Difference between revisions of "R"
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[[Category:Mathematics and science]] | [[Category:Mathematics and science]] | ||
[[Category:Programming language]] | [[Category:Programming language]] | ||
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''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/). | ||
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=== Initial configuration === | === Initial configuration === | ||
| − | The | + | Please refer to [http://stat.ethz.ch/R-manual/R-devel/library/base/html/Startup.html Initialization at Start of an R Session] to get a detailed understanding of startup process. |
| + | The home directory of the {{ic|R}} installation is {{ic|usr/bin/R}}. Base packages are found in {{ic|usr/bin/R/library/base}} and '''site''' configuration files in {{ic|/etc/R/}}. Aspects of the [[Locale]] are accessed by the functions {{ic|Sys.getlocale}} and {{ic|Sys.localeconv}} within the {{ic|R}} session. Locales will be the one defined in your system. | ||
| + | |||
| + | To start a {{ic|R}} session, open your terminal and type this command: | ||
| + | $ 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|>}} | ||
| + | * '''site''' refers to '''system-wide''' in R Documentation}} | ||
| + | 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. | ||
| + | |||
| + | 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, functions. The saved image is stored in {{ic|.RData}} format and 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(image.RData)}} command, save as many images as you want (eg : ''image1.RData'', ''image2.RData''). You can load image with the {{ic|load.iamge(image.RData)}} command at any time of your session. | ||
| − | + | {{Tip| | |
| + | * Tired of R's verbose startup message ? Then start {{ic|R}} with the {{ic|--quiet}} command-line option. | ||
| + | {{ic|$ R --quiet}} | ||
| + | You can {{ic|alias R ="R --quiet"}} in one of your [[Startup_files]] | ||
| + | * Unless explicitly defined somewhere in your configuration files, {{ic|R}} will start in your $HOME directory. If you want to start in a specific directory. first time you create the directory do this: | ||
$ R | $ R | ||
| − | + | > setwd("path/to/your/directory") | |
| − | + | > q() | |
| + | Save workspace image? [y/n/c]: y | ||
| + | {{ic|R}} will create a '''.RData''' image file of your current environment. Then, when double-clicking this file, {{ic|R}} will automatically change its working directory to the file's directory. | ||
| + | }} | ||
| − | + | ===Variables=== | |
| + | {{ic|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 {{ic|$R_ENVIRON}} and ''profile files'', defined by {{ic|$R_PROFILE}}. | ||
| − | + | Most important variables can be found on [http://stat.ethz.ch/R-manual/R-devel/library/base/html/EnvVar.html Environment Variables R Documentation]]. | |
| − | + | ====R_ENVIRON==== | |
| + | At startup, {{ic|R}} search at early stage for '''site''' and '''user''' {{ic|.Renviron}} files to process for setting [[Environment variables]]. The '''site''' file is located in {{ic|/etc/R}}, and generated by configure. | ||
| − | + | The name of the user file can be specified by the {{ic|R_ENVIRON_USER}} [[Environment variables]]. | |
| − | {{ | + | If you don't specify any file, {{ic|R}} will automatically read {{ic|.Renviron}} in your home directory if there is one. In case you want to use another emplacement for this file, append this line {{ic| 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'''. |
| + | |||
| + | ====R_PROFILE==== | ||
| + | Then {{ic|R}} searches for the '''site-wilde''' {{ic|Rprofile.site}} defined by the {{ic|R_PROFILE}} [[Environment variables]]. This file does not exist after a fresh installation. | ||
| + | Finally, {{ic|R}} seraches for '''user''' {{ic|R_PROFILE_USER}}. if unset, a file called {{ic|.Rprofile}} is searched for in the current directory, returned by the {{ic|R}} command {{ic|> getwd()}} or in the user's home directory. This is the place to put all your custom {{ic|R}} code. | ||
| + | |||
| + | == Installing R packages == | ||
| + | There are many add-on {{ic|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 {{ic|R}} using the {{ic|'''install.packages(''pkgname'')''' command}}. {{ic|R}} can install its packages locally as '''per user''' local settings or '''system wide'''. | ||
| + | |||
| + | Within your {{ic|R }} session, run this command to check that your user library exists and is set correctly: | ||
| + | {{hc|> Sys.getenv("R_LIBS_USER")| | ||
| + | [1] "/path/to/directory/R/packages"}} | ||
