Difference between revisions of "R"

From ArchWiki
Jump to: navigation, search
(Initial configuration: explain site R Documentation)
m (Variables)
Line 26: Line 26:
  
 
===Variables===
 
===Variables===
{{ic|R}} can be confusing when it comes to [[Environment Variables]].{{ic|R}} search for '''site''' (understand '''system wide''') and user files to process for setting them. Most important ones can be found on [http://stat.ethz.ch/R-manual/R-devel/library/base/html/EnvVar.html R Documentation]. The ''site'' {{ic|R_ENVIRON}} file is ${R_HOME}/etc/Renviron. To see {{ic|R_HOME}} variable, run the {{ic|Sys.getenv()}} command within your {{ic|R}} session: {{hc|> Sys.getenv("R_HOME")|[1] "/usr/lib64/R"}}
+
{{ic|R}} can be confusing when it comes to [[Environment Variables]].{{ic|R}} search for '''site''' and '''user''' files to process for setting them. Most important variables can be found on [http://stat.ethz.ch/R-manual/R-devel/library/base/html/EnvVar.html Environment Variables]. The '''site''' {{ic|R_ENVIRON}} file is ${R_HOME}/etc/Renviron. To see {{ic|R_HOME}} variable, run the {{ic|Sys.getenv()}} command within your {{ic|R}} session: {{hc|> Sys.getenv("R_HOME")|[1] "/usr/lib64/R"}}
 
{{Note|/usr/lib64/R/etc/Renviron is a symlink to /etc/R/Renviron}}
 
{{Note|/usr/lib64/R/etc/Renviron is a symlink to /etc/R/Renviron}}
 
The name of the user file can be specified by the {{ic|R_ENVIRON_USER}} ''environment variable''. You can append this line in your [[Bashrc]]: {{bc|
 
The name of the user file can be specified by the {{ic|R_ENVIRON_USER}} ''environment variable''. You can append this line in your [[Bashrc]]: {{bc|
Line 34: Line 34:
 
To set the location of your local {{ic|R}} package library, append the following line in your {{ic|Renviron}} file:
 
To set the location of your local {{ic|R}} package library, append the following line in your {{ic|Renviron}} file:
 
{{bc|R_LIBS_USER=/path/to/directory/R/packages}}
 
{{bc|R_LIBS_USER=/path/to/directory/R/packages}}
 
  
 
== Installing R packages ==
 
== Installing R packages ==

Revision as of 16:31, 5 October 2013

Tango-document-new.pngThis article is a stub.Tango-document-new.png

Notes: please use the first argument of the template to provide more detailed indications. (Discuss in Talk:R#)

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 main main script is usr/bin/R, basic packages are found in $HOME/R/ and site configuration files in /etc/R/.

Make sure R has been installed correctly by running the following command in a terminal to start a R session:

$ R
Note:
  • Use Shift+u for the command (some terminals use the r letter to repeat the last entered command). Once in your R session, the prompt will change to >
  • site refers to system-wide in R Documentation

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. The saved image is stored in .RData 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() command.

Variables

R can be confusing when it comes to Environment Variables.R search for site and user files to process for setting them. Most important variables can be found on Environment Variables. The site R_ENVIRON file is ${R_HOME}/etc/Renviron. To see R_HOME variable, run the Sys.getenv() command within your R session:
> Sys.getenv("R_HOME")
[1] "/usr/lib64/R"
Note: /usr/lib64/R/etc/Renviron is a symlink to /etc/R/Renviron
The name of the user file can be specified by the R_ENVIRON_USER environment variable. You can append this line in your Bashrc:
export R_HOME_USER=/path/to/your/Renviron

R packages are installed into libraries which are directories in the file system containing a subdirectory for each package installed there. To set the location of your local R package library, append the following line in your Renviron file:

R_LIBS_USER=/path/to/directory/R/packages

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

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 rkwardAUR 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-binAUR (binary version from the Rstudio project website) or rstudio-desktop-gitAUR (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.