Applications/R

From HPC
Jump to: navigation , search

Application Details

  • Description: R is an open source programming language and software environment for statistical computing and graphics
  • Version: 3.3.0, 3.4.1
  • Modules: R/3.3.0,R/3.4.1
  • Licence: GNU

Information

R is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language and environment which was developed at Bell Laboratories (formerly AT&T, now Lucent Technologies) by John Chambers and colleagues. R can be considered as a different implementation of S. There are some important differences, but much code written for S runs unaltered under R.

R provides a wide variety of statistical (linear and non-linear modelling, classical statistical tests, time-series analysis, classification, clustering, …) and graphical techniques, and is highly extensible. The S language is often the vehicle of choice for research in statistical methodology, and R provides an Open Source route to participation in that activity.

One of R’s strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control.

Usage Examples

Note: Use version 3.4.1, version 3.3.0 will be deprecated in the future.

Interactive

Note: R supports interactive mode (as below) and execution mode running as an interpreted script.


[username@login01 ~]$ interactive
salloc: Granted job allocation 402968
Job ID 402968 connecting to c059, please wait...
Last login: Wed Jul 12 16:23:48 2017 from 10.254.5.246
[username@c059 ~]$ module load R/3.4.1
[username@c059~]$ R


3.3.0

This version is to be deprecated, all new work should be done with version 3.4.1

3.4.1

This version has compiled support for these additional libraries:

  • --enable-R-shlib
  • --with-x --with-readline
  • --with-cairo
  • --with-tcltk
  • --with-libpng
  • --with-jpeglib

Install an R package



[username@login01 ~]$ module load R/3.4.1
[username@login01 ~]$ R

R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages("ggplot2")

Batch Submission

#!/bin/bash
#SBATCH -J My_R_job              # Job name, you can change it to whatever you want
#SBATCH -N 1                # Number of nodes 
#SBATCH -o %N.%j.out        # Standard output will be written here
#SBATCH -e %N.%j.err        # Standard error will be written here
#SBATCH -p compute          # Slurm partition, where you want the job to be queued 
#SBATCH --exclusive            # run on one node without any other users
#SBATCH --mem=64G       # reserve 64Gbytes of RAM for my job (optional)
 
module purge
module add R/3.4.1
 
R CMD BATCH Random.R
[username@login01 ~]$ sbatch Rtest.job
Submitted batch job 289522


Further Information