| + | Installation within your {{ic|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: | ||
| + | |||
| + | {{bc|$ R CMD INSTALL -l $R_LIBS_USER ''pkg1 pkg2 ...''}} | ||
=== Upgrading R packages === | === Upgrading R packages === | ||
| Line 32: | Line 65: | ||
Or when you also need to rebuild packages which were built for an older version: | Or when you also need to rebuild packages which were built for an older version: | ||
> update.packages(ask=FALSE,checkBuilt=TRUE) | > update.packages(ask=FALSE,checkBuilt=TRUE) | ||
| + | |||
| + | ==Configuration files== | ||
| + | |||
| + | The two user configuration files you want in your home folder are {{ic|.Renviron}} and {{ic|Rprofile.r}}. If you want to keep your {{ic|$HOME}} directory as clean as possible, a good practice will be to make the {{ic|~/.config/r}} directory, put the {{ic|Rprofile.r}} file at the root of the directory and append all your {{ic|R}} code in this file. | ||
| + | ===.Renviron=== | ||
| + | Lines in {{ic|Renviron}} file should be either comment lines starting with '''#''' or lines of the form ''name=value''.Here is a very basic {{ic|.Renviron}} you can start with: | ||
| + | {{hc|.Renviron| | ||
| + | R_HOME_USER = /path/to/your/r/directory | ||
| + | R_PROFILE_USER = ${HOME}/.config/r/Rprofile.r | ||
| + | R_LIBS_USER = /path/to/your/r/library | ||
| + | R_HISTFILE = /path/to/your/filename.Rhistory # Do not forget to append the '''.Rhistory''' | ||
| + | }} | ||
| + | |||
| + | ===Rprofile.r=== | ||
| + | For convenient reasons, you can put a specific {{ic|Rprofile.r}} in each of your usual working directories. One facility would be to dedicate one directory per project, with its specific profile. When {{ic|R}} will change to the working directory, it will then read the {{ic|Rprofile.r}} file inside it. | ||
| + | |||
| + | Here is a very short list of useful options and code: | ||
| + | {{hc|Rprofile.r| | ||
| + | options(prompt = paste(paste (Sys.info () [c ("user", "nodename")], collapse = "@"),"[R] ")) # customize your R prompt with username and hostname in this format: '''user@hostname [R]''' | ||
| + | options(digits = 4) # number of digits to print | ||
| + | options(stringsAsFactors = FALSE) | ||
| + | options(show.signif.stars = FALSE) | ||
| + | error = quote(dump.frames("${R_HOME_USER}/testdump", TRUE)) # post-mortem debugiging facilities | ||
| + | }} | ||
| + | You can add more [http://stat.ethz.ch/R-manual/R-devel/library/base/html/options.html global options] to customize your {{ic|R}} environment. | ||
| + | See this [http://stackoverflow.com/questions/1189759/expert-r-users-whats-in-your-rprofile post] for more user configurations. | ||
== Adding a graphical frontend to R == | == Adding a graphical frontend to R == | ||
Revision as of 09:10, 23 February 2014
R is a free software environment for statistical computing and graphics (http://www.r-project.org/).
Contents
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].
R_ENVIRON
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.
R_PROFILE
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 .Renviron and Rprofile.r. If you want to keep your $HOME directory as clean as possible, a good practice will be to make the ~/.config/r directory, put the Rprofile.r file at the root of the directory and append all your R code in this file.
.Renviron
Lines in Renviron file should be either comment lines starting with # or lines of the form name=value.Here is a very basic .Renviron you can start with:
.Renviron
R_HOME_USER = /path/to/your/r/directory
R_PROFILE_USER = ${HOME}/.config/r/Rprofile.r
R_LIBS_USER = /path/to/your/r/library
R_HISTFILE = /path/to/your/filename.Rhistory # Do not forget to append the .Rhistory
Rprofile.r
For convenient reasons, you can put a specific Rprofile.r in each of your usual working directories. One facility would be to dedicate one directory per project, with its specific profile. When R will change to the working directory, it will then read the Rprofile.r file inside it.
Here is a very short list of useful options and code:
Rprofile.r
options(prompt = paste(paste (Sys.info () [c ("user", "nodename")], collapse = "@"),"[R] ")) # customize your R prompt with username and hostname in this format: user@hostname [R]
options(digits = 4) # number of digits to print
options(stringsAsFactors = FALSE)
options(show.signif.stars = FALSE)
error = quote(dump.frames("${R_HOME_USER}/testdump", TRUE)) # post-mortem debugiging facilities
You can add more global options to customize your R environment.
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 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.