8")
Pandoc.brew(file = paste0(name, ".md"), output = paste0(-name, "docx"), convert = "docx")

Note that once we have used knitr command to create a md file, we can use pandoc shell command to convert it to different formats:

• A pdf file: pandoc -s report.md -t latex -o report.pdf
• A html file: pandoc -s report.md -o report.html (with the -c flag html files can be added easily)
• Openoffice: pandoc report.md -o report.odt
• Word docx: pandoc report.md -o report.docx

We can also create the epub file for reading on Kobo ereader. For example, download this file and save it as example.Rmd. I need to remove the line containing the link to http://i.imgur.com/RVNmr.jpg since it creates an error when I run pandoc (not sure if it is the pandoc version I have is too old). Now we just run these 2 lines to get the epub file. Amazing!

knit("example.Rmd")
pandoc("example.md", format="epub")

PS. If we don't remove the link, we will get an error message (pandoc 1.10.1 on Windows 7)

> pandoc("Rmd_to_Epub.md", format="epub")
executing pandoc   -f markdown -t epub -o Rmd_to_Epub.epub "Rmd_to_Epub.utf8md"
pandoc.exe: .\.\http://i.imgur.com/RVNmr.jpg: openBinaryFile: invalid argument (Invalid argument)
Error in (function (input, format, ext, cfg)  : conversion failed
In addition: Warning message:
running command 'pandoc   -f markdown -t epub -o Rmd_to_Epub.epub "Rmd_to_Epub.utf8md"' had status 1

pander

Try pandoc[1] with a minimal reproducible example, you might give a try to my "pander" package [2] too:

library(pander)
Pandoc.brew(system.file('examples/minimal.brew', package='pander'),
            output = tempfile(), convert = 'docx')

Where the content of the "minimal.brew" file is something you might have got used to with Sweave - although it's using "brew" syntax instead. See the examples of pander [3] for more details. Please note that pandoc should be installed first, which is pretty easy on Windows.

1. http://johnmacfarlane.net/pandoc/
2. http://rapporter.github.com/pander/
3. http://rapporter.github.com/pander/#examples

R2wd

Use R2wd package. However, only 32-bit R is allowed and sometimes it can not produce all 'table's.

> library(R2wd)
> wdGet()
Loading required package: rcom
Loading required package: rscproxy
rcom requires a current version of statconnDCOM installed.
To install statconnDCOM type
     installstatconnDCOM()

This will download and install the current version of statconnDCOM

You will need a working Internet connection
because installation needs to download a file.
Error in if (wdapp[["Documents"]][["Count"]] == 0) wdapp[["Documents"]]$Add() : 
  argument is of length zero 

The solution is to launch 32-bit R instead of 64-bit R since statconnDCOM does not support 64-bit R.

Convert from pdf to word

The best rendering of advanced tables is done by converting from pdf to Word. See http://biostat.mc.vanderbilt.edu/wiki/Main/SweaveConvert

rtf

Use rtf package for Rich Text Format (RTF) Output.

xtable

Package xtable will produce html output. If you save the file and then open it with Word, you will get serviceable results. I've had better luck copying the output from xtable and pasting it into Excel.

ReporteRs

Microsoft Word, Microsoft Powerpoint and HTML documents generation from R. The source code is hosted on https://github.com/davidgohel/ReporteRs

A quick exploration

R Graphs Gallery

• Romain François
• R Graph Catalog written using R + Shiny. The source code is available on Github.
• Forest plot

COM client or server

Client

RDCOMClient where excel.link depends on it.

Server

RDCOMServer

Use R under proxy

http://support.rstudio.org/help/kb/faq/configuring-r-to-use-an-http-proxy

What is the best place to save Rconsole on Windows platform

Put it in C:/Users/USERNAME/Documents folder so no matter how R was upgraded/downgraded, it always find my preference.

Web scraping

http://www.slideshare.net/schamber/web-data-from-r#btnNext

pubmed.mineR

Text mining of PubMed Abstracts (http://www.ncbi.nlm.nih.gov/pubmed). The algorithms are designed for two formats (text and XML) from PubMed.

RStudio

• Github
• Installing RStudio (1.0.44) on Ubuntu will not install Java even the source code contains 37.5% Java??

Launch RStudio

If multiple versions of R was detected, Rstudio can not be launched successfully. A java-like clock will be spinning without a stop. The trick is to click Ctrl key and click the Rstudio at the same time. After done that, it will show up a selection of R to choose from.

List files using regular expression

• Extension

list.files(pattern = "\\.txt$")

where the dot (.) is a metacharacter. It is used to refer to any character.

• Start with

list.files(pattern = "^Something")

Using Sys.glob()"' as

> Sys.glob("~/Downloads/*.txt")
[1] "/home/brb/Downloads/ip.txt"       "/home/brb/Downloads/valgrind.txt"

Hidden tool: rsync in Rtools

c:\Rtools\bin>rsync -avz "/cygdrive/c/users/limingc/Downloads/a.exe" "/cygdrive/c/users/limingc/Documents/"
sending incremental file list
a.exe

sent 323142 bytes  received 31 bytes  646346.00 bytes/sec
total size is 1198416  speedup is 3.71

c:\Rtools\bin>

And rsync works best when we need to sync folder.

c:\Rtools\bin>rsync -avz "/cygdrive/c/users/limingc/Downloads/binary" "/cygdrive/c/users/limingc/Documents/"
sending incremental file list
binary/
binary/Eula.txt
binary/cherrytree.lnk
binary/depends64.chm
binary/depends64.dll
binary/depends64.exe
binary/mtputty.exe
binary/procexp.chm
binary/procexp.exe
binary/pscp.exe
binary/putty.exe
binary/sqlite3.exe
binary/wget.exe

sent 4115294 bytes  received 244 bytes  1175868.00 bytes/sec
total size is 8036311  speedup is 1.95

c:\Rtools\bin>rm c:\users\limingc\Documents\binary\procexp.exe
cygwin warning:
  MS-DOS style path detected: c:\users\limingc\Documents\binary\procexp.exe
  Preferred POSIX equivalent is: /cygdrive/c/users/limingc/Documents/binary/procexp.exe
  CYGWIN environment variable option "nodosfilewarning" turns off this warning.
  Consult the user's guide for more details about POSIX paths:
    http://cygwin.com/cygwin-ug-net/using.html#using-pathnames

c:\Rtools\bin>rsync -avz "/cygdrive/c/users/limingc/Downloads/binary" "/cygdrive/c/users/limingc/Documents/"
sending incremental file list
binary/
binary/procexp.exe

sent 1767277 bytes  received 35 bytes  3534624.00 bytes/sec
total size is 8036311  speedup is 4.55

c:\Rtools\bin>

Unforunately, if the destination is a network drive, I could get a permission denied (13) error. See also http://superuser.com/questions/69620/rsync-file-permissions-on-windows

Install rgdal package on ubuntu

sudo apt-get install libgdal1-dev libproj-dev
R
> install.packages("rgdal")

Set up Emacs on Windows

Edit the file C:\Program Files\GNU Emacs 23.2\site-lisp\site-start.el with something like

(setq-default inferior-R-program-name
              "c:/program files/r/r-2.15.2/bin/i386/rterm.exe")

Database

RSQLite

[http://blog.sobbayi.com/sql

sqldf

Manipulate R data frames using SQL. Depends on RSQLite. A use of gsub, reshape2 and sqldf with healthcare data

RMySQL

• http://datascienceplus.com/bringing-the-powers-of-sql-into-r/

MongoDB

• http://www.r-bloggers.com/r-and-mongodb/
• http://watson.nci.nih.gov/~sdavis/blog/rmongodb-using-R-with-mongo/

Github

R source

https://github.com/wch/r-source/ Daily update, interesting, should be visited every day. Clicking 1000+ commits to look at daily changes.

If we are interested in a certain branch (say 3.2), look for R-3-2-branch.

R packages (only) source (metacran)

• https://github.com/cran/ by Gábor Csárdi, the author of igraph software.

Bioconductor packages source

• Announcement
• https://github.com/Bioconductor-mirror

Send local repository to Github in R by using reports package

http://www.youtube.com/watch?v=WdOI_-aZV0Y

My collection

• https://github.com/arraytools
• https://gist.github.com/4383351 heatmap using leukemia data
• https://gist.github.com/4382774 heatmap using sequential data
• https://gist.github.com/4484270 biocLite

How to download

Clone ~ Download.

• Command line

git clone https://gist.github.com/4484270.git

This will create a subdirectory called '4484270' with all cloned files there.

• Within R

library(devtools)
source_gist("4484270")

or First download the json file from

https://api.github.com/users/MYUSERLOGIN/gists

and then

library(RJSONIO)
x <- fromJSON("~/Downloads/gists.json")
setwd("~/Downloads/")
gist.id <- lapply(x, "[[", "id")
lapply(gist.id, function(x){
  cmd <- paste0("git clone https://gist.github.com/", x, ".git")
  system(cmd)
})

Jekyll

An Easy Start with Jekyll, for R-Bloggers

Connect R with Arduino

• http://lamages.blogspot.com/2012/10/connecting-real-world-to-r-with-arduino.html
• http://jean-robert.github.io/2012/11/11/thermometer-R-using-Arduino-Java.html
• http://bio7.org/?p=2049
• http://www.rforge.net/Arduino/svn.html

Android App

• R Instructor $4.84
• Statistical Distribution (Not R related app)

Time series stock price plot

• http://blog.revolutionanalytics.com/2015/08/plotting-time-series-in-r.html (ggplot2, xts, dygraphs)

Circular plot

• http://freakonometrics.hypotheses.org/20667 which uses https://cran.r-project.org/web/packages/circlize/ circlize] package.
• https://www.biostars.org/p/17728/
• RCircos package from CRAN.
• OmicCircos from Bioconductor.

Venn Diagram

• limma http://www.ats.ucla.edu/stat/r/faq/venn.htm - only black and white?
• VennDiagram - input has to be the numbers instead of the original vector?
• http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual#TOC-Venn-Diagrams and the R code or the Bioc package systemPipeR

# systemPipeR package method
library(systemPipeR)
setlist <- list(A=sample(letters, 18), B=sample(letters, 16), C=sample(letters, 20), D=sample(letters, 22), E=sample(letters, 18)) 
OLlist <- overLapper(setlist[1:3], type="vennsets")
vennPlot(list(OLlist))                             

# R script source method
source("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/overLapper.R") 
setlist <- list(A=sample(letters, 18), B=sample(letters, 16), C=sample(letters, 20), D=sample(letters, 22), E=sample(letters, 18)) 
# or (obtained by dput(setlist))
setlist <- structure(list(A = c("o", "h", "u", "p", "i", "s", "a", "w", 
"b", "z", "n", "c", "k", "j", "y", "m", "t", "q"), B = c("h", 
"r", "x", "y", "b", "t", "d", "o", "m", "q", "g", "v", "c", "u", 
"f", "z"), C = c("b", "e", "t", "u", "s", "j", "o", "k", "d", 
"l", "g", "i", "w", "n", "p", "a", "y", "x", "m", "z"), D = c("f", 
"g", "b", "k", "j", "m", "e", "q", "i", "d", "o", "l", "c", "t", 
"x", "r", "s", "u", "w", "a", "z", "n"), E = c("u", "w", "o", 
"k", "n", "h", "p", "z", "l", "m", "r", "d", "q", "s", "x", "b", 
"v", "t"), F = c("o", "j", "r", "c", "l", "l", "u", "b", "f", 
"d", "u", "m", "y", "t", "y", "s", "a", "g", "t", "m", "x", "m"
)), .Names = c("A", "B", "C", "D", "E", "F"))

OLlist <- overLapper(setlist[1:3], type="vennsets")
counts <- list(sapply(OLlist$Venn_List, length))  
vennPlot(counts=counts)

Amazing plots

New R logo 2/11/2016

• http://rud.is/b/2016/02/11/plot-the-new-svg-r-logo-with-ggplot2/
• https://www.stat.auckland.ac.nz/~paul/Reports/Rlogo/Rlogo.html

library(sp)
library(maptools)
library(ggplot2)
library(ggthemes)
# rgeos requires the installation of GEOS from http://trac.osgeo.org/geos/
system("curl http://download.osgeo.org/geos/geos-3.5.0.tar.bz2 | tar jx")
system("cd geos-3.5.0; ./configure; make; sudo make install")
library(rgeos)
 
r_wkt_gist_file <- "https://gist.githubusercontent.com/hrbrmstr/07d0ccf14c2ff109f55a/raw/db274a39b8f024468f8550d7aeaabb83c576f7ef/rlogo.wkt"
if (!file.exists("rlogo.wkt")) download.file(r_wkt_gist_file, "rlogo.wkt")
rlogo <- readWKT(paste0(readLines("rlogo.wkt", warn=FALSE))) # rgeos
 
rlogo_shp <- SpatialPolygonsDataFrame(rlogo, data.frame(poly=c("halo", "r"))) # sp
rlogo_poly <- fortify(rlogo_shp, region="poly") # ggplot2
 
ggplot(rlogo_poly) + 
  geom_polygon(aes(x=long, y=lat, group=id, fill=id)) + 
  scale_fill_manual(values=c(halo="#b8babf", r="#1e63b5")) +
  coord_equal() + 
  theme_map() + 
  theme(legend.position="none")

3D plot

Using persp function to create the following plot.

