Difference between revisions of "R"

Revision as of 16:21, 27 October 2013

R is a free software environment for statistical computing and graphics (http://www.r-project.org/).

Installation

Install the r package available in the official repositories

Some external packages may require to be compile in Fortran as well, so installing the gcc-fortran can be a good idea

Initial configuration

Please refer to Initialization at Start of an R Session to get a detailed understanding of startup process. The home directory of the R installation is usr/bin/R. Base packages are found in usr/bin/R/library/base and site configuration files in /etc/R/. Aspects of the Locale are accessed by the functions Sys.getlocale and Sys.localeconv within the R session. Locales will be the one defined in your system.

To start a R session, open your terminal and type this command:

$ R

Run help(startup) to read the documentation about system file configuration, help() for the on-line help,help.start() for the HTML browser interface to help, demo() for some demos and q() to close the session and quit.

When closing the session, you will be prompted : Save workspace Image ?[y/n/c]. The workspace is your current working environment and include any user-defined objects, functions. The saved image is stored in .RData format and will be automatically reloaded the next time R is started. You can manually save the workspace at any time in the session with the save.image(image.RData) command, save as many images as you want (eg : image1.RData, image2.RData). You can load image with the load.iamge(image.RData) command at any time of your session.

Variables

R can be confusing when it comes to Environment Variables, as they are large and duplicated following the site or user sides. There are two sorts of files used in startup: environment files, defined by $R_ENVIRON and profile files, defined by $R_PROFILE.

Most important variables can be found on Environment Variables R Documentation].

Renviron

At startup, R search at early stage for site and user .Renviron files to process for setting Environment_Variables. The site file is located in /etc/R, and generated by configure.

The name of the user file can be specified by the R_ENVIRON_USER Environment_Variables. If you don't specify any file, R will automatically read .Renviron in your home directory if there is one. In case you want to use another emplacement for this file, append this line export R_ENVIRON_USER ="path/to/.Renviron" in one of your Startup_files. This is the place to set all kind of environment variables using the R syntax.

Rprofile

Then R searches for the site-wilde Rprofile.site defined by the R_PROFILE Environment_Variables. This file does not exist after a fresh installation. Finally, R seraches for user R_PROFILE_USER. if unset, a file called .Rprofile is searched for in the current directory, returned by the R command > getwd() or in the user's home directory. This is the place to put all your custom R code.

Installing R packages

There are many add-on R packages, which can be browsed on The R Website.. They can be installed from within R using the install.packages(pkgname) command. R can install its packages locally as per user local settings or system wide.

Within your R session, run this command to check that your user library exists and is set correctly:

> Sys.getenv("R_LIBS_USER")

[1] "/path/to/directory/R/packages"

Installation within your R session is the safest way and won't conflict with the pacman package management, but there is another method to install packages. Run the following command in your terminal:

$ R CMD INSTALL -l $R_LIBS_USER pkg1 pkg2 ...

Upgrading R packages

> update.packages(ask=FALSE)

Or when you also need to rebuild packages which were built for an older version:

> update.packages(ask=FALSE,checkBuilt=TRUE)

Configuration files

The two user configuration files you want in your home folder are .Rprofile and Renviron.r. If you want to keep your $HOME directory as clean as possible, a good practice will be to make the ~/.config/r directory and append all your environment #Variables in the Renviron.r file : $HOME/.config/r/Renviron.r. Then, at the root of your $HOME directory, append the following line to ~/.Rprofile:

 source ("~/.config/r/Renviron.r")

Renviron.r file

Here is a very basic Renviron.r you can start with:

Renviron.r

                                       
Sys.setenv(R_HOME_USER = "/path/to/your/r/directory")
Sys.setenv(R_ENVIRON_USER = "${HOME}/.config/r/.Renviron.r")
Sys.setenv(R_LIBS_USER = "/path/to/your/r/library")
Sys.setenv(R_HISTFILE = "/path/to/your/filename.Rhistory")   # Do not forget to append the .Rhistory
Sys.setenv(R_HISTSIZE ='5000')

readRenviron("/path/to/any/custom_startup_file")             # read any custom startup file

You can add more global options to customize your R environment. Here is a very short list:

Renviron.r

options(prompt = paste(paste (Sys.info () [c ("user", "nodename")], collapse = "@"),"[R] "))  # customize your R prompt with username and hostname in this format: user@hostname [R]
options(digits = 4)                                                                           # number of digits to print
options(stringsAsFactors = FALSE)
options(show.signif.stars = FALSE)
error = quote(dump.frames("${R_HOME_USER}/testdump", TRUE))                                   # post-mortem debugiging facilities

See this post for more user configurations.

Adding a graphical frontend to R

The linux version of R does not include a graphical user interface. However, third-party user interfaces for R are available, such as R commander and RKWard.

R Commander frontend

R Commander is a popular user interface to R. There is no Arch linux package available to install R commander, but it is an R package so it can be installed easily from within R. R Commander requires Tk:

# pacman -S tk

To install R Commander, run 'R' from the command line. Then type:

> install.packages("Rcmdr", dependencies=TRUE)

This can take some time.

You can then start R Commander from within R using the library command:

> library("Rcmdr")

RKWard frontend

RKWard is an open-source frontend which allows for data import and browsing as well as running common statistical tests and plots. You can install rkward^AUR from AUR.

Rstudio IDE

RStudio an open-source R IDE. It includes many modern conveniences such as parentheses matching, tab-completion, tool-tip help popups, and a spreadsheet-like data viewer.

Install rstudio-desktop-bin^AUR (binary version from the Rstudio project website) or rstudio-desktop-git^AUR (development version) from AUR.

The R library path is often configured with the R_LIBS environment variable. RStudio ignores this, so the user must set R_LIBS_USER in ~/.Renviron, as documented above.