# R

## Description

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R is a free software environment for statistical computing and graphics.
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## Available versions

**Note: File a support ticket to request installation of additional libraries.**

- 2.14.1
- 2.14.1-mpi - R base package MPI-enabled via the Rmpi library.
- 2.14.2 (default)

## Running the application using modules

To use R with the environment modules system at HPC the following commands are available:

Get module information for r:

$module spider R

Load the default application module:

$module load R

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

- HPC_R_DIR - directory where R is located.
- HPC_R_BIN - executable directory
- HPC_R_LIB - library directory
- HPC_R_INCLUDE - includes directory

To use the version of R built for parallel execution with MPI via the Rmpi library load the following modules:

module load intel/11.1 openmpi/1.4.3 R

## Installed Packages

**Note: ** Many of the packages in the R library shown below are installed as a part of Bioconductor meta-library. The list is generated from the default R version.

affy Methods for Affymetrix Oligonucleotide Arrays affydata Affymetrix Data for Demonstration Purpose affyio Tools for parsing Affymetrix data files affyPLM Methods for fitting probe-level models affyQCReport QC Report Generation for affyBatch objects akima Interpolation of irregularly spaced data annaffy Annotation tools for Affymetrix biological metadata annotate Annotation for microarrays AnnotationDbi Annotation Database Interface ape Analyses of Phylogenetics and Evolution base The R Base Package baySeq Empirical Bayesian analysis of patterns of differential expression in count data Biobase Biobase: Base functions for Bioconductor BiocInstaller Install/Update Bioconductor and CRAN Packages Biostrings String objects representing biological sequences, and matching algorithms bitops Functions for Bitwise operations boot Bootstrap Functions (originally by Angelo Canty for S) caTools Tools: moving window statistics, GIF, Base64, ROC AUC, etc. class Functions for Classification cluster Cluster Analysis Extended Rousseeuw et al. CNVtools A package to test genetic association with CNV data codetools Code Analysis Tools for R colorspace Color Space Manipulation compiler The R Compiler Package datasets The R Datasets Package DBI R Database Interface DESeq Differential gene expression analysis based on the negative binomial distribution dichromat Color schemes for dichromats digest Create cryptographic hash digests of R objects DynDoc Dynamic document tools edgeR Empirical analysis of digital gene expression data in R foreign Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase, ... gcrma Background Adjustment Using Sequence Information gdata Various R programming tools for data manipulation gee Generalized Estimation Equation solver geiger Analysis of evolutionary diversification genefilter genefilter: methods for filtering genes from microarray experiments geneplotter Graphics related functions for Bioconductor GenomicRanges Representation and manipulation of genomic intervals ggplot2 An implementation of the Grammar of Graphics glmmADMB Generalized Linear Mixed Models Using AD Model Builder GO.db A set of annotation maps describing the entire Gene Ontology gplots Various R programming tools for plotting data graphics The R Graphics Package grDevices The R Graphics Devices and Support for Colours and Fonts grid The Grid Graphics Package gtools Various R programming tools hacks Convenient R Functions hgu95av2.db Affymetrix Human Genome U95 Set annotation data (chip hgu95av2) HilbertVis Hilbert curve visualization Hmisc Harrell Miscellaneous IRanges Infrastructure for manipulating intervals on sequences iterators Iterator construct for R itertools Iterator Tools KEGG.db A set of annotation maps for KEGG KernSmooth Functions for kernel smoothing for Wand & Jones (1995) lattice Lattice Graphics leaps regression subset selection limma Linear Models for Microarray Data locfit Local Regression, Likelihood and Density Estimation. maanova Tools for analyzing Micro Array experiments marray Exploratory analysis for two-color spotted microarray data MASS Support Functions and Datasets for Venables and Ripley's MASS Matrix Sparse and Dense Matrix Classes and Methods memoise Memoise functions methods Formal Methods and Classes mgcv GAMs with GCV/AIC/REML smoothness estimation and GAMMs by PQL msm Multi-state Markov and hidden Markov models in continuous time multicore Parallel processing of R code on machines with multiple cores or CPUs multtest Resampling-based multiple hypothesis testing munsell Munsell colour system mvtnorm Multivariate Normal and t Distributions nlme Linear and Nonlinear Mixed Effects Models nnet Feed-forward Neural Networks and Multinomial Log-Linear Models org.Hs.eg.db Genome wide annotation for Human ouch Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses parallel Support for Parallel computation in R pheatmap Pretty Heatmaps plyr Tools for splitting, applying and combining data preprocessCore A collection of pre-processing functions proto Prototype object-based programming R2admb ADMB to R interface functions RColorBrewer ColorBrewer palettes reshape2 Flexibly reshape data: a reboot of the reshape package. rpart Recursive Partitioning RSQLite SQLite interface for R Rwave Time-Frequency analysis of 1-D signals scales Scale functions for graphics. simpleaffy Very simple high level analysis of Affymetrix data spatial Functions for Kriging and Point Pattern Analysis splines Regression Spline Functions and Classes statmod Statistical Modeling stats The R Stats Package stats4 Statistical Functions using S4 Classes stringr Make it easier to work with strings. subplex Subplex optimization algorithm survival Survival analysis, including penalised likelihood. tcltk Tcl/Tk Interface tools Tools for Package Development utils The R Utils Package vsn Variance stabilization and calibration for microarray data waveslim Basic wavelet routines for one-, two- and three-dimensional signal processing wavethresh Wavelets statistics and transforms. XML Tools for parsing and generating XML within R and S-Plus. xtable Export tables to LaTeX or HTML zlibbioc An R packaged zlib-1.2.5

Example of using the parallel module to run MPI jobs under R 2.14.1+

{{#fileAnchor: rmpi_test.R}} Download raw source of the [{{#fileLink: rmpi_test.R}} rmpi_test.R] file.

```
# Load the R MPI package if it is not already loaded.
if (!is.loaded("mpi_initialize")) {
library("Rmpi")
}
# Spawn as many slaves as possible
mpi.spawn.Rslaves()
# In case R exits unexpectedly, have it automatically clean up
# resources taken up by Rmpi (slaves, memory, etc...)
.Last <- function(){
if (is.loaded("mpi_initialize")){
if (mpi.comm.size(1) > 0){
print("Please use mpi.close.Rslaves() to close slaves.")
mpi.close.Rslaves()
}
print("Please use mpi.quit() to quit R")
.Call("mpi_finalize")
}
}
# Tell all slaves to return a message identifying themselves
mpi.remote.exec(paste("I am",mpi.comm.rank(),"of",mpi.comm.size()))
# Tell all slaves to close down, and exit the program