### Random pattern
 # Create matrix with random values with dimension of final grid
  rand <- rnorm(441, mean=0.3, sd=0.1)
  mat.rand <- matrix(rand, nrow=21)
 
# Create another matrix for the colors. Start by making all cells green
  fill <- matrix("green3", nr = 21, nc = 21) 
 
# Change colors in each cell based on corresponding mat.rand value
  fcol <- fill
  fcol[] <- terrain.colors(40)[cut(mat.rand,
     stats::quantile(mat.rand, seq(0,1, len = 41),
     na.rm=T), include.lowest = TRUE)]
 
# Create concave surface using expontential function
  x <- -10:10
  y <- x^2
  y <- as.matrix(y)
  y1 <- y
  for(i in 1:20){tmp <- cbind(y,y1); y1 <- tmp[,1]; y <- tmp;}
  mat <- tmp[1:21, 1:21]
 
# Plot it up!
  persp(1:21, 1:21, t(mat)/10, theta = 90, phi = 35,col=fcol,
     scale = FALSE, axes = FALSE, box = FALSE)

### Organized pattern
# Same as before
  rand <- rnorm(441, mean=0.3, sd=0.1)
 
# Create concave surface using expontential function
  x <- -10:10
  y <- x^2
  y <- as.matrix(y)
  for(i in 1:20){tmp <- cbind(y,y); y1 <- tmp[,1]; y <- tmp;}
  mat <- tmp[1:21, 1:21]
 
###Organize rand by y and put into matrix form
  o <- order(rand,as.vector(mat))
  o.tmp <- cbind(rand[o], rev(sort(as.vector(mat))))
  mat.org <- matrix(o.tmp[,1], nrow=21)
  half.1 <- mat.org[,seq(1,21,2)]
  half.2 <- mat.org[,rev(seq(2,20,2))]
  full <- cbind(half.1, half.2)
  full <- t(full)
 
# Again, create color matrix and populate using rand values
zi <- full[-1, -1] + full[-1, -21] + full[-21,-1] + full[-21, -21] 
fill <- matrix("green3", nr = 20, nc = 20) 
fcol <- fill
fcol[] <- terrain.colors(40)[cut(zi,
        stats::quantile(zi, seq(0,1, len = 41), na.rm=T),
        include.lowest = TRUE)]
 
# Plot it up!        
persp(1:21, 1:21, t(mat)/10, theta = 90, phi = 35,col=t(fcol),
     scale = FALSE, axes = FALSE, box = FALSE)

Christmas tree

http://wiekvoet.blogspot.com/2014/12/merry-christmas.html

# http://blogs.sas.com/content/iml/2012/12/14/a-fractal-christmas-tree/
# Each row is a 2x2 linear transformation 
# Christmas tree 
L <-  matrix(
    c(0.03,  0,     0  ,  0.1,
        0.85,  0.00,  0.00, 0.85,
        0.8,   0.00,  0.00, 0.8,
        0.2,  -0.08,  0.15, 0.22,
        -0.2,   0.08,  0.15, 0.22,
        0.25, -0.1,   0.12, 0.25,
        -0.2,   0.1,   0.12, 0.2),
    nrow=4)
# ... and each row is a translation vector
B <- matrix(
    c(0, 0,
        0, 1.5,
        0, 1.5,
        0, 0.85,
        0, 0.85,
        0, 0.3,
        0, 0.4),
    nrow=2)

prob = c(0.02, 0.6,.08, 0.07, 0.07, 0.07, 0.07)

# Iterate the discrete stochastic map 
N = 1e5 #5  #   number of iterations 
x = matrix(NA,nrow=2,ncol=N)
x[,1] = c(0,2)   # initial point
k <- sample(1:7,N,prob,replace=TRUE) # values 1-7 

for (i in 2:N) 
  x[,i] = crossprod(matrix(L[,k[i]],nrow=2),x[,i-1]) + B[,k[i]] # iterate 

# Plot the iteration history 
png('card.png')
par(bg='darkblue',mar=rep(0,4))    
plot(x=x[1,],y=x[2,],
    col=grep('green',colors(),value=TRUE),
    axes=FALSE,
    cex=.1,
    xlab='',
    ylab='' )#,pch='.')

bals <- sample(N,20)
points(x=x[1,bals],y=x[2,bals]-.1,
    col=c('red','blue','yellow','orange'),
    cex=2,
    pch=19
)
text(x=-.7,y=8,
    labels='Merry',
    adj=c(.5,.5),
    srt=45,
    vfont=c('script','plain'),
    cex=3,
    col='gold'
)
text(x=0.7,y=8,
    labels='Christmas',
    adj=c(.5,.5),
    srt=-45,
    vfont=c('script','plain'),
    cex=3,
    col='gold'
)

Happy Thanksgiving

Turkey

treemap

http://ipub.com/treemap/

Voronoi diagram

• https://www.stat.auckland.ac.nz/~paul/Reports/VoronoiTreemap/voronoiTreeMap.html
• http://letstalkdata.com/2014/05/creating-voronoi-diagrams-with-ggplot/

Silent Night

# https://aschinchon.wordpress.com/2014/03/13/the-lonely-acacia-is-rocked-by-the-wind-of-the-african-night/
depth <- 9
angle<-30 #Between branches division
L <- 0.90 #Decreasing rate of branches by depth
nstars <- 300 #Number of stars to draw
mstars <- matrix(runif(2*nstars), ncol=2)
branches <- rbind(c(1,0,0,abs(jitter(0)),1,jitter(5, amount = 5)), data.frame())
colnames(branches) <- c("depth", "x1", "y1", "x2", "y2", "inertia")
for(i in 1:depth)
{
  df <- branches[branches$depth==i,]
  for(j in 1:nrow(df))
  {
    branches <- rbind(branches, c(df[j,1]+1, df[j,4], df[j,5], df[j,4]+L^(2*i+1)*sin(pi*(df[j,6]+angle)/180), df[j,5]+L^(2*i+1)*cos(pi*(df[j,6]+angle)/180), df[j,6]+angle+jitter(10, amount = 8)))
    branches <- rbind(branches, c(df[j,1]+1, df[j,4], df[j,5], df[j,4]+L^(2*i+1)*sin(pi*(df[j,6]-angle)/180), df[j,5]+L^(2*i+1)*cos(pi*(df[j,6]-angle)/180), df[j,6]-angle+jitter(10, amount = 8)))
  }
}
nodes <- rbind(as.matrix(branches[,2:3]), as.matrix(branches[,4:5]))
png("image.png", width = 1200, height = 600)
plot.new()
par(mai = rep(0, 4), bg = "gray12")
plot(nodes, type="n", xlim=c(-7, 3), ylim=c(0, 5))
for (i in 1:nrow(mstars)) 
{
  points(x=10*mstars[i,1]-7, y=5*mstars[i,2], col = "blue4", cex=.7, pch=16)
  points(x=10*mstars[i,1]-7, y=5*mstars[i,2], col = "blue",  cex=.3, pch=16)
  points(x=10*mstars[i,1]-7, y=5*mstars[i,2], col = "white", cex=.1, pch=16)
}
# The moon
points(x=-5, y=3.5, cex=40, pch=16, col="lightyellow")
# The tree
for (i in 1:nrow(branches)) {lines(x=branches[i,c(2,4)], y=branches[i,c(3,5)], col = paste("gray", as.character(sample(seq(from=50, to=round(50+5*branches[i,1]), by=1), 1)), sep = ""), lwd=(65/(1+3*branches[i,1])))}
rm(branches)
dev.off()

Google Analytics

GAR package

http://www.analyticsforfun.com/2015/10/query-your-google-analytics-data-with.html

Linear Programming

http://www.r-bloggers.com/modeling-and-solving-linear-programming-with-r-free-book/

Read rrd file

• https://en.wikipedia.org/wiki/RRDtool
• http://oss.oetiker.ch/rrdtool/
• https://github.com/pldimitrov/Rrd
• http://plamendimitrov.net/blog/2014/08/09/r-package-for-working-with-rrd-files/

Amazon Alexa

• http://blagrants.blogspot.com/2016/02/theres-party-at-alexas-place.html

Tricks

Getting help

• http://stackoverflow.com/questions/tagged/r
• https://stat.ethz.ch/pipermail/r-help/
• https://stat.ethz.ch/pipermail/r-devel/

Better Coder

• http://www.mango-solutions.com/wp/2015/10/10-top-tips-for-becoming-a-better-coder/

Change default R repository

Edit global Rprofile file. On *NIX platforms, it's located in /usr/lib/R/library/base/R/Rprofile although local .Rprofile settings take precedence.

For example, I can specify the R mirror I like by creating a single line <.Rprofile> file under my home directory.

options(repos = "http://cran.rstudio.com/")

Change the default web browser

When I run help.start() function in LXLE, it cannot find its default web browser (seamonkey).

> help.start()
If the browser launched by 'xdg-open' is already running, it is *not*
    restarted, and you must switch to its window.
Otherwise, be patient ...
> /usr/bin/xdg-open: 461: /usr/bin/xdg-open: x-www-browser: not found
/usr/bin/xdg-open: 461: /usr/bin/xdg-open: firefox: not found
/usr/bin/xdg-open: 461: /usr/bin/xdg-open: mozilla: not found
/usr/bin/xdg-open: 461: /usr/bin/xdg-open: epiphany: not found
/usr/bin/xdg-open: 461: /usr/bin/xdg-open: konqueror: not found
/usr/bin/xdg-open: 461: /usr/bin/xdg-open: chromium-browser: not found
/usr/bin/xdg-open: 461: /usr/bin/xdg-open: google-chrome: not found
/usr/bin/xdg-open: 461: /usr/bin/xdg-open: links2: not found
/usr/bin/xdg-open: 461: /usr/bin/xdg-open: links: not found
/usr/bin/xdg-open: 461: /usr/bin/xdg-open: lynx: not found
/usr/bin/xdg-open: 461: /usr/bin/xdg-open: w3m: not found
xdg-open: no method available for opening 'http://127.0.0.1:27919/doc/html/index.html'

The solution is to put

options(browser='seamonkey')

in the .Rprofile of your home directory. If the browser is not in the global PATH, we need to put the full path above.

For one-time only purpose, we can use the browser option in help.start() function:

> help.start(browser="seamonkey")
If the browser launched by 'seamonkey' is already running, it is *not*
    restarted, and you must switch to its window.
Otherwise, be patient ...

We can work made a change (or create the file) ~/.Renviron or etc/Renviron. See

• Changing default browser in options().
• https://stat.ethz.ch/R-manual/R-devel/library/utils/html/browseURL.html

Rconsole, Rprofile.site, Renviron.site files

• https://cran.r-project.org/doc/manuals/r-release/R-admin.html (Rprofile.site)
• https://cran.r-project.org/doc/manuals/r-release/R-intro.html (Rprofile.site, Renviron.site, Rconsole (Windows only))
• https://cran.r-project.org/doc/manuals/r-release/R-exts.html (Renviron.site)
• How to store and use webservice keys and authentication details
• Use your .Rprofile to give you important notifications

If we like to install R packages to a personal directory, follow this. Just add the line

R_LIBS_SITE=F:/R/library

to the file R_HOME/etc/x64/Renviron.site.

Note that on Windows OS, R/etc contains

$ ls -l /c/Progra~1/r/r-3.2.0/etc
total 142
-rw-r--r--    1   Administ     1043 Jun 20  2013 Rcmd_environ
-rw-r--r--    1   Administ     1924 Mar 17  2010 Rconsole
-rw-r--r--    1   Administ      943 Oct  3  2011 Rdevga
-rw-r--r--    1   Administ      589 May 20  2013 Rprofile.site
-rw-r--r--    1   Administ   251894 Jan 17  2015 curl-ca-bundle.crt
drwxr-xr-x    1   Administ        0 Jun  8 10:30 i386
-rw-r--r--    1   Administ     1160 Dec 31  2014 repositories
-rw-r--r--    1   Administ    30188 Mar 17  2010 rgb.txt
drwxr-xr-x    3   Administ        0 Jun  8 10:30 x64

$ ls /c/Progra~1/r/r-3.2.0/etc/i386
Makeconf

$ cat /c/Progra~1/r/r-3.2.0/etc/Rconsole
# Optional parameters for the console and the pager
# The system-wide copy is in R_HOME/etc.
# A user copy can be installed in `R_USER'.

## Style
# This can be `yes' (for MDI) or `no' (for SDI).
  MDI = yes
# MDI = no

# the next two are only relevant for MDI
toolbar = yes
statusbar = no

## Font.
# Please use only fixed width font.
# If font=FixedFont the system fixed font is used; in this case
# points and style are ignored. If font begins with "TT ", only
# True Type fonts are searched for.
font = TT Courier New
points = 10
style = normal # Style can be normal, bold, italic

# Dimensions (in characters) of the console.
rows = 25
columns = 80
# Dimensions (in characters) of the internal pager.
pgrows = 25
pgcolumns = 80
# should options(width=) be set to the console width?
setwidthonresize = yes

# memory limits for the console scrolling buffer, in chars and lines
# NB: bufbytes is in bytes for R < 2.7.0, chars thereafter.
bufbytes = 250000
buflines = 8000

# Initial position of the console (pixels, relative to the workspace for MDI)
# xconsole = 0
# yconsole = 0

# Dimension of MDI frame in pixels
# Format (w*h+xorg+yorg) or use -ve w and h for offsets from right bottom
# This will come up maximized if w==0
# MDIsize = 0*0+0+0
# MDIsize = 1000*800+100+0
# MDIsize = -50*-50+50+50  # 50 pixels space all round

# The internal pager can displays help in a single window
# or in multiple windows (one for each topic)
# pagerstyle can be set to `singlewindow' or `multiplewindows'
pagerstyle = multiplewindows

## Colours for console and pager(s)
# (see rwxxxx/etc/rgb.txt for the known colours).
background = White
normaltext = NavyBlue
usertext = Red
highlight = DarkRed

## Initial position of the graphics window
## (pixels, <0 values from opposite edge)
xgraphics = -25
ygraphics = 0

## Language for messages
language =

## Default setting for console buffering: 'yes' or 'no'
buffered = yes

and on Linux

brb@brb-T3500:~$ whereis R
R: /usr/bin/R /etc/R /usr/lib/R /usr/bin/X11/R /usr/local/lib/R /usr/share/R /usr/share/man/man1/R.1.gz

brb@brb-T3500:~$ ls /usr/lib/R
bin  COPYING  etc  lib  library  modules  site-library  SVN-REVISION

brb@brb-T3500:~$ ls /usr/lib/R/etc
javaconf  ldpaths  Makeconf  Renviron  Renviron.orig  Renviron.site  Renviron.ucf  repositories  Rprofile.site

brb@brb-T3500:~$ ls /usr/local/lib/R
site-library

and

brb@brb-T3500:~$ cat /usr/lib/R/etc/Rprofile.site
##                                              Emacs please make this -*- R -*-
## empty Rprofile.site for R on Debian
##
## Copyright (C) 2008 Dirk Eddelbuettel and GPL'ed
##
## see help(Startup) for documentation on ~/.Rprofile and Rprofile.site

# ## Example of .Rprofile
# options(width=65, digits=5)
# options(show.signif.stars=FALSE)
# setHook(packageEvent("grDevices", "onLoad"),
#         function(...) grDevices::ps.options(horizontal=FALSE))
# set.seed(1234)
# .First <- function() cat("\n   Welcome to R!\n\n")
# .Last <- function()  cat("\n   Goodbye!\n\n")

# ## Example of Rprofile.site
# local({
#  # add MASS to the default packages, set a CRAN mirror
#  old <- getOption("defaultPackages"); r <- getOption("repos")
#  r["CRAN"] <- "http://my.local.cran"
#  options(defaultPackages = c(old, "MASS"), repos = r)
#})
brb@brb-T3500:~$ cat /usr/lib/R/etc/Renviron.site
##                                              Emacs please make this -*- R -*-
## empty Renviron.site for R on Debian
##
## Copyright (C) 2008 Dirk Eddelbuettel and GPL'ed
##
## see help(Startup) for documentation on ~/.Renviron and Renviron.site

# ## Example ~/.Renviron on Unix
# R_LIBS=~/R/library
# PAGER=/usr/local/bin/less

# ## Example .Renviron on Windows
# R_LIBS=C:/R/library
# MY_TCLTK="c:/Program Files/Tcl/bin"

# ## Example of setting R_DEFAULT_PACKAGES (from R CMD check)
# R_DEFAULT_PACKAGES='utils,grDevices,graphics,stats'
# # this loads the packages in the order given, so they appear on
# # the search path in reverse order.
brb@brb-T3500:~$

R release versions

rversions: Query the main 'R' 'SVN' repository to find the released versions & dates.

R package managment

Package related functions from package 'utils'

• available.packages(); see packageStatus().
• download.packages()
• packageStatus(), update(), upgrade(). packageStatus() will return a list with two components:

1. inst - a data frame with columns as the matrix returned by installed.packages plus "Status", a factor with levels c("ok", "upgrade"). Note: the manual does not mention "unavailable" case (but I do get it) in R 3.2.0?
2. avail - a data frame with columns as the matrix returned by available.packages plus "Status", a factor with levels c("installed", "not installed", "unavailable"). Note: I don't get the "unavailable" case in R 3.2.0?

