Difference between revisions of "R"

From ArchWiki
Jump to: navigation, search
(Upgrading R packages: R documentation seems to be wrong; not just needed for a minor version)
(Installing R: Added some useful missing informations and started to reorganize the wiki. More edits shall follow in coming days with 2 new sections : configuration files & Invoking R from the command line)
Line 5: Line 5:
 
''R is a free software environment for statistical computing and graphics''  (http://www.r-project.org/).
 
''R is a free software environment for statistical computing and graphics''  (http://www.r-project.org/).
  
== Installing R ==
+
== Installation ==
  
It is very easy to install R in Arch Linux:
+
[[pacman|Install]] the {{Pkg|r}} package available in the [[official repositories]]
# pacman -S r
+
  
R has some dependencies in tcl and tk (required to install an R package from R). To install then:
+
Some external packages may require to be compile in Fortran as well, so [[pacman|installing]] the {{Pkg|gcc-fortran}} can be a good idea
# pacman -S tcl tk
+
  
Some external packages may require to be compile in Fortran as well, so installing gcc-fortran can be a good idea:
+
=== Initial configuration ===
# pacman -S gcc-fortran
+
  
=== Installing R packages ===
+
Make sure {{ic|R}} has been installed correctly by running the following command in a terminal to start a {{ic|R}} session:
There are many add-on R packages, which can be browsed on [http://cran.r-project.org/ The R Website.]. They can be installed from within R using the R install.packages command. It is not necessary to be superuser or have root privileges when doing this -- R can install its packages locally for the individual user. This is the safest way to install R packages and won't conflict with the pacman package management.
+
$ R
 +
{{Note|Use {{ic|Shift+u}} for the command (some terminals use the {{ic|r}} letter to repeat the last entered command). Once in your {{ic|R}} session, the prompt will change to {{ic|>}}}}
 +
run {{ic|help(startup)}} to read the documentation about system file  configuration, {{ic|help()}} for the on-line help,{{ic|help.start()}} for the HTML browser interface to help, {{ic|demo()}} for some demos and {{ic|q()}} to close the session and quit.
  
To set the location of your local R package library, create a {{ic|~/.Renviron}} file and set R_LIBS_USER:
+
When closing the session, you will be prompted : {{ic|Save workspace Image ?[y/n/c]}}. The ''workspace'' is your current working environment and include any user-defined objects. The saved image will be automatically reloaded the next time {{ic|R}} is started. You can manually save the workspace at any time in the session with the {{ic|save.image()}} command.
 +
 
 +
=== Installing R packages ===
 +
There are many add-on R packages, which can be browsed on [http://cran.r-project.org/web/packages/available_packages_by_date.html The R Website.]. They can be installed from within R using the R install.packages command. It is not necessary to be superuser or have root privileges when doing this -- R can install its packages locally for the individual user. This is the safest way to install R packages and won't conflict with the pacman package management.
  
{{hc|~/.Renviron|
+
To set the location of your local R package library, create a {{ic|~/.Renviron}} file and append the following line:
R_LIBS_USER=/home/username/path/to/R/packages}}
+
{{bc|R_LIBS_USER=/path/to/directory/R/packages}}
  
 
=== Upgrading R packages ===
 
=== Upgrading R packages ===

Revision as of 23:28, 25 September 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

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 >

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 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.

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 R install.packages command. It is not necessary to be superuser or have root privileges when doing this -- R can install its packages locally for the individual user. This is the safest way to install R packages and won't conflict with the pacman package management.

To set the location of your local R package library, create a ~/.Renviron file and append the following line:

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

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)

Running R

R can be run from the command line, by using the R command:

$ R

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.