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"R is a system for statistical computation and graphics. It consists of a language plus a run-time environment with graphics, a debugger, access to certain system functions, and the ability to run programs stored in script files." | "R is a system for statistical computation and graphics. It consists of a language plus a run-time environment with graphics, a debugger, access to certain system functions, and the ability to run programs stored in script files." | ||
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Even though R was not developed for high performance computing (HPC), its popularity with scientists from a variety of disciplines, including engineering, mathematics, statistics, bioinformatics, etc. makes it an essential tool on HPC installations dedicated to academic research. Features such as C extensions, byte-compiled code and parallelisation allow for reasonable performance in single-node jobs. Thanks to R’s modular nature, users can customize the R functions available to them by installing packages from the Comprehensive R Archive Network ([https://cran.r-project.org/ CRAN]) into their home directories. | Even though R was not developed for high performance computing (HPC), its popularity with scientists from a variety of disciplines, including engineering, mathematics, statistics, bioinformatics, etc. makes it an essential tool on HPC installations dedicated to academic research. Features such as C extensions, byte-compiled code and parallelisation allow for reasonable performance in single-node jobs. Thanks to R’s modular nature, users can customize the R functions available to them by installing packages from the Comprehensive R Archive Network ([https://cran.r-project.org/ CRAN]) into their home directories. | ||
== The R interpreter == | == The R interpreter == <!--T:3--> | ||
You need to begin by loading an R module; there will typically be several versions available and you can see a list of all of them using the command | You need to begin by loading an R module; there will typically be several versions available and you can see a list of all of them using the command | ||
{{Command | {{Command | ||
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Platform: x86_64-pc-linux-gnu (64-bit) | Platform: x86_64-pc-linux-gnu (64-bit) | ||
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R is free software and comes with ABSOLUTELY NO WARRANTY. | R is free software and comes with ABSOLUTELY NO WARRANTY. | ||
You are welcome to redistribute it under certain conditions. | You are welcome to redistribute it under certain conditions. | ||
Type 'license()' or 'licence()' for distribution details. | Type 'license()' or 'licence()' for distribution details. | ||
Natural language support but running in an English locale | <!--T:5--> | ||
Natural language support but running in an English locale | |||
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R is a collaborative project with many contributors. | R is a collaborative project with many contributors. | ||
Type 'contributors()' for more information and | Type 'contributors()' for more information and | ||
'citation()' on how to cite R or R packages in publications. | 'citation()' on how to cite R or R packages in publications. | ||
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Type 'demo()' for some demos, 'help()' for on-line help, or | Type 'demo()' for some demos, 'help()' for on-line help, or | ||
'help.start()' for an HTML browser interface to help. | 'help.start()' for an HTML browser interface to help. | ||
Type 'q()' to quit R. | Type 'q()' to quit R. | ||
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> values <- c(3,5,7,9) | > values <- c(3,5,7,9) | ||
> values[0] | > values[0] | ||
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To execute R scripts, use the <tt>Rscript</tt> front-end with the file containing the R commands as an argument: | To execute R scripts, use the <tt>Rscript</tt> front-end with the file containing the R commands as an argument: | ||
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{{Command|Rscript computation.R}} | {{Command|Rscript computation.R}} | ||
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This front-end will automatically pass scripting-appropriate options <tt>--slave</tt> and <tt>--no-restore</tt> to the R interpreter. These also imply the <tt>--no-save</tt> option, preventing the creation of useless workspace files on exit. | This front-end will automatically pass scripting-appropriate options <tt>--slave</tt> and <tt>--no-restore</tt> to the R interpreter. These also imply the <tt>--no-save</tt> option, preventing the creation of useless workspace files on exit. | ||
== Installing R packages == | == Installing R packages == <!--T:11--> | ||
To install packages from [https://cran.r-project.org/ CRAN], you can use the <tt>install.packages</tt> facility inside the R interpreter. For example, to install the <tt>sp</tt> package that provides classes and methods for spatial data, use the following command on a login node: | To install packages from [https://cran.r-project.org/ CRAN], you can use the <tt>install.packages</tt> facility inside the R interpreter. For example, to install the <tt>sp</tt> package that provides classes and methods for spatial data, use the following command on a login node: | ||
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{{Command | {{Command | ||
|R | |R | ||
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}} | }} | ||
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When asked, select an appropriate mirror for download. Ideally, it will be geographically close to the cluster you're working on. | When asked, select an appropriate mirror for download. Ideally, it will be geographically close to the cluster you're working on. | ||
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Some packages require defining the environment variable <tt>TMPDIR</tt> before installing. | Some packages require defining the environment variable <tt>TMPDIR</tt> before installing. | ||
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To install a package that you downloaded (i.e. not from CRAN), you can install it the following way. Assuming the package is named <tt>archive_package.tgz</tt>, run the following command in a shell: | To install a package that you downloaded (i.e. not from CRAN), you can install it the following way. Assuming the package is named <tt>archive_package.tgz</tt>, run the following command in a shell: | ||
{{Command | {{Command | ||