> x <- packageStatus()
> names(x)
[1] "inst"  "avail"
> dim(x[['inst']])
[1] 225  17
> x[['inst']][1:3, ]
              Package                            LibPath Version Priority               Depends Imports
acepack       acepack C:/Program Files/R/R-3.1.2/library 1.3-3.3     <NA>                  <NA>    <NA>
adabag         adabag C:/Program Files/R/R-3.1.2/library     4.0     <NA> rpart, mlbench, caret    <NA>
affxparser affxparser C:/Program Files/R/R-3.1.2/library  1.38.0     <NA>          R (>= 2.6.0)    <NA>
           LinkingTo                                                        Suggests Enhances
acepack         <NA>                                                            <NA>     <NA>
adabag          <NA>                                                            <NA>     <NA>
affxparser      <NA> R.oo (>= 1.18.0), R.utils (>= 1.32.4),\nAffymetrixDataTestFiles     <NA>
                      License License_is_FOSS License_restricts_use OS_type MD5sum NeedsCompilation Built
acepack    MIT + file LICENSE            <NA>                  <NA>    <NA>   <NA>              yes 3.1.2
adabag             GPL (>= 2)            <NA>                  <NA>    <NA>   <NA>               no 3.1.2
affxparser        LGPL (>= 2)            <NA>                  <NA>    <NA>   <NA>             <NA> 3.1.1
                Status
acepack             ok
adabag              ok
affxparser unavailable
> dim(x[['avail']])
[1] 6538   18
> x[['avail']][1:3, ]
                Package Version Priority                        Depends        Imports LinkingTo
A3                   A3   0.9.2     <NA> R (>= 2.15.0), xtable, pbapply           <NA>      <NA>
ABCExtremes ABCExtremes     1.0     <NA>      SpatialExtremes, combinat           <NA>      <NA>
ABCanalysis ABCanalysis   1.0.1     <NA>                    R (>= 2.10) Hmisc, plotrix      <NA>
                       Suggests Enhances    License License_is_FOSS License_restricts_use OS_type Archs
A3          randomForest, e1071     <NA> GPL (>= 2)            <NA>                  <NA>    <NA>  <NA>
ABCExtremes                <NA>     <NA>      GPL-2            <NA>                  <NA>    <NA>  <NA>
ABCanalysis                <NA>     <NA>      GPL-3            <NA>                  <NA>    <NA>  <NA>
            MD5sum NeedsCompilation File                                      Repository        Status
A3            <NA>             <NA> <NA> http://cran.rstudio.com/bin/windows/contrib/3.1 not installed
ABCExtremes   <NA>             <NA> <NA> http://cran.rstudio.com/bin/windows/contrib/3.1 not installed
ABCanalysis   <NA>             <NA> <NA> http://cran.rstudio.com/bin/windows/contrib/3.1 not installed

• packageVersion(), packageDescription()
• install.packages(), remove.packages().
• installed.packages(); see packageStatus().
• update.packages(), old.packages(), new.packages()
• setRepositories()
• contrib.url()
• chooseCRANmirror(), chooseBioCmirror()
• suppressForeignCheck()

install.packages()

By default, install.packages() will check versions and install uninstalled packages shown in 'Depends', 'Imports', and 'LinkingTo' fields. See R-exts manual.

If we want to install packages listed in 'Suggests' field, we should specify it explicitly by using dependencies argument:

install.packages(XXXX, dependencies = c("Depends", "Imports", "Suggests", "LinkingTo"))
# OR
install.packages(XXXX, dependencies = TRUE)

For example, if I use a plain install.packages() command to install downloader package

install.packages("downloader")

it will only install 'digest' and 'downloader' packages. If I use

install.packages("downloader", dependencies=TRUE)

it will also install 'testhat' package.

The install.packages function source code can be found in R -> src -> library -> utils -> R -> packages2.R file from Github repository (put 'install.packages' in the search box).

install a tar.gz from a local directory

R CMD INSTALL <package-name>.tar.gz

Or in R:

install.packages(<pathtopackage>, repos = NULL, type="source")

Query an R package installed locally

packageDescription("MASS")
packageVersion("MASS")

Query an R package (from CRAN) basic information

packageStatus() # Summarize information about installed packages

available.packages() # List Available Packages at CRAN-like Repositories

The available.packages() command is useful for understanding package dependency. Use setRepositories() or 'RGUI -> Packages -> select repositories' to select repositories and options()$repos to check or change the repositories.

Also the packageStatus() is another useful function for query how many packages are in the repositories, how many have been installed, and individual package status (installed or not, needs to be upgraded or not).

> options()$repos 

> packageStatus() 
Number of installed packages:
                                    
                                      ok upgrade unavailable
  C:/Program Files/R/R-3.0.1/library 110       0           1

Number of available packages (each package counted only once):
                                                                                   
                                                                                    installed not installed
  http://watson.nci.nih.gov/cran_mirror/bin/windows/contrib/3.0                            76          4563
  http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.0                                0             5
  http://www.bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0                   16           625
  http://www.bioconductor.org/packages/2.12/data/annotation/bin/windows/contrib/3.0         4           686
> tmp <- available.packages()
> str(tmp)
 chr [1:5975, 1:17] "A3" "ABCExtremes" "ABCp2" "ACCLMA" "ACD" "ACNE" "ADGofTest" "ADM3" "AER" ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:5975] "A3" "ABCExtremes" "ABCp2" "ACCLMA" ...
  ..$ : chr [1:17] "Package" "Version" "Priority" "Depends" ...
> tmp[1:3,]
            Package       Version Priority Depends                     Imports LinkingTo Suggests             
A3          "A3"          "0.9.2" NA       "xtable, pbapply"           NA      NA        "randomForest, e1071"
ABCExtremes "ABCExtremes" "1.0"   NA       "SpatialExtremes, combinat" NA      NA        NA                   
ABCp2       "ABCp2"       "1.1"   NA       "MASS"                      NA      NA        NA                   
            Enhances License      License_is_FOSS License_restricts_use OS_type Archs MD5sum NeedsCompilation File
A3          NA       "GPL (>= 2)" NA              NA                    NA      NA    NA     NA               NA  
ABCExtremes NA       "GPL-2"      NA              NA                    NA      NA    NA     NA               NA  
ABCp2       NA       "GPL-2"      NA              NA                    NA      NA    NA     NA               NA  
            Repository                                                     
A3          "http://watson.nci.nih.gov/cran_mirror/bin/windows/contrib/3.0"
ABCExtremes "http://watson.nci.nih.gov/cran_mirror/bin/windows/contrib/3.0"
ABCp2       "http://watson.nci.nih.gov/cran_mirror/bin/windows/contrib/3.0"

And the following commands find which package depends on Rcpp and also which are from bioconductor repository.

> pkgName <- "Rcpp"
> rownames(tmp)[grep(pkgName, tmp[,"Depends"])]
> tmp[grep("Rcpp", tmp[,"Depends"]), "Depends"]

> ind <- intersect(grep(pkgName, tmp[,"Depends"]), grep("bioconductor", tmp[, "Repository"]))
> rownames(grep)[ind]
NULL
> rownames(tmp)[ind]
 [1] "ddgraph"            "DESeq2"             "GeneNetworkBuilder" "GOSemSim"           "GRENITS"           
 [6] "mosaics"            "mzR"                "pcaMethods"         "Rdisop"             "Risa"              
[11] "rTANDEM"    

Install personal R packages after upgrade R, .libPaths()

Scenario: We already have installed many R packages under R 3.1.X in the user's directory. Now we upgrade R to a new version (3.2.X). We like to have these packages available in R 3.2.X.

For Windows OS, refer to R for Windows FAQ

The follow method works on Linux and Windows.

Make sure only one instance of R is running

# Step 1. update R's built-in packages and install them on my personal directory
update.packages(ask=FALSE, checkBuilt = TRUE, repos="http://cran.rstudio.com")

# Step 2. update Bioconductor packages
.libPaths() # The first one is my personal directory
# [1] "/home/brb/R/x86_64-pc-linux-gnu-library/3.2"
# [2] "/usr/local/lib/R/site-library"
# [3] "/usr/lib/R/site-library"
# [4] "/usr/lib/R/library"

Sys.getenv("R_LIBS_USER") # equivalent to .libPaths()[1]
ul <- unlist(strsplit(Sys.getenv("R_LIBS_USER"), "/"))
src <- file.path(paste(ul[1:(length(ul)-1)], collapse="/"), "3.1") 
des <- file.path(paste(ul[1:(length(ul)-1)], collapse="/"), "3.2") 
pkg <- dir(src, full.names = TRUE)
if (!file.exists(des)) dir.create(des)  # If 3.2 subdirectory does not exist yet!
file.copy(pkg, des, overwrite=FALSE, recursive = TRUE)
source("http://www.bioconductor.org/biocLite.R")
biocLite(ask = FALSE)

From Robert Kabacoff (R in Action)

• If you have a customized Rprofile.site file (see appendix B), save a copy outside of R.
• Launch your current version of R and issue the following statements

oldip <- installed.packages()[,1]
save(oldip, file="path/installedPackages.Rdata")

where path is a directory outside of R.

• Download and install the newer version of R.
• If you saved a customized version of the Rprofile.site file in step 1, copy it into the new installation.
• Launch the new version of R, and issue the following statements

load("path/installedPackages.Rdata")
newip <- installed.packages()[,1]
for(i in setdiff(oldip, newip))
  install.packages(i)

where path is the location specified in step 2.

• Delete the old installation (optional).

This approach will install only packages that are available from the CRAN. It won’t find packages obtained from other locations. In fact, the process will display a list of packages that can’t be installed For example for packages obtained from Bioconductor, use the following method to update packages

source(http://bioconductor.org/biocLite.R)
biocLite(PKGNAME)

List vignettes from a package

vignette(package=PACKAGENAME)

List data from a package

data(package=PACKAGENAME)

List installed packages and versions

• http://heuristicandrew.blogspot.com/2015/06/list-of-user-installed-r-packages-and.html
• checkpoint package

ip <- as.data.frame(installed.packages()[,c(1,3:4)])
rownames(ip) <- NULL
unique(ip$Priority)
# [1] <NA>        base        recommended
# Levels: base recommended
ip <- ip[is.na(ip$Priority),1:2,drop=FALSE]
print(ip, row.names=FALSE)

Query the names of outdated packages

psi <- packageStatus()$inst
subset(psi, Status == "upgrade", drop = FALSE)
#                     Package                                  LibPath     Version    Priority                Depends
# RcppArmadillo RcppArmadillo C:/Users/brb/Documents/R/win-library/3.2 0.5.100.1.0        <NA>                   <NA>
# Matrix               Matrix       C:/Program Files/R/R-3.2.0/library       1.2-0 recommended R (>= 2.15.2), methods
#                                             Imports LinkingTo                 Suggests
# RcppArmadillo                      Rcpp (>= 0.11.0)      Rcpp RUnit, Matrix, pkgKitten
# Matrix        graphics, grid, stats, utils, lattice      <NA>               expm, MASS
#                                            Enhances    License License_is_FOSS License_restricts_use OS_type MD5sum
# RcppArmadillo                                  <NA> GPL (>= 2)            <NA>                  <NA>    <NA>   <NA>
# Matrix        MatrixModels, graph, SparseM, sfsmisc GPL (>= 2)            <NA>                  <NA>    <NA>   <NA>
#               NeedsCompilation Built  Status
# RcppArmadillo              yes 3.2.0 upgrade
# Matrix                     yes 3.2.0 upgrade

The above output does not show the package version from the latest packages on CRAN. So the following snippet does that.

psi <- packageStatus()$inst
pl <- unname(psi$Package[psi$Status == "upgrade"])  # List package names

out <- cbind(subset(psi, Status == "upgrade")[, c("Package", "Version")], ap[match(pl, ap$Package), "Version"])
colnames(out)[2:3] <- c("OldVersion", "NewVersion")
rownames(out) <- NULL
out
#         Package  OldVersion  NewVersion
# 1 RcppArmadillo 0.5.100.1.0 0.5.200.1.0
# 2        Matrix       1.2-0       1.2-1

To consider also the packages from Bioconductor, we have the following code. Note that "3.1" means the Bioconductor version and "3.2" is the R version. See Bioconductor release versions page.

psic <- packageStatus(repos = c(contrib.url(getOption("repos")),
                                "http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2",
                                "http://www.bioconductor.org/packages/3.1/data/annotation/bin/windows/contrib/3.2"))$inst
subset(psic, Status == "upgrade", drop = FALSE)
pl <- unname(psic$Package[psic$Status == "upgrade"])

# ap <- as.data.frame(available.packages()[, c(1,2,3)], stringsAsFactors = FALSE)
ap   <- as.data.frame(available.packages(c(contrib.url(getOption("repos")),
                                "http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2",
                                "http://www.bioconductor.org/packages/3.1/data/annotation/bin/windows/contrib/3.2"))[, c(1:3)], 
                      stringAsFactors = FALSE)

out <- cbind(subset(psic, Status == "upgrade")[, c("Package", "Version")], ap[match(pl, ap$Package), "Version"])
colnames(out)[2:3] <- c("OldVersion", "NewVersion")
rownames(out) <- NULL
out
#         Package  OldVersion  NewVersion
# 1         limma      3.24.5      3.24.9
# 2 RcppArmadillo 0.5.100.1.0 0.5.200.1.0
# 3        Matrix       1.2-0       1.2-1

Fishing for packages in CRAN

• http://blog.revolutionanalytics.com/2015/06/fishing-for-packages-in-cran.html

Query top downloaded packages

• cranlogs package - Download Logs from the RStudio CRAN Mirror
• http://blog.revolutionanalytics.com/2015/06/working-with-the-rstudio-cran-logs.html

Top new packages in 2015

• 2015 R packages roundup by CHRISTOPH SAFFERLING
• R trends in 2015 by MAX GORDON

Warning: cannot remove prior installation of package

http://stackoverflow.com/questions/15932152/unloading-and-removing-a-loaded-package-withouth-restarting-r

Instance 1.

# Install the latest hgu133plus2cdf package
# Remove/Uninstall hgu133plus2.db package
# Put/Install an old version of IRanges (eg version 1.18.2 while currently it is version 1.18.3)
# Test on R 3.0.1
library(hgu133plus2cdf) # hgu133pluscdf does not depend or import IRanges
source("http://bioconductor.org/biocLite.R")
biocLite("hgu133plus2.db", ask=FALSE) # hgu133plus2.db imports IRanges
# Warning:cannot remove prior installation of package 'IRanges'
# Open Windows Explorer and check IRanges folder. Only see libs subfolder.

Note:

• In the above example, all packages were installed under C:\Program Files\R\R-3.0.1\library\.
• In another instance where I cannot reproduce the problem, new R packages were installed under C:\Users\xxx\Documents\R\win-library\3.0\. The different thing is IRanges package CAN be updated but if I use packageVersion("IRanges") command in R, it still shows the old version.
• The above were tested on a desktop.

Instance 2.

# On a fresh R 3.2.0, I install Bioconductor's depPkgTools & lumi packages. Then I close R, re-open it, 
# and install depPkgTools package again.
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.1 (BiocInstaller 1.18.2), ?biocLite for help
> biocLite("pkgDepTools")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.2), R version 3.2.0.
Installing package(s) ‘pkgDepTools’
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/pkgDepTools_1.34.0.zip'
Content type 'application/zip' length 390579 bytes (381 KB)
downloaded 381 KB

package ‘pkgDepTools’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘pkgDepTools’

The downloaded binary packages are in
        C:\Users\brb\AppData\Local\Temp\RtmpYd2l7i\downloaded_packages
> library(pkgDepTools)
Error in library(pkgDepTools) : there is no package called ‘pkgDepTools’

The pkgDepTools library folder appears in C:\Users\brb\Documents\R\win-library\3.2, but it is empty. The weird thing is if I try the above steps again, I cannot reproduce the problem.

Warning: Unable to move temporary installation

The problem seems to happen only on virtual machines (Virtualbox).

• Warning: unable to move temporary installation `C:\Users\brb\Documents\R\win-library\3.0\fileed8270978f5\quadprog` to `C:\Users\brb\Documents\R\win-library\3.0\quadprog` when I try to run 'install.packages("forecast").
• Warning: unable to move temporary installation ‘C:\Users\brb\Documents\R\win-library\3.2\file5e0104b5b49\plyr’ to ‘C:\Users\brb\Documents\R\win-library\3.2\plyr’ when I try to run 'biocLite("lumi")'. The other dependency packages look fine although I am not sure if any unknown problem can happen (it does, see below).

Here is a note of my trouble shooting.

1. If I try to ignore the warning and load the lumi package. I will get an error.
2. If I try to run biocLite("lumi") again, it will only download & install lumi without checking missing 'plyr' package. Therefore, when I try to load the lumi package, it will give me an error again.
3. Even I install the plyr package manually, library(lumi) gives another error - missing mclust package.

> biocLite("lumi")
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/BiocInstaller_1.18.2.zip'
Content type 'application/zip' length 114097 bytes (111 KB)
downloaded 111 KB
...
package ‘lumi’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\brb\AppData\Local\Temp\RtmpyUjsJD\downloaded_packages
Old packages: 'BiocParallel', 'Biostrings', 'caret', 'DESeq2', 'gdata', 'GenomicFeatures', 'gplots', 'Hmisc', 'Rcpp', 'RcppArmadillo', 'rgl',
  'stringr'
Update all/some/none? [a/s/n]: a
also installing the dependencies ‘Rsamtools’, ‘GenomicAlignments’, ‘plyr’, ‘rtracklayer’, ‘gridExtra’, ‘stringi’, ‘magrittr’

trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/Rsamtools_1.20.1.zip'
Content type 'application/zip' length 8138197 bytes (7.8 MB)
downloaded 7.8 MB
...
package ‘Rsamtools’ successfully unpacked and MD5 sums checked
package ‘GenomicAlignments’ successfully unpacked and MD5 sums checked
package ‘plyr’ successfully unpacked and MD5 sums checked
Warning: unable to move temporary installation ‘C:\Users\brb\Documents\R\win-library\3.2\file5e0104b5b49\plyr’ 
         to ‘C:\Users\brb\Documents\R\win-library\3.2\plyr’
package ‘rtracklayer’ successfully unpacked and MD5 sums checked
package ‘gridExtra’ successfully unpacked and MD5 sums checked
package ‘stringi’ successfully unpacked and MD5 sums checked
package ‘magrittr’ successfully unpacked and MD5 sums checked
package ‘BiocParallel’ successfully unpacked and MD5 sums checked
package ‘Biostrings’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘Biostrings’
package ‘caret’ successfully unpacked and MD5 sums checked
package ‘DESeq2’ successfully unpacked and MD5 sums checked
package ‘gdata’ successfully unpacked and MD5 sums checked
package ‘GenomicFeatures’ successfully unpacked and MD5 sums checked
package ‘gplots’ successfully unpacked and MD5 sums checked
package ‘Hmisc’ successfully unpacked and MD5 sums checked
package ‘Rcpp’ successfully unpacked and MD5 sums checked
package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
package ‘rgl’ successfully unpacked and MD5 sums checked
package ‘stringr’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\brb\AppData\Local\Temp\RtmpyUjsJD\downloaded_packages
> library(lumi)
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘plyr’
Error: package or namespace load failed for ‘lumi’
> search()
 [1] ".GlobalEnv"            "package:BiocInstaller" "package:Biobase"       "package:BiocGenerics"  "package:parallel"      "package:stats"        
 [7] "package:graphics"      "package:grDevices"     "package:utils"         "package:datasets"      "package:methods"       "Autoloads"            
[13] "package:base"         
> biocLite("lumi")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.2), R version 3.2.0.
Installing package(s) ‘lumi’
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/lumi_2.20.1.zip'
Content type 'application/zip' length 18185326 bytes (17.3 MB)
downloaded 17.3 MB

package ‘lumi’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\brb\AppData\Local\Temp\RtmpyUjsJD\downloaded_packages
> search()
 [1] ".GlobalEnv"            "package:BiocInstaller" "package:Biobase"       "package:BiocGenerics"  "package:parallel"      "package:stats"        
 [7] "package:graphics"      "package:grDevices"     "package:utils"         "package:datasets"      "package:methods"       "Autoloads"            
[13] "package:base"         
> library(lumi)
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘plyr’
Error: package or namespace load failed for ‘lumi’
> biocLite("plyr")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.2), R version 3.2.0.
Installing package(s) ‘plyr’
trying URL 'http://cran.rstudio.com/bin/windows/contrib/3.2/plyr_1.8.2.zip'
Content type 'application/zip' length 1128621 bytes (1.1 MB)
downloaded 1.1 MB

package ‘plyr’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\brb\AppData\Local\Temp\RtmpyUjsJD\downloaded_packages

> library(lumi)
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘mclust’
Error: package or namespace load failed for ‘lumi’

> ?biocLite
Warning messages:
1: In read.dcf(file.path(p, "DESCRIPTION"), c("Package", "Version")) :
  cannot open compressed file 'C:/Users/brb/Documents/R/win-library/3.2/Biostrings/DESCRIPTION', probable reason 'No such file or directory'
2: In find.package(if (is.null(package)) loadedNamespaces() else package,  :
  there is no package called ‘Biostrings’
> library(lumi)
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘mclust’
In addition: Warning messages:
1: In read.dcf(file.path(p, "DESCRIPTION"), c("Package", "Version")) :
  cannot open compressed file 'C:/Users/brb/Documents/R/win-library/3.2/Biostrings/DESCRIPTION', probable reason 'No such file or directory'
2: In find.package(if (is.null(package)) loadedNamespaces() else package,  :
  there is no package called ‘Biostrings’
Error: package or namespace load failed for ‘lumi’

Other people also have the similar problem. The possible cause is the virus scanner locks the file and R cannot move them.

Some possible solutions:

1. Delete ALL folders under R/library (e.g. C:/Progra~1/R/R-3.2.0/library) folder and install the main package again using install.packages() or biocLite().
2. For specific package like 'lumi' from Bioconductor, we can find out all dependency packages and then install them one by one.
3. Find out and install the top level package which misses dependency packages.
   1. This is based on the fact that install.packages() or biocLite() sometimes just checks & installs the 'Depends' and 'Imports' packages and won't install all packages recursively
   2. we can do a small experiment by removing a package which is not directly dependent/imported by another package; e.g. 'iterators' is not dependent/imported by 'glment' directly but indirectly. So if we run remove.packages("iterators"); install.packages("glmnet"), then the 'iterator' package is still missing.
   3. A real example is if the missing packages are 'Biostrings', 'limma', 'mclust' (these are packages that 'minfi' directly depends/imports although they should be installed when I run biocLite("lumi") command), then I should just run the command remove.packages("minfi"); biocLite("minfi"). If we just run biocLite("lumi") or biocLite("methylumi"), the missing packages won't be installed.

Error in download.file(url, destfile, method, mode = "wb", ...) and cache

HTTP status was '404 Not Found'

Tested on an existing R-3.2.0 session. Note that VariantAnnotation 1.14.4 was just uploaded to Bioc.

> biocLite("COSMIC.67")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.3), R version 3.2.0.
Installing package(s) ‘COSMIC.67’
also installing the dependency ‘VariantAnnotation’

trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/VariantAnnotation_1.14.3.zip'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/VariantAnnotation_1.14.3.zip'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open: HTTP status was '404 Not Found'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘VariantAnnotation’ failed
installing the source package ‘COSMIC.67’

trying URL 'http://bioconductor.org/packages/3.1/data/experiment/src/contrib/COSMIC.67_1.4.0.tar.gz'
Content type 'application/x-gzip' length 40999037 bytes (39.1 MB)

However, when I tested on a new R-3.2.0 (just installed in VM), the COSMIC package installation is successful. That VariantAnnotation version 1.14.4 was installed (this version was just updated today from Bioconductor).

The cause of the error is the available.package() function will read the rds file first from cache in a tempdir (C:\Users\XXXX\AppData\Local\Temp\RtmpYYYYYY). See lines 51-55 of <packages.R>.

 dest <- file.path(tempdir(),
                   paste0("repos_", URLencode(repos, TRUE), ".rds"))
 if(file.exists(dest)) {
    res0 <- readRDS(dest)
 } else {
    ...
 }  

Since my R was opened 1 week ago, the rds file it reads today contains old information. Note that Bioconductor does not hold the source code or binary code for the old version of packages. This explains why biocLite() function broke. When I restart R, the original problem is gone.

If we look at the source code of available.packages(), we will see we could use cacheOK option in download.file() function.

download.file(url, destfile, method, cacheOK = FALSE, quiet = TRUE, mode ="wb")

Error in unloadNamespace(package)

> d3heatmap(mtcars, scale = "column", colors = "Blues")
Error: 'col_numeric' is not an exported object from 'namespace:scales'
> packageVersion("scales")
[1] ‘0.2.5’
> library(scales)
Error in unloadNamespace(package) : 
  namespace ‘scales’ is imported by ‘ggplot2’ so cannot be unloaded
In addition: Warning message:
package ‘scales’ was built under R version 3.2.1 
Error in library(scales) : 
  Package ‘scales’ version 0.2.4 cannot be unloaded
> search()
 [1] ".GlobalEnv"             "package:d3heatmap"      "package:ggplot2"       
 [4] "package:microbenchmark" "package:COSMIC.67"      "package:BiocInstaller" 
 [7] "package:stats"          "package:graphics"       "package:grDevices"     
[10] "package:utils"          "package:datasets"       "package:methods"       
[13] "Autoloads"              "package:base" 

If I open a new R session, the above error will not happen!

The problem occurred because the 'scales' package version required by the d3heatmap package/function is old. See this post. And when I upgraded the 'scales' package, it was locked by the package was imported by the ggplot2 package.

Unload a package

See an example below.

require(splines)
detach(package:splines, unload=TRUE)

METACRAN - Search and browse all CRAN/R packages

• Source code on https://github.com/metacran. The 'PACKAGES' file is updated regularly to Github.
• Announcement on R/mailing list
• Author's homepage on http://gaborcsardi.org/.

New R packages as reported by CRANberries

http://blog.revolutionanalytics.com/2015/07/mranspackages-spotlight.html

#----------------------------
# SCRAPE CRANBERRIES FILES TO COUNT NEW PACKAGES AND PLOT
#
library(ggplot2)
# Build a vextor of the directories of interest
year <- c("2013","2014","2015")
month <- c("01","02","03","04","05","06","07","08","09","10","11","12")
span <-c(rep(month,2),month[1:7])
dir <- "http://dirk.eddelbuettel.com/cranberries"

url2013 <- file.path(dir,"2013",month)
url2014 <- file.path(dir,"2014",month)
url2015 <- file.path(dir,"2015",month[1:7])
url <- c(url2013,url2014,url2015)

# Read each directory and count the new packages
new_p <- vector()
for(i in url){
  raw.data <- readLines(i)
  new_p[i] <- length(grep("New package",raw.data,value=TRUE))
}

# Plot
time <- seq(as.Date("2013-01-01"), as.Date("2015-07-01"), by="months")
new_pkgs <- data.frame(time,new_p)

ggplot(new_pkgs, aes(time,y=new_p)) +
  geom_line() + xlab("") + ylab("Number of new packages") + 
  geom_smooth(method='lm') + ggtitle("New R packages as reported by CRANberries") 

R package dependencies

• Package tools' functions package.dependencies(), pkgDepends(), etc are deprecated now, mostly in favor of package_dependencies() which is both more flexible and efficient. See R 3.3.0 News.

Bioconductor's pkgDepTools package

The is an example of querying the dependencies of the notorious 'lumi' package which often broke the installation script. I am using R 3.2.0 and Bioconductor 3.1.

The getInstallOrder function is useful to get a list of all (recursive) dependency packages.

source("http://bioconductor.org/biocLite.R")
if (!require(pkgDepTools)) {
  biocLite("pkgDepTools", ask = FALSE)
  library(pkgDepTools)
}
MkPlot <- FALSE

library(BiocInstaller)
biocUrl <- biocinstallRepos()["BioCsoft"]
biocDeps <- makeDepGraph(biocUrl, type="source", dosize=FALSE) # pkgDepTools defines its makeDepGraph()

PKG <- "lumi"
if (MkPlot) {
  if (!require(Biobase))  {
    biocLite("Biobase", ask = FALSE)
    library(Biobase)
  }
  if (!require(Rgraphviz))  {
    biocLite("Rgraphviz", ask = FALSE) 
    library(Rgraphviz)
  }
  categoryNodes <- c(PKG, names(acc(biocDeps, PKG)[[1]]))  
  categoryGraph <- subGraph(categoryNodes, biocDeps) 
  nn <- makeNodeAttrs(categoryGraph, shape="ellipse") 
  plot(categoryGraph, nodeAttrs=nn)   # Complete but plot is too complicated & font is too small.
}

system.time(allDeps <- makeDepGraph(biocinstallRepos(), type="source",
                           keep.builtin=TRUE, dosize=FALSE)) # takes a little while
#    user  system elapsed 
# 175.737  10.994 186.875 
# Warning messages:
# 1: In .local(from, to, graph) : edges replaced: ‘SNPRelate|gdsfmt’
# 2: In .local(from, to, graph) :
#   edges replaced: ‘RCurl|methods’, ‘NA|bitops’

# When needed.only=TRUE, only those dependencies not currently installed are included in the list.
x1 <- sort(getInstallOrder(PKG, allDeps, needed.only=TRUE)$packages); x1
 [1] "affy"                              "affyio"                           
 [3] "annotate"                          "AnnotationDbi"                    
 [5] "base64"                            "beanplot"                         
 [7] "Biobase"                           "BiocParallel"                     
 [9] "biomaRt"                           "Biostrings"                       
[11] "bitops"                            "bumphunter"                       
[13] "colorspace"                        "DBI"                              
[15] "dichromat"                         "digest"                           
[17] "doRNG"                             "FDb.InfiniumMethylation.hg19"     
[19] "foreach"                           "futile.logger"                    
[21] "futile.options"                    "genefilter"                       
[23] "GenomeInfoDb"                      "GenomicAlignments"                
[25] "GenomicFeatures"                   "GenomicRanges"                    
[27] "GEOquery"                          "ggplot2"                          
[29] "gtable"                            "illuminaio"                       
[31] "IRanges"                           "iterators"                        
[33] "labeling"                          "lambda.r"                         
[35] "limma"                             "locfit"                           
[37] "lumi"                              "magrittr"                         
[39] "matrixStats"                       "mclust"                           
[41] "methylumi"                         "minfi"                            
[43] "multtest"                          "munsell"                          
[45] "nleqslv"                           "nor1mix"                          
[47] "org.Hs.eg.db"                      "pkgmaker"                         
[49] "plyr"                              "preprocessCore"                   
[51] "proto"                             "quadprog"                         
[53] "RColorBrewer"                      "Rcpp"                             
[55] "RCurl"                             "registry"                         
[57] "reshape"                           "reshape2"                         
[59] "rngtools"                          "Rsamtools"                        
[61] "RSQLite"                           "rtracklayer"                      
[63] "S4Vectors"                         "scales"                           
[65] "siggenes"                          "snow"                             
[67] "stringi"                           "stringr"                          
[69] "TxDb.Hsapiens.UCSC.hg19.knownGene" "XML"                              
[71] "xtable"                            "XVector"                          
[73] "zlibbioc"                         

# When needed.only=FALSE the complete list of dependencies is given regardless of the set of currently installed packages.
x2 <- sort(getInstallOrder(PKG, allDeps, needed.only=FALSE)$packages); x2
 [1] "affy"                              "affyio"                            "annotate"                         
 [4] "AnnotationDbi"                     "base64"                            "beanplot"                         
 [7] "Biobase"                           "BiocGenerics"                      "BiocInstaller"                    
[10] "BiocParallel"                      "biomaRt"                           "Biostrings"                       
[13] "bitops"                            "bumphunter"                        "codetools"                        
[16] "colorspace"                        "DBI"                               "dichromat"                        
[19] "digest"                            "doRNG"                             "FDb.InfiniumMethylation.hg19"     
[22] "foreach"                           "futile.logger"                     "futile.options"                   
[25] "genefilter"                        "GenomeInfoDb"                      "GenomicAlignments"                
[28] "GenomicFeatures"                   "GenomicRanges"                     "GEOquery"                         
[31] "ggplot2"                           "graphics"                          "grDevices"                        
[34] "grid"                              "gtable"                            "illuminaio"                       
[37] "IRanges"                           "iterators"                         "KernSmooth"                       
[40] "labeling"                          "lambda.r"                          "lattice"                          
[43] "limma"                             "locfit"                            "lumi"                             
[46] "magrittr"                          "MASS"                              "Matrix"                           
[49] "matrixStats"                       "mclust"                            "methods"                          
[52] "methylumi"                         "mgcv"                              "minfi"                            
[55] "multtest"                          "munsell"                           "nleqslv"                          
[58] "nlme"                              "nor1mix"                           "org.Hs.eg.db"                     
[61] "parallel"                          "pkgmaker"                          "plyr"                             
[64] "preprocessCore"                    "proto"                             "quadprog"                         
[67] "RColorBrewer"                      "Rcpp"                              "RCurl"                            
[70] "registry"                          "reshape"                           "reshape2"                         
[73] "rngtools"                          "Rsamtools"                         "RSQLite"                          
[76] "rtracklayer"                       "S4Vectors"                         "scales"                           
[79] "siggenes"                          "snow"                              "splines"                          
[82] "stats"                             "stats4"                            "stringi"                          
[85] "stringr"                           "survival"                          "tools"                            
[88] "TxDb.Hsapiens.UCSC.hg19.knownGene" "utils"                             "XML"                              
[91] "xtable"                            "XVector"                           "zlibbioc" 

> sort(setdiff(x2, x1)) # Not all R's base packages are included; e.g. 'base', 'boot', ...
 [1] "BiocGenerics"  "BiocInstaller" "codetools"     "graphics"      "grDevices"    
 [6] "grid"          "KernSmooth"    "lattice"       "MASS"          "Matrix"       
[11] "methods"       "mgcv"          "nlme"          "parallel"      "splines"      
[16] "stats"         "stats4"        "survival"      "tools"         "utils"  

miniCRAN package

miniCRAN package can be used to identify package dependencies or create a local CRAN repository. It can be used on repositories other than CRAN, such as Bioconductor.

• http://blog.revolutionanalytics.com/2014/07/dependencies-of-popular-r-packages.html
• http://www.r-bloggers.com/introducing-minicran-an-r-package-to-create-a-private-cran-repository/
• http://www.magesblog.com/2014/09/managing-r-package-dependencies.html
• Using miniCRAN in Azure ML
• developing internal CRAN Repositories

Before we go into R, we need to install some packages from Ubuntu terminal. See here.

# Consider glmnet package (today is 4/29/2015)
# Version:	2.0-2
# Depends:	Matrix (≥ 1.0-6), utils, foreach
# Suggests:	survival, knitr, lars
if (!require("miniCRAN"))  {
  install.packages("miniCRAN", dependencies = TRUE, repos="http://cran.rstudio.com") # include 'igraph' in Suggests.
  library(miniCRAN)
}
if (!"igraph" %in% installed.packages()[,1]) install.packages("igraph")

tags <- "glmnet"
pkgDep(tags, suggests=TRUE, enhances=TRUE) # same as pkgDep(tags)
#  [1] "glmnet"    "Matrix"    "foreach"   "codetools" "iterators" "lattice"   "evaluate"  "digest"   
#  [9] "formatR"   "highr"     "markdown"  "stringr"   "yaml"      "mime"      "survival"  "knitr"    
# [17] "lars"   

dg <- makeDepGraph(tags, suggests=TRUE, enhances=TRUE) # miniCRAN defines its makeDepGraph()
plot(dg, legendPosition = c(-1, 1), vertex.size=20)

We can also display the dependence for a package from the Bioconductor repository.

tags <- "DESeq2"
# Depends	S4Vectors, IRanges, GenomicRanges, Rcpp (>= 0.10.1), RcppArmadillo (>= 0.3.4.4)
# Imports	BiocGenerics(>= 0.7.5), Biobase, BiocParallel, genefilter, methods, locfit, geneplotter, ggplot2, Hmisc
# Suggests	RUnit, gplots, knitr, RColorBrewer, BiocStyle, airway,\npasilla (>= 0.2.10), DESeq, vsn
# LinkingTo     Rcpp, RcppArmadillo
index <- function(url, type="source", filters=NULL, head=5, cols=c("Package", "Version")){
  contribUrl <- contrib.url(url, type=type)
  available.packages(contribUrl, type=type, filters=filters)
}

bioc <- local({
  env <- new.env()
  on.exit(rm(env))
  evalq(source("http://bioconductor.org/biocLite.R", local=TRUE), env)
  biocinstallRepos() # return URLs
})

bioc
#                                               BioCsoft 
#            "http://bioconductor.org/packages/3.0/bioc" 
#                                                BioCann 
# "http://bioconductor.org/packages/3.0/data/annotation" 
#                                                BioCexp 
# "http://bioconductor.org/packages/3.0/data/experiment" 
#                                              BioCextra 
#           "http://bioconductor.org/packages/3.0/extra" 
#                                                   CRAN 
#                                "http://cran.fhcrc.org" 
#                                              CRANextra 
#                   "http://www.stats.ox.ac.uk/pub/RWin" 
str(index(bioc["BioCsoft"])) # similar to cranJuly2014 object 

system.time(dg <- makeDepGraph(tags, suggests=TRUE, enhances=TRUE, availPkgs = index(bioc["BioCsoft"]))) # Very quick!
plot(dg, legendPosition = c(-1, 1), vertex.size=20)

The dependencies of GenomicFeature and GenomicAlignments are more complicated. So we turn the 'suggests' option to FALSE.

tags <- "GenomicAlignments"
dg <- makeDepGraph(tags, suggests=FALSE, enhances=FALSE, availPkgs = index(bioc["BioCsoft"]))
plot(dg, legendPosition = c(-1, 1), vertex.size=20)

MRAN (CRAN only)

• http://blog.revolutionanalytics.com/2014/10/explore-r-package-connections-at-mran.html

Reverse dependence

• http://romainfrancois.blog.free.fr/index.php?post/2011/10/30/Rcpp-reverse-dependency-graph

Create a new R package, namespace, documentation

• http://cran.r-project.org/doc/contrib/Leisch-CreatingPackages.pdf (highly recommend)
• https://stat.ethz.ch/pipermail/r-devel/2013-July/066975.html
• Benefit of import in a namespace
• This youtube video from Tyler Rinker teaches how to use RStudio to develop an R package and also use Git to do version control. Very useful!
• Developing R packages by Jeff Leek in Johns Hopkins University.
• R packages book by Hadley Wickham.
• R package primer a minimal tutorial from Karl Broman].

R package depends vs imports

• http://stackoverflow.com/questions/8637993/better-explanation-of-when-to-use-imports-depends
• http://stackoverflow.com/questions/9893791/imports-and-depends
• https://stat.ethz.ch/pipermail/r-devel/2013-August/067082.html

In the namespace era Depends is never really needed. All modern packages have no technical need for Depends anymore. Loosely speaking the only purpose of Depends today is to expose other package's functions to the user without re-exporting them.

load = functions exported in myPkg are available to interested parties as myPkg::foo or via direct imports - essentially this means the package can now be used

attach = the namespace (and thus all exported functions) is attached to the search path - the only effect is that you have now added the exported functions to the global pool of functions - sort of like dumping them in the workspace (for all practical purposes, not technically)

import a function into a package = make sure that this function works in my package regardless of the search path (so I can write fn1 instead of pkg1::fn1 and still know it will come from pkg1 and not someone's workspace or other package that chose the same name)

---

• https://stat.ethz.ch/pipermail/r-devel/2013-September/067451.html

The distinction is between "loading" and "attaching" a package. Loading it (which would be done if you had MASS::loglm, or imported it) guarantees that the package is initialized and in memory, but doesn't make it visible to the user without the explicit MASS:: prefix. Attaching it first loads it, then modifies the user's search list so the user can see it.

Loading is less intrusive, so it's preferred over attaching. Both library() and require() would attach it.

Create R package with devtools and roxygen2

A useful post by Jacob Montgomery. Do watch the youtube video there.

The process requires 3 components: RStudio software, devtools and roxygen2 (creating documentation from R code) packages.

Minimal R package for submission

https://stat.ethz.ch/pipermail/r-devel/2013-August/067257.html and CRAN Repository Policy.

Travis-CI

• A Beginner's Guide to Travis-CI
• testhat package

Submit packages to cran

• http://f.briatte.org/r/submitting-packages-to-cran
• https://rmhogervorst.github.io/cleancode/blog/2016/07/09/submtting-to-cran-first-experience.html

Build R package faster using multicore

http://www.rexamine.com/2015/07/speeding-up-r-package-installation-process/

The idea is edit the /lib64/R/etc/Renviron file (where /lib64/R/etc/ is the result to a call to the R.home() function in R) and set:

MAKE='make -j 8' # submit 8 jobs at once

Then build R package as regular, for example,

$ time R CMD INSTALL ~/R/stringi --preclean --configure-args='--disable-pkg-config'

Detect number of running R instances in Windows

• http://stackoverflow.com/questions/15935931/detect-number-of-running-r-instances-in-windows-within-r

C:\Program Files\R>tasklist /FI "IMAGENAME eq Rscript.exe"
INFO: No tasks are running which match the specified criteria.

C:\Program Files\R>tasklist /FI "IMAGENAME eq Rgui.exe"

Image Name                     PID Session Name        Session#    Mem Usage
========================= ======== ================ =========== ============
Rgui.exe                      1096 Console                    1     44,712 K

C:\Program Files\R>tasklist /FI "IMAGENAME eq Rserve.exe"

Image Name                     PID Session Name        Session#    Mem Usage
========================= ======== ================ =========== ============
Rserve.exe                    6108 Console                    1    381,796 K

In R, we can use

> system('tasklist /FI "IMAGENAME eq Rgui.exe" ', intern = TRUE)
[1] ""                                                                            
[2] "Image Name                     PID Session Name        Session#    Mem Usage"
[3] "========================= ======== ================ =========== ============"
[4] "Rgui.exe                      1096 Console                    1     44,804 K"

> length(system('tasklist /FI "IMAGENAME eq Rgui.exe" ', intern = TRUE))-3

Editor

http://en.wikipedia.org/wiki/R_(programming_language)#Editors_and_IDEs

• Emacs + ESS. The ESS is useful in the case I want to tidy R code (the tidy_source() function in the formatR package sometimes gives errors; eg when I tested it on an R file like <GetComparisonResults.R> from BRB-ArrayTools v4.4 stable).
• Rstudio - editor/R terminal/R graphics/file browser/package manager. The new version (0.98) also provides a new feature for debugging step-by-step. See also RStudio Tricks
• geany - I like the feature that it shows defined functions on the side panel even for R code. RStudio can also do this (see the bottom of the code panel).
• Rgedit which includes a feature of splitting screen into two panes and run R in the bottom panel. See here.
• Komodo IDE with browser preview http://www.youtube.com/watch?v=wv89OOw9roI at 4:06 and http://docs.activestate.com/komodo/4.4/editor.html

GUI for Data Analysis

Rcmdr

http://cran.r-project.org/web/packages/Rcmdr/index.html

Deducer

http://cran.r-project.org/web/packages/Deducer/index.html

Scope

See Assignments within functions in the An Introduction to R manual.

Note that any ordinary assignments done within the function are local and temporary and are lost after exit from the function.

Example 1.

> ttt <- data.frame(type=letters[1:5], JpnTest=rep("999", 5), stringsAsFactors = F)
> ttt
  type JpnTest
1    a     999
2    b     999
3    c     999
4    d     999
5    e     999
> jpntest <- function() { ttt$JpnTest[1] ="N5"; print(ttt)}
> jpntest()
  type JpnTest
1    a      N5
2    b     999
3    c     999
4    d     999
5    e     999
> ttt
  type JpnTest
1    a     999
2    b     999
3    c     999
4    d     999
5    e     999

Example 2. How can we set global variables inside a function? The answer is to use the "<<-" operator or assign(, , envir = .GlobalEnv) function.

Other resource: Advanced R by Hadley Wickham.

Speedup R code

• Strategies to speedup R code from DataScience+

Vectorization

http://www.noamross.net/blog/2014/4/16/vectorization-in-r--why.html

Mean of duplicated rows

• rowsum()
• use ave() and unique()
• data.table package
• plyr package
• aggregate() function. Too slow! http://slowkow.com/2015/01/28/data-table-aggregate/. Don't use aggregate post.

> attach(mtcars)
> head(mtcars)
                   mpg cyl disp  hp drat    wt  qsec vs am gear carb
Mazda RX4         21.0   6  160 110 3.90 2.620 16.46  0  1    4    4
Mazda RX4 Wag     21.0   6  160 110 3.90 2.875 17.02  0  1    4    4
Datsun 710        22.8   4  108  93 3.85 2.320 18.61  1  1    4    1
Hornet 4 Drive    21.4   6  258 110 3.08 3.215 19.44  1  0    3    1
Hornet Sportabout 18.7   8  360 175 3.15 3.440 17.02  0  0    3    2
Valiant           18.1   6  225 105 2.76 3.460 20.22  1  0    3    1
> aggdata <-aggregate(mtcars, by=list(cyl,vs), 
+   FUN=mean, na.rm=TRUE)
> print(aggdata)
  Group.1 Group.2      mpg cyl   disp       hp     drat       wt     qsec vs
1       4       0 26.00000   4 120.30  91.0000 4.430000 2.140000 16.70000  0
2       6       0 20.56667   6 155.00 131.6667 3.806667 2.755000 16.32667  0
3       8       0 15.10000   8 353.10 209.2143 3.229286 3.999214 16.77214  0
4       4       1 26.73000   4 103.62  81.8000 4.035000 2.300300 19.38100  1
5       6       1 19.12500   6 204.55 115.2500 3.420000 3.388750 19.21500  1
         am     gear     carb
1 1.0000000 5.000000 2.000000
2 1.0000000 4.333333 4.666667
3 0.1428571 3.285714 3.500000
4 0.7000000 4.000000 1.500000
5 0.0000000 3.500000 2.500000
> detach(mtcars)

Apply family

Vectorize, aggregate, apply, by, eapply, lapply, mapply, rapply, replicate, scale, sapply, split, tapply, and vapply. Check out this.

• apply – Apply a Functions Over Array Margins
• sapply – Apply a Function over a List or Vector
• lapply – Apply a Function over a List or Vector
• tapply – Apply a Function Over a "Ragged" Array
• mapply – Multivariate version of sapply
• rapply – A recursive version of lapply
• eapply – Apply a Function over values in an environment

However, apply is just a wrap of a loop. The performance is not better than a for loop. See

• http://tolstoy.newcastle.edu.au/R/help/06/05/27255.html (answered by Brian Ripley)
• https://stat.ethz.ch/pipermail/r-help/2014-October/422455.html (has one example)

The package 'pbapply' creates a text-mode progress bar - it works on any platforms. On Windows platform, check out this post. It uses winProgressBar() and setWinProgressBar() functions.

Progress bar

What is the cost of a progress bar in R?

lapply and Map

• Examples of using lapply + split on a data frame. See rollingyours.wordpress.com.
• Map() and Reduce() in functional programming

sapply & vapply

This discusses why vapply is safer and faster than sapply.

rapply - recursive version of lapply

• http://4dpiecharts.com/tag/recursive/
• Search in R source code. Mainly r-source/src/library/stats/R/dendrogram.R.

plyr and dplyr packages

Paper in J. Stat Software.

A quick introduction to plyr with a summary of apply functions in R and compare them with functions in plyr package.

1. plyr has a common syntax -- easier to remember
2. plyr requires less code since it takes care of the input and output format
3. plyr can easily be run in parallel -- faster

Tutorials

• A video of dplyr package can be found on vimeo.
• Hands-on dplyr tutorial for faster data manipulation in R from dataschool.io.

Examples of using dplyr:

• Medicines under evaluation
• CBI GEO Metadata Survey
• Logistic Regression by Page Piccinini. mutate(), inner_join() and %>%.
• DESeq2 post analysis select(), gather(), arrange() and %>%.

llply()

llply is equivalent to lapply except that it will preserve labels and can display a progress bar. This is handy if we want to do a crazy thing.

LLID2GOIDs <- lapply(rLLID, function(x) get("org.Hs.egGO")[[x]])

where rLLID is a list of entrez ID. For example,

get("org.Hs.egGO")[["6772"]]

returns a list of 49 GOs.

ddply()

http://lamages.blogspot.com/2012/06/transforming-subsets-of-data-in-r-with.html

ldply()

An R Script to Automatically download PubMed Citation Counts By Year of Publication

mclapply()

paralle package is a mult-core version of lapply()

Note that Windows OS can not take advantage of it.

Another choice for Windows OS is to use parLapply() function in parallel package.

ncores <- as.integer( Sys.getenv('NUMBER_OF_PROCESSORS') )
cl <- makeCluster(getOption("cl.cores", ncores))
LLID2GOIDs2 <- parLapply(cl, rLLID, function(x) {
                                    library(org.Hs.eg.db); get("org.Hs.egGO")[[x]]} 
                        )
stopCluster(cl)

It does work. Cut the computing time from 100 sec to 29 sec on 4 cores.

The mclapply() implementation relies on forking and Windows does not support forking. mclapply from the parallel package is implemented as a serial function on Windows systems. The parallelsugar package was created based on the above idea.

parallelsugar package

• http://edustatistics.org/nathanvan/2015/10/14/parallelsugar-an-implementation-of-mclapply-for-windows/

If we load parallelsugar, the default implementation of parallel::mclapply, which used fork based clusters, will be overwritten by parallelsugar::mclapply, which is implemented with socket clusters.

library(parallel) 

system.time( mclapply(1:4, function(xx){ Sys.sleep(10) }) )
##    user  system elapsed 
##    0.00    0.00   40.06 

library(parallelsugar)
## 
## Attaching package: ‘parallelsugar’
## 
## The following object is masked from ‘package:parallel’:
## 
##     mclapply

system.time( mclapply(1:4, function(xx){ Sys.sleep(10) }) )
##    user  system elapsed 
##    0.04    0.08   12.98

Regular Expression

• ?grep and ?regexpr in R
• http://biostat.mc.vanderbilt.edu/wiki/pub/Main/SvetlanaEdenRFiles/regExprTalk.pdf
• http://www.johndcook.com/r_language_regex.html
• http://en.wikibooks.org/wiki/R_Programming/Text_Processing#Regular_Expressions
• http://rpubs.com/Lionel/19068
• http://ucfagls.wordpress.com/2012/08/15/processing-sample-labels-using-regular-expressions-in-r/
• http://www.dummies.com/how-to/content/how-to-use-regular-expressions-in-r.html
• http://www.r-bloggers.com/example-8-27-using-regular-expressions-to-read-data-with-variable-number-of-words-in-a-field/
• http://www.r-bloggers.com/using-regular-expressions-in-r-case-study-in-cleaning-a-bibtex-database/
• http://cbio.ensmp.fr/~thocking/papers/2011-08-16-directlabels-and-regular-expressions-for-useR-2011/2011-useR-named-capture-regexp.pdf
• http://stackoverflow.com/questions/5214677/r-find-the-last-dot-in-a-string
• http://stackoverflow.com/questions/10294284/remove-all-special-characters-from-a-string-in-r

Specific to R

• https://en.wikipedia.org/wiki/Regular_expression
• PCRE and newlines tells the differences of \r\n (newline for Windows), \r (newline for UNIX, hex 0D) and \n (newline for old Mac, hex 0A). The tab \t has hex 09.
• http://www.autohotkey.com/docs/misc/RegEx-QuickRef.htm
• http://opencompany.org/download/regex-cheatsheet.pdf
• http://r-exercises.com/2016/10/30/regular-expressions-part-1/

Syntax

The following table is from endmemo.com.

Syntax	Description
\\d	Digit, 0,1,2 ... 9
\\D	Not Digit
\\s	Space
\\S	Not Space
\\w	Word
\\W	Not Word
\\t	Tab
\\n	New line
^	Beginning of the string
$	End of the string
\	Escape special characters, e.g. \\ is "\", \+ is "+"
	d)n/ matches "en" and "dn"
•	Any character, except \n or line terminator
[ab]	a or b
[^ab]	Any character except a and b
[0-9]	All Digit
[A-Z]	All uppercase A to Z letters
[a-z]	All lowercase a to z letters
[A-z]	All Uppercase and lowercase a to z letters
i+	i at least one time
i*	i zero or more times
i?	i zero or 1 time
i{n}	i occurs n times in sequence
i{n1,n2}	i occurs n1 - n2 times in sequence
i{n1,n2}?	non greedy match, see above example
i{n,}	i occures >= n times
[:alnum:]	Alphanumeric characters: [:alpha:] and [:digit:]
[:alpha:]	Alphabetic characters: [:lower:] and [:upper:]
[:blank:]	Blank characters: e.g. space, tab
[:cntrl:]	Control characters
[:digit:]	Digits: 0 1 2 3 4 5 6 7 8 9
[:graph:]	Graphical characters: [:alnum:] and [:punct:]
[:lower:]	Lower-case letters in the current locale
[:print:]	Printable characters: [:alnum:], [:punct:] and space
[:punct:]	} ~
[:space:]	Space characters: tab, newline, vertical tab, form feed, carriage return, space
[:upper:]	Upper-case letters in the current locale
[:xdigit:]	Hexadecimal digits: 0 1 2 3 4 5 6 7 8 9 A B C D E F a b c d e f

sub() and gsub()

The sub function changes only the first occurrence of the regular expression, while the gsub function performs the substitution on all occurrences within the string.

regexpr() and gregexpr()

The output from these functions is a vector of starting positions of the regular expressions which were found; if no match occurred, a value of -1 is returned.

The regexpr function will only provide information about the first match in its input string(s), while the gregexpr function returns information about all matches found.

Note that in C++, the std::string::find() and Qt's QRegExp::indexIn() can do R's regexpr() does. I am not aware of any gregexpr()-equivalent function in C++.

The following example is coming from the book 'Data Manipulation with R' by Phil Spector, Chapter 7, Character Manipulation.

tst = c('one x7 two b1', 'three c5 four b9', 'five six seven', 'a8 eight nine')
wh = regexpr('[a-z][0-9]', tst)
wh
# [1] 5 7 -1 1
# attr(,"match.length")
# [1] 2 2 -1 2

wh1 = gregexpr('[a-z][0-9]',tst) # return a list just like strsplit()
wh1

# [[1]]
# [1]  5 12
# attr(,"match.length")
# [1] 2 2
# attr(,"useBytes")
# [1] TRUE
#
# [[2]]
# [1]  7 15
# attr(,"match.length")
# [1] 2 2
# attr(,"useBytes")
# [1] TRUE
#
# [[3]]
# [1] -1
# attr(,"match.length")
# [1] -1
# attr(,"useBytes")
# [1] TRUE
#
# [[4]]
# [1] 1
# attr(,"match.length")
# [1] 2
# attr(,"useBytes")
# [1] TRUE

gregexpr("'", "|3'-5'") # find the apostrophe character
# [[1]]
# [1] 3 6
# attr(,"match.length")
# [1] 1 1
# attr(,"useBytes")
# [1] TRUE

Examples

• sub("^.*boundary=", "", string) will substitute a substring which starts with 0 or more characters and then 'boundary=' with an empty. Here ^ means beginning, dot means any character and star means the preceding item 0 or more times.
• grep("\\.zip$", pkgs) or grep("\\.tar.gz$", pkgs) will search for the string ending with .zip or .tar.gz
• grep("9.11", string) will search for the string containing '9', any character (to split 9 & 11) and '11'.
• pipe metacharacter; it is translated to 'or'. flood|fire will match strings containing floor or fire.
• [^?.]$ will match anyone ([]) not (^) ending ($) with the question mark (?) or period (.).
• ^[Gg]ood|[Bb]ad will match strings starting with Good/good and anywhere containing Bad/bad.
• ^([Gg]ood|[Bb]ad) will look for strings beginning with Good/good/Bad/bad.
• ? character; it means optional. [Gg]eorge( [Ww]\.)? [Bb]ush will match strings like 'george bush', 'George W. Bush' or 'george bushes'. Note that we escape the metacharacter dot by '\.' so it becomes a literal period.
• star and plus sign. star means any number including none and plus means at least one. For example, (.*) matches 'abc(222 )' and '()'.
• [0-9]+ (.*) [0-9]+ will match one number and following by any number of characters and a number; e.g. 'afda1080 p' and '4 by 5 size'.
• gsub("space:+", " ", " ab c ") will replace multiple spaces with 1 space.
• {} refers to as interval quantifiers; specify the minimum and maximum number of match of an expression.
• trimws() function to remove trailing/leading whitespace. The function is used in several places.

trimws <-
function(x, which = c("both", "left", "right"))
{
    which <- match.arg(which)
    mysub <- function(re, x) sub(re, "", x, perl = TRUE)
    if(which == "left")
        return(mysub("^[ \t\r\n]+", x))
    if(which == "right")
        return(mysub("[ \t\r\n]+$", x))
    mysub("[ \t\r\n]+$", mysub("^[ \t\r\n]+", x))
}

• Another solution to trim leading/trailing space is

# returns string w/o leading whitespace
trim.leading <- function (x)  sub("^\\s+", "", x)

# returns string w/o trailing whitespace
trim.trailing <- function (x) sub("\\s+$", "", x)

# returns string w/o leading or trailing whitespace
trim <- function (x) gsub("^\\s+|\\s+$", "", x)

Clipboard

source("clipboard")
read.table("clipboard")

read/manipulate binary data

• x <- readBin(fn, raw(), file.info(fn)$size)
• rawToChar(x[1:16])
• See Biostrings C API

String Manipulation

• ebook by Gaston Sanchez.
• Chapter 7 of the book 'Data Manipulation with R' by Phil Spector.
• Chapter 7 of the book 'R Cookbook' by Paul Teetor.
• Chapter 2 of the book 'Using R for Data Management, Statistical Analysis and Graphics' by Horton and Kleinman.
• http://www.endmemo.com/program/R/deparse.php. It includes lots of examples for each R function it lists.

HTTPs connection

HTTPS connection becomes default in R 3.2.2. See

• http://blog.rstudio.org/2015/08/17/secure-https-connections-for-r/
• http://blog.revolutionanalytics.com/2015/08/good-advice-for-security-with-r.html

setInternet2

There was a bug in ftp downloading in R 3.2.2 (r69053) Windows though it is fixed now in R 3.2 patch.

Read the discussion reported on 8/8/2015. The error only happened on ftp not http connection. The final solution is explained in this post. The following demonstrated the original problem.

url <- paste0("ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/",
              "GCF_000001405.13.assembly.txt")
f1 <- tempfile()
download.file(url, f1)

It seems the bug was fixed in R 3.2-branch. See 8/16/2015 patch r69089 where a new argument INTERNET_FLAG_PASSIVE was added to InternetOpenUrl() function of wininet library. This article and this post explain differences of active and passive FTP.

The following R command will show the exact svn revision for the R you are currently using.

R.Version()$"svn rev"

If setInternet2(T), then https protocol is supported in download.file().

When setInternet(T) is enabled by default, download.file() does not work for ftp protocol (this is used in getGEO() function of the GEOquery package). If I use setInternet(F), download.file() works again for ftp protocol.

The setInternet2() function is defined in R> src> library> utils > R > windows > sysutils.R.

R up to 3.2.2

setInternet2 <- function(use = TRUE) .Internal(useInternet2(use))

See also

• <src/include/Internal.h> (declare do_setInternet2()),
• <src/main/names.c> (show do_setInternet2() in C)
• <src/main/internet.c> (define do_setInternet2() in C).

Note that: setInternet2(T) becomes default in R 3.2.2. To revert to the previous default use setInternet2(FALSE). See the <doc/NEWS.pdf> file. If we use setInternet2(F), then it solves the bug of getGEO() error. But it disables the https file download using the download.file() function. In R < 3.2.2, it is also possible to download from https by setIneternet2(T).

R 3.3.0

setInternet2 <- function(use = TRUE) {
    if(!is.na(use)) stop("use != NA is defunct")
    NA
}

Note that setInternet2.Rd says As from \R 3.3.0 it changes nothing, and only \code{use = NA} is accepted. Also NEWS.Rd says setInternet2() has no effect and will be removed in due course.

read/download/source a file from internet

Simple text file http

retail <- read.csv("http://robjhyndman.com/data/ausretail.csv",header=FALSE)

Zip file and url() function

con = gzcon(url('http://www.systematicportfolio.com/sit.gz', 'rb'))
source(con)
close(con)

Here url() function is like file(), gzfile(), bzfile(), xzfile(), unz(), pipe(), fifo(), socketConnection(). They are used to create connections. By default, the connection is not opened (except for ‘socketConnection’), but may be opened by setting a non-empty value of argument ‘open’. See ?url.

Another example of using url() is

load(url("http:/www.example.com/example.RData"))

downloader package

This package provides a wrapper for the download.file function, making it possible to download files over https on Windows, Mac OS X, and other Unix-like platforms. The RCurl package provides this functionality (and much more) but can be difficult to install because it must be compiled with external dependencies. This package has no external dependencies, so it is much easier to install.

Google drive file based on https using RCurl package

require(RCurl)
myCsv <- getURL("https://docs.google.com/spreadsheet/pub?hl=en_US&hl=en_US&key=0AkuuKBh0jM2TdGppUFFxcEdoUklCQlJhM2kweGpoUUE&single=true&gid=0&output=csv")
read.csv(textConnection(myCsv))

Google sheet file using googlesheets package

Reading data from google sheets into R

Github files https using RCurl package

• http://support.rstudio.org/help/kb/faq/configuring-r-to-use-an-http-proxy
• http://tonybreyal.wordpress.com/2011/11/24/source_https-sourcing-an-r-script-from-github/

x = getURL("https://gist.github.com/arraytools/6671098/raw/c4cb0ca6fe78054da8dbe253a05f7046270d5693/GeneIDs.txt", 
            ssl.verifypeer = FALSE)
read.table(text=x)

• gistr package

Create publication tables using tables package

See p13 for example in http://www.ianwatson.com.au/stata/tabout_tutorial.pdf

R's tables packages is the best solution. For example,

> library(tables)
> tabular( (Species + 1) ~ (n=1) + Format(digits=2)*
+          (Sepal.Length + Sepal.Width)*(mean + sd), data=iris )
                                                  
                Sepal.Length      Sepal.Width     
 Species    n   mean         sd   mean        sd  
 setosa      50 5.01         0.35 3.43        0.38
 versicolor  50 5.94         0.52 2.77        0.31
 virginica   50 6.59         0.64 2.97        0.32
 All        150 5.84         0.83 3.06        0.44
> str(iris)
'data.frame':   150 obs. of  5 variables:
 $ Sepal.Length: num  5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
 $ Sepal.Width : num  3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...
 $ Petal.Length: num  1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
 $ Petal.Width : num  0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
 $ Species     : Factor w/ 3 levels "setosa","versicolor",..: 1 1 1 1 1 1 1 1 1 1 ...

and

# This example shows some of the less common options         
> Sex <- factor(sample(c("Male", "Female"), 100, rep=TRUE))
> Status <- factor(sample(c("low", "medium", "high"), 100, rep=TRUE))
> z <- rnorm(100)+5
> fmt <- function(x) {
  s <- format(x, digits=2)
  even <- ((1:length(s)) %% 2) == 0
  s[even] <- sprintf("(%s)", s[even])
  s
}
> tabular( Justify(c)*Heading()*z*Sex*Heading(Statistic)*Format(fmt())*(mean+sd) ~ Status )
                  Status              
 Sex    Statistic high   low    medium
 Female mean       4.88   4.96   5.17 
        sd        (1.20) (0.82) (1.35)
 Male   mean       4.45   4.31   5.05 
        sd        (1.01) (0.93) (0.75)

See also a collection of R packages related to reproducible research in http://cran.r-project.org/web/views/ReproducibleResearch.html

Tabulizer- extracting tables from PDFs

extracting Tables from PDFs in R

Create flat tables in R console using ftable()

> ftable(Titanic, row.vars = 1:3)
                   Survived  No Yes
Class Sex    Age                   
1st   Male   Child            0   5
             Adult          118  57
      Female Child            0   1
             Adult            4 140
2nd   Male   Child            0  11
             Adult          154  14
      Female Child            0  13
             Adult           13  80
3rd   Male   Child           35  13
             Adult          387  75
      Female Child           17  14
             Adult           89  76
Crew  Male   Child            0   0
             Adult          670 192
      Female Child            0   0
             Adult            3  20
> ftable(Titanic, row.vars = 1:2, col.vars = "Survived")
             Survived  No Yes
Class Sex                    
1st   Male            118  62
      Female            4 141
2nd   Male            154  25
      Female           13  93
3rd   Male            422  88
      Female          106  90
Crew  Male            670 192
      Female            3  20
> ftable(Titanic, row.vars = 2:1, col.vars = "Survived")
             Survived  No Yes
Sex    Class                 
Male   1st            118  62
       2nd            154  25
       3rd            422  88
       Crew           670 192
Female 1st              4 141
       2nd             13  93
       3rd            106  90
       Crew             3  20
> str(Titanic)
 table [1:4, 1:2, 1:2, 1:2] 0 0 35 0 0 0 17 0 118 154 ...
 - attr(*, "dimnames")=List of 4
  ..$ Class   : chr [1:4] "1st" "2nd" "3rd" "Crew"
  ..$ Sex     : chr [1:2] "Male" "Female"
  ..$ Age     : chr [1:2] "Child" "Adult"
  ..$ Survived: chr [1:2] "No" "Yes"
> x <- ftable(mtcars[c("cyl", "vs", "am", "gear")])
> x
          gear  3  4  5
cyl vs am              
4   0  0        0  0  0
       1        0  0  1
    1  0        1  2  0
       1        0  6  1
6   0  0        0  0  0
       1        0  2  1
    1  0        2  2  0
       1        0  0  0
8   0  0       12  0  0
       1        0  0  2
    1  0        0  0  0
       1        0  0  0
> ftable(x, row.vars = c(2, 4))
        cyl  4     6     8   
        am   0  1  0  1  0  1
vs gear                      
0  3         0  0  0  0 12  0
   4         0  0  0  2  0  0
   5         0  1  0  1  0  2
1  3         1  0  2  0  0  0
   4         2  6  2  0  0  0
   5         0  1  0  0  0  0
> 
> ## Start with expressions, use table()'s "dnn" to change labels
> ftable(mtcars$cyl, mtcars$vs, mtcars$am, mtcars$gear, row.vars = c(2, 4),
         dnn = c("Cylinders", "V/S", "Transmission", "Gears"))

          Cylinders     4     6     8   
          Transmission  0  1  0  1  0  1
V/S Gears                               
0   3                   0  0  0  0 12  0
    4                   0  0  0  2  0  0
    5                   0  1  0  1  0  2
1   3                   1  0  2  0  0  0
    4                   2  6  2  0  0  0
    5                   0  1  0  0  0  0

tracemem, data type, copy

How to avoid copying a long vector

Tell if the current R is running in 32-bit or 64-bit mode

8 * .Machine$sizeof.pointer

where sizeof.pointer returns the number of *bytes* in a C SEXP type and '8' means number of bits per byte.

32- and 64-bit

See R-admin.html.

• For speed you may want to use a 32-bit build, but to handle large datasets a 64-bit build.
• Even on 64-bit builds of R there are limits on the size of R objects, some of which stem from the use of 32-bit integers (especially in FORTRAN code). For example, the dimensionas of an array are limited to 2^31 -1.
• Since R 2.15.0, it is possible to select '64-bit Files' from the standard installer even on a 32-bit version of Windows (2012/3/30).

Handling length 2^31 and more in R 3.0.0

From R News for 3.0.0 release:

There is a subtle change in behaviour for numeric index values 2^31 and larger. These never used to be legitimate and so were treated as NA, sometimes with a warning. They are now legal for long vectors so there is no longer a warning, and x[2^31] <- y will now extend the vector on a 64-bit platform and give an error on a 32-bit one.

In R 2.15.2, if I try to assign a vector of length 2^31, I will get an error

> x <- seq(1, 2^31)
Error in from:to : result would be too long a vector

However, for R 3.0.0 (tested on my 64-bit Ubuntu with 16GB RAM. The R was compiled by myself):

> system.time(x <- seq(1,2^31))
   user  system elapsed
  8.604  11.060 120.815
> length(x)
[1] 2147483648
> length(x)/2^20
[1] 2048
> gc()
             used    (Mb) gc trigger    (Mb)   max used    (Mb)
Ncells     183823     9.9     407500    21.8     350000    18.7
Vcells 2147764406 16386.2 2368247221 18068.3 2148247383 16389.9
>

Note:

1. 2^31 length is about 2 Giga length. It takes about 16 GB (2^31*8/2^20 MB) memory.
2. On Windows, it is almost impossible to work with 2^31 length of data if the memory is less than 16 GB because virtual disk on Windows does not work well. For example, when I tested on my 12 GB Windows 7, the whole Windows system freezes for several minutes before I force to power off the machine.
3. My slide in http://goo.gl/g7sGX shows the screenshots of running the above command on my Ubuntu and RHEL machines. As you can see the linux is pretty good at handling large (> system RAM) data. That said, as long as your linux system is 64-bit, you can possibly work on large data without too much pain.
4. For large dataset, it makes sense to use database or specially crafted packages like bigmemory or ff.

NA in index

• Question: what is seq(1, 3)[c(1, 2, NA)]?

Answer: It will reserve the element with NA in indexing and return the value NA for it.

• Question: What is TRUE & NA?

Answer: NA

• Question: What is FALSE & NA?

Answer: FALSE

• Question: c("A", "B", NA) != "" ?

Answer: TRUE TRUE NA

• Question: which(c("A", "B", NA) != "") ?

Answer: 1 2

• Question: c(1, 2, NA) != "" & !is.na(c(1, 2, NA)) ?

Answer: TRUE TRUE FALSE

• Question: c("A", "B", NA) != "" & !is.na(c("A", "B", NA)) ?

Answer: TRUE TRUE FALSE

Conclusion: In order to exclude empty or NA for numerical or character data type, we can use which() or a convenience function keep.complete(x) <- function(x) x != "" & !is.na(x). This will guarantee return logical values and not contain NAs.

Don't just use x != "" OR !is.na(x).

Constant

Add 'L' after a constant. For example,

for(i in 1L:n) { }

if (max.lines > 0L) { }

label <- paste0(n-i+1L, ": ")

n <- length(x);  if(n == 0L) { }

Data frame

• http://blog.datacamp.com/15-easy-solutions-data-frame-problems-r/

data.frame to vector

> a= matrix(1:6, 2,3)
> rownames(a) <- c("a", "b")
> colnames(a) <- c("x", "y", "z")
> a
  x y z
a 1 3 5
b 2 4 6
> unlist(data.frame(a))
x1 x2 y1 y2 z1 z2 
 1  2  3  4  5  6 

matrix vs data.frame

ip1 <- installed.packages()[,c(1,3:4)] # class(ip1) = 'matrix'
unique(ip1$Priority)
# Error in ip1$Priority : $ operator is invalid for atomic vectors
unique(ip1[, "Priority"])   # OK

ip2 <- as.data.frame(installed.packages()[,c(1,3:4)], stringsAsFactors = FALSE) # matrix -> data.frame
unique(ip2$Priority)     # OK

Print a vector by suppressing names

Use unname.

sprintf does not print

Use cat() or print() outside sprintf(). sprintf() do not print in a non interactive mode.

cat(sprintf('%5.2f\t%i\n',1.234, l234))

Creating publication quality graphs in R

• http://teachpress.environmentalinformatics-marburg.de/2013/07/creating-publication-quality-graphs-in-r-7/

Write unix format files on Windows and vice versa

https://stat.ethz.ch/pipermail/r-devel/2012-April/063931.html

with() and within() functions

within() is similar to with() except it is used to create new columns and merge them with the original data sets. See youtube video.

closePr <- with(mariokart, totalPr - shipPr)
head(closePr, 20)

mk <- within(mariokart, {
             closePr <- totalPr - shipPr
     })
head(mk) # new column closePr

mk <- mariokart
aggregate(. ~ wheels + cond, mk, mean)
# create mean according to each level of (wheels, cond)

aggregate(totalPr ~ wheels + cond, mk, mean)

tapply(mk$totalPr, mk[, c("wheels", "cond")], mean)

Graphical Parameters, Axes and Text, Combining Plots

statmethods.net

15 Questions All R Users Have About Plots

See http://blog.datacamp.com/15-questions-about-r-plots/. This is a tremendous post. It covers

1. How To Draw An Empty R Plot?
2. How To Set The Axis Labels And Title Of The R Plots?
3. How To Add And Change The Spacing Of The Tick Marks Of Your R Plot
4. How To Create Two Different X- or Y-axes
5. How To Add Or Change The R Plot’s Legend?
6. How To Draw A Grid In Your R Plot?
7. How To Draw A Plot With A PNG As Background?
8. How To Adjust The Size Of Points In An R Plot?
9. How To Fit A Smooth Curve To Your R Data
10. How To Add Error Bars In An R Plot
11. How To Save A Plot As An Image On Disc
12. How To Plot Two R Plots Next To Each Other?
13. How To Plot Multiple Lines Or Points?
14. How To Fix The Aspect Ratio For Your R Plots
15. What Is The Function Of hjust And vjust In ggplot2?

Scatterplot with rugs

require(stats)  # both 'density' and its default method
with(faithful, {
    plot(density(eruptions, bw = 0.15))
    rug(eruptions)
    rug(jitter(eruptions, amount = 0.01), side = 3, col = "light blue")
})

Draw a single plot with two different y-axes

• http://www.gettinggeneticsdone.com/2015/04/r-single-plot-with-two-different-y-axes.html

Barplot with values

• barplot(), text() and axis() functions. The data can be from a table() object.
• two bars in one factor (stack). The data can be a 2-dim matrix with numerical values.
• two bars in one factor (next to each other)

Draw Color Palette

• http://teachpress.environmentalinformatics-marburg.de/2013/07/creating-publication-quality-graphs-in-r-7/

SVG

Embed svg in html

• http://www.magesblog.com/2016/02/using-svg-graphics-in-blog-posts.html

svglite

https://blog.rstudio.org/2016/11/14/svglite-1-2-0/

read.table

clipboard

source("clipboard")
read.table("clipboard")

inline text

mydf <- read.table(header=T, text='
 cond yval
    A 2
    B 2.5
    C 1.6
')

http(s) connection

temp = getURL("https://gist.github.com/arraytools/6743826/raw/23c8b0bc4b8f0d1bfe1c2fad985ca2e091aeb916/ip.txt", 
                           ssl.verifypeer = FALSE)
ip <- read.table(textConnection(temp), as.is=TRUE)

read only specific columns

Use 'colClasses' option in read.table, read.delim, .... For example, the following example reads only the 3rd column of the text file and also changes its data type from a data frame to a vector. Note that we have include double quotes around NULL.

x <- read.table("var_annot.vcf", colClasses = c(rep("NULL", 2), "character", rep("NULL", 7)), 
                skip=62, header=T, stringsAsFactors = FALSE)[, 1]
# 
system.time(x <- read.delim("Methylation450k.txt", 
                colClasses = c("character", "numeric", rep("NULL", 188)), stringsAsFactors = FALSE))

To know the number of columns, we might want to read the first row first.

library(magrittr)
scan("var_annot.vcf", sep="\t", what="character", skip=62, nlines=1, quiet=TRUE) %>% length()

Read excel files

• http://www.milanor.net/blog/?p=779

My experience is to save the Excel file as csv file (before it can be read into R) if it is possible.

Serialization

If we want to pass an R object to C (use recv() function), we can use writeBin() to output the stream size and then use serialize() function to output the stream to a file. See the post on R mailing list.

> a <- list(1,2,3)
> a_serial <- serialize(a, NULL)
> a_length <- length(a_serial)
> a_length
[1] 70
> writeBin(as.integer(a_length), connection, endian="big")
> serialize(a, connection)

In C++ process, I receive one int variable first to get the length, and then read <length> bytes from the connection.

socketConnection

See ?socketconnection.

Simple example

from the socketConnection's manual.

Open one R session

con1 <- socketConnection(port = 22131, server = TRUE) # wait until a connection from some client
writeLines(LETTERS, con1)
close(con1)

Open another R session (client)

con2 <- socketConnection(Sys.info()["nodename"], port = 22131)
# as non-blocking, may need to loop for input
readLines(con2)
while(isIncomplete(con2)) {
   Sys.sleep(1)
   z <- readLines(con2)
   if(length(z)) print(z)
}
close(con2)

Use nc in client

The client does not have to be the R. We can use telnet, nc, etc. See the post here. For example, on the client machine, we can issue

nc localhost 22131   [ENTER]

Then the client will wait and show anything written from the server machine. The connection from nc will be terminated once close(con1) is given.

If I use the command

nc -v -w 2 localhost -z 22130-22135

then the connection will be established for a short time which means the cursor on the server machine will be returned. If we issue the above nc command again on the client machine it will show the connection to the port 22131 is refused. PS. "-w" switch denotes the number of seconds of the timeout for connects and final net reads.

Some post I don't have a chance to read. http://digitheadslabnotebook.blogspot.com/2010/09/how-to-send-http-put-request-from-r.html

Use curl command in client

On the server,

con1 <- socketConnection(port = 8080, server = TRUE)

On the client,

curl --trace-ascii debugdump.txt http://localhost:8080/

Then go to the server,

while(nchar(x <- readLines(con1, 1)) > 0) cat(x, "\n")

close(con1) # return cursor in the client machine

Use telnet command in client

On the server,

con1 <- socketConnection(port = 8080, server = TRUE)

On the client,

sudo apt-get install telnet
telnet localhost 8080
abcdefg
hijklmn
qestst

Go to the server,

readLines(con1, 1)
readLines(con1, 1)
readLines(con1, 1)
close(con1) # return cursor in the client machine

Some tutorial about using telnet on http request. And this is a summary of using telnet.

Subsetting

Subset assignment of R Language Definition and Manipulation of functions.

The result of the command x[3:5] <- 13:15 is as if the following had been executed

`*tmp*` <- x
x <- "[<-"(`*tmp*`, 3:5, value=13:15)
rm(`*tmp*`)

S3 and S4

• Software for Data Analysis: Programming with R by John Chambers
• Programming with Data: A Guide to the S Language by John Chambers
• https://www.rmetrics.org/files/Meielisalp2009/Presentations/Chalabi1.pdf
• https://www.stat.auckland.ac.nz/S-Workshop/Gentleman/S4Objects.pdf
• packS4: Toy Example of S4 Package
• http://www.cyclismo.org/tutorial/R/s4Classes.html
• http://adv-r.had.co.nz/S4.html

To get the source code of S4 methods, we can use showMethod(), getMethod() and showMethod(). For example

library(qrqc)
showMethods("gcPlot")
getMethod("gcPlot", "FASTQSummary") # get an error
showMethods("gcPlot", "FASTQSummary") # good.

• getClassDef() in S4 (Bioconductor course).

library(IRanges)
ir <- IRanges(start=c(10, 20, 30), width=5)
ir

class(ir)
## [1] "IRanges"
## attr(,"package")
## [1] "IRanges"

getClassDef(class(ir))
## Class "IRanges" [package "IRanges"]
## 
## Slots:
##                                                                       
## Name:            start           width           NAMES     elementType
## Class:         integer         integer characterORNULL       character
##                                       
## Name:  elementMetadata        metadata
## Class: DataTableORNULL            list
## 
## Extends: 
## Class "Ranges", directly
## Class "IntegerList", by class "Ranges", distance 2
## Class "RangesORmissing", by class "Ranges", distance 2
## Class "AtomicList", by class "Ranges", distance 3
## Class "List", by class "Ranges", distance 4
## Class "Vector", by class "Ranges", distance 5
## Class "Annotated", by class "Ranges", distance 6
## 
## Known Subclasses: "NormalIRanges"

mcols() and DataFrame() from Bioc S4Vectors package

• mcols: Get or set the metadata columns.
• colData: SummarizedExperiment instances from GenomicRanges
• DataFrame: The DataFrame class extends the DataTable virtual class and supports the storage of any type of object (with length and [ methods) as columns.

For example, in Shrinkage of logarithmic fold changes vignette of the DESeq2paper package

> mcols(ddsNoPrior[genes, ])
DataFrame with 2 rows and 21 columns
   baseMean   baseVar   allZero dispGeneEst    dispFit dispersion  dispIter dispOutlier   dispMAP
  <numeric> <numeric> <logical>   <numeric>  <numeric>  <numeric> <numeric>   <logical> <numeric>
1  163.5750  8904.607     FALSE  0.06263141 0.03862798  0.0577712         7       FALSE 0.0577712
2  175.3883 59643.515     FALSE  2.25306109 0.03807917  2.2530611        12        TRUE 1.6011440
  Intercept strain_DBA.2J_vs_C57BL.6J SE_Intercept SE_strain_DBA.2J_vs_C57BL.6J WaldStatistic_Intercept
  <numeric>                 <numeric>    <numeric>                    <numeric>               <numeric>
1  6.210188                  1.735829    0.1229354                    0.1636645               50.515872
2  6.234880                  1.823173    0.6870629                    0.9481865                9.074686
  WaldStatistic_strain_DBA.2J_vs_C57BL.6J WaldPvalue_Intercept WaldPvalue_strain_DBA.2J_vs_C57BL.6J
                                <numeric>            <numeric>                            <numeric>
1                                10.60602         0.000000e+00                         2.793908e-26
2                                 1.92280         1.140054e-19                         5.450522e-02
   betaConv  betaIter  deviance  maxCooks
  <logical> <numeric> <numeric> <numeric>
1      TRUE         3  210.4045 0.2648753
2      TRUE         9  243.7455 0.3248949

findInterval()

Related functions are cuts() and split(). See also

• R Graphs Cookbook
• Hadley Wickham

do.call, rbind, lapply

Lots of examples. See for example this one for creating a data frame from a vector.

x <- readLines(textConnection("---CLUSTER 1 ---
 3
 4
 5
 6
 ---CLUSTER 2 ---
 9
 10
 8
 11"))

 # create a list of where the 'clusters' are
 clust <- c(grep("CLUSTER", x), length(x) + 1L)

 # get size of each cluster
 clustSize <- diff(clust) - 1L

 # get cluster number
 clustNum <- gsub("[^0-9]+", "", x[grep("CLUSTER", x)])

 result <- do.call(rbind, lapply(seq(length(clustNum)), function(.cl){
     cbind(Object = x[seq(clust[.cl] + 1L, length = clustSize[.cl])]
         , Cluster = .cl
         )
     }))

 result

     Object Cluster
[1,] "3"    "1"
[2,] "4"    "1"
[3,] "5"    "1"
[4,] "6"    "1"
[5,] "9"    "2"
[6,] "10"   "2"
[7,] "8"    "2"
[8,] "11"   "2"

A 2nd example is to sort a data frame by using do.call(order, list()).

How to get examples from help file

See this post. Method 1:

example(acf, give.lines=TRUE)

Method 2:

Rd <- utils:::.getHelpFile(?acf)
tools::Rd2ex(Rd)

"[" and "[[" with the sapply() function

Suppose we want to extract string from the id like "ABC-123-XYZ" before the first hyphen.

sapply(strsplit("ABC-123-XYZ", "-"), "[", 1)

is the same as

sapply(strsplit("ABC-123-XYZ", "-"), function(x) x[1])

Dealing with date

d1 = date()
class(d1) # "character"
d2 = Sys.Date()
class(d2) # "Date"

format(d2, "%a %b %d")

library(lubridate); ymd("20140108") # "2014-01-08 UTC"
mdy("08/04/2013") # "2013-08-04 UTC"
dmy("03-04-2013") # "2013-04-03 UTC"
ymd_hms("2011-08-03 10:15:03") # "2011-08-03 10:15:03 UTC"
ymd_hms("2011-08-03 10:15:03", tz="Pacific/Auckland") 
# "2011-08-03 10:15:03 NZST"
?Sys.timezone
x = dmy(c("1jan2013", "2jan2013", "31mar2013", "30jul2013"))
wday(x[1]) # 3
wday(x[1], label=TRUE) # Tues

• http://www.r-statistics.com/2012/03/do-more-with-dates-and-times-in-r-with-lubridate-1-1-0/
• http://cran.r-project.org/web/packages/lubridate/vignettes/lubridate.html
• http://rpubs.com/seandavi/GEOMetadbSurvey2014
• We want our dates and times as class "Date" or the class "POSIXct", "POSIXlt". For more information type ?POSIXlt.

Nonstandard evaluation

• substitute(expr, env) - capture expression. substitute() is often paired with deparse() to create informative labels for data sets and plots.
• quote(expr) - similar to substitute() but do nothing??
• eval(expr, envir), evalq(expr, envir) - eval evaluates its first argument in the current scope before passing it to the evaluator: evalq avoids this.
• deparse(expr) - turns unevaluated expressions into character strings. For example,

> deparse(args(lm))
[1] "function (formula, data, subset, weights, na.action, method = \"qr\", " 
[2] "    model = TRUE, x = FALSE, y = FALSE, qr = TRUE, singular.ok = TRUE, "
[3] "    contrasts = NULL, offset, ...) "                                    
[4] "NULL"     

> deparse(args(lm), width=20)
[1] "function (formula, data, "        "    subset, weights, "           
[3] "    na.action, method = \"qr\", " "    model = TRUE, x = FALSE, "   
[5] "    y = FALSE, qr = TRUE, "       "    singular.ok = TRUE, "        
[7] "    contrasts = NULL, "           "    offset, ...) "               
[9] "NULL"

• parse(text) - returns the parsed but unevaluated expressions in a list. See Create a Simple Socket Server in R for the application of eval(parse(text)).

The ‘…’ argument

See Section 10.4 of An Introduction to R. Especially, the expression list(...) evaluates all such arguments and returns them in a named list

Lazy evaluation in R functions arguments

• http://adv-r.had.co.nz/Functions.html
• https://stat.ethz.ch/pipermail/r-devel/2015-February/070688.html

R function arguments are lazy — they’re only evaluated if they’re actually used.

• Example 1. By default, R function arguments are lazy.

f <- function(x) {
  999
}
f(stop("This is an error!"))
#> [1] 999

• Example 2. If you want to ensure that an argument is evaluated you can use force().

add <- function(x) {
  force(x)
  function(y) x + y
}
adders2 <- lapply(1:10, add)
adders2[[1]](10)
#> [1] 11
adders2[[10]](10)
#> [1] 20

• Example 3. Default arguments are evaluated inside the function.

f <- function(x = ls()) {
  a <- 1
  x
}

# ls() evaluated inside f:
f()
# [1] "a" "x"

# ls() evaluated in global environment:
f(ls())
# [1] "add"    "adders" "f" 

• Example 4. Laziness is useful in if statements — the second statement below will be evaluated only if the first is true.

x <- NULL
if (!is.null(x) && x > 0) {

}

Backtick sign, infix/prefix/postfix operators

The backtick sign ` (not the single quote) refers to functions or variables that have otherwise reserved or illegal names; e.g. '&&', '+', '(', 'for', 'if', etc. See some examples in this note.

infix operator.

1 + 2    # infix
+ 1 2    # prefix
1 2 +    # postfix

List data type

Calling a function given a list of arguments

> args <- list(c(1:10, NA, NA), na.rm = TRUE)
> do.call(mean, args)
[1] 5.5
> mean(c(1:10, NA, NA), na.rm = TRUE)
[1] 5.5

Error handling and exceptions

• http://adv-r.had.co.nz/Exceptions-Debugging.html
• try() allows execution to continue even after an error has occurred. You can suppress the message with try(..., silent = TRUE).

out <- try({
  a <- 1
  b <- "x"
  a + b
})

elements <- list(1:10, c(-1, 10), c(T, F), letters)
results <- lapply(elements, log)
is.error <- function(x) inherits(x, "try-error")
succeeded <- !sapply(results, is.error)

• tryCatch(): With tryCatch() you map conditions to handlers (like switch()), named functions that are called with the condition as an input. Note that try() is a simplified version of tryCatch().

tryCatch(expr, ..., finally)

show_condition <- function(code) {
  tryCatch(code,
    error = function(c) "error",
    warning = function(c) "warning",
    message = function(c) "message"
  )
}
show_condition(stop("!"))
#> [1] "error"
show_condition(warning("?!"))
#> [1] "warning"
show_condition(message("?"))
#> [1] "message"
show_condition(10)
#> [1] 10

Below is another snippet from available.packages() function,

z <- tryCatch(download.file(....), error = identity)
if (!inherits(z, "error")) STATEMENTS

Using list type

Avoid if-else or switch

?plot.stepfun.

y0 <- c(1,2,4,3)
sfun0  <- stepfun(1:3, y0, f = 0)
sfun.2 <- stepfun(1:3, y0, f = .2)
sfun1  <- stepfun(1:3, y0, right = TRUE)

for(i in 1:3)
  lines(list(sfun0, sfun.2, stepfun(1:3, y0, f = 1))[[i]], col = i)
legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty = 1, y.intersp = 1)

Open a new Window device

X11() or dev.new()

par()

?par

layout

http://datascienceplus.com/adding-text-to-r-plot/

mtext vs title

http://datascienceplus.com/adding-text-to-r-plot/

mgp

The margin line (in ‘mex’ units) for the axis title, axis labels and axis line. Note that ‘mgp[1]’ affects ‘title’ whereas ‘mgp[2:3]’ affect ‘axis’. The default is ‘c(3, 1, 0)’.

If we like to make the axis labels closer to an axis, we can use mgp=c(2.3, 1, 0) for example.

lty

1=solid (default), 2=dashed, 3=dotted, 4=dotdash, 5=longdash, 6=twodash

oma

The following trick is useful when we want to draw multiple plots with a common title.

par(mfrow=c(1,2),oma = c(0, 0, 2, 0))  # oma=c(0, 0, 0, 0) by default
plot(1:10,  main="Plot 1")
plot(1:100,  main="Plot 2")
mtext("Title for Two Plots", outer = TRUE, cex = 1.5) # outer=FALSE by default

Suppress warnings

op <- options("warn")
options(warn = -1)
....
options(op)

save() vs saveRDS()

1. saveRDS() can only save one R object while save() does not have this constraint.
2. saveRDS() doesn’t save the both the object and its name it just saves a representation of the object. As a result, the saved object can be loaded into a named object within R that is different from the name it had when originally serialized. See this post.

x <- 5
saveRDS(x, "myfile.rds")
x2 <- readRDS("myfile.rds")
identical(mod, mod2, ignore.environment = TRUE)

all.equal(), identical()

• all.equal: compare R objects x and y testing ‘near equality’
• identical: The safe and reliable way to test two objects for being exactly equal.

x <- 1.0; y <- 0.99999999999
all.equal(x, y)
# [1] TRUE
identical(x, y)
# [1] FALSE

See also the testhat package.

Numerical Pitfall

Numerical pitfalls in computing variance

.1 - .3/3
## [1] 0.00000000000000001388

Sys.getpid()

This can be used to monitor R process memory usage or stop the R process. See this post.

How to debug an R code

Using assign() in functions

For example, insert the following line to your function

 assign(envir=globalenv(), "GlobalVar", localvar)

Debug R source code

Build R with debug information

• R -> Build R from its source on Windows
• http://www.stats.uwo.ca/faculty/murdoch/software/debuggingR/
• http://www.stats.uwo.ca/faculty/murdoch/software/debuggingR/gdb.shtml
• My note of debugging cor() function

.Call

• Writing R Extensions manual.

Registering native routines

https://cran.rstudio.com/doc/manuals/r-release/R-exts.html#Registering-native-routines

Pay attention to the prefix argument .fixes (eg .fixes = "C_") in useDynLib() function in the NAMESPACE file.

Example of debugging cor() function

Note that R's cor() function called a C function cor().

stats::cor
....
 .Call(C_cor, x, y, na.method, method == "kendall")

A step-by-step screenshot of debugging using the GNU debugger gdb can be found on my Github repository https://github.com/arraytools/r-debug.

Locale bug (grep did not handle UTF-8 properly PR#16264)

https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16264

Resource

Books

• A list of recommended books http://blog.revolutionanalytics.com/2015/11/r-recommended-reading.html
• Learning R programming by reading books: A book list
• Modern Applied Statistics with S by William N. Venables and Brian D. Ripley
• Seamless R and C++ Integration with Rcpp by Dirk Eddelbuettel
• Advanced R by Hadley Wickham
• Functional programming and unit testing for data munging with R by Bruno Rodrigues
• R Cookbook by Paul Teetor
• Machine Learning with R by Brett Lantz
• R for Everyone by Jared P. Lander
• The Art of R Programming by Norman Matloff
• Applied Predictive Modeling by Max Kuhn
• R in Action by Robert Kabacoff
• The R Book by Michael J. Crawley
• Regression Modeling Strategies, with Applications to Linear Models, Survival Analysis and Logistic Regression by Frank E. Harrell
• Data Manipulation with R by Phil Spector

Webinar

• RStudio & its github repository

Blogs, Tips

• Why R is hard to learn by Bob Musenchen.
• My 15 practical tips for a bioinformatician

Bug Tracking System

https://bugs.r-project.org/bugzilla3/ and Search existing bug reports. Remember to select 'All' in the Status drop-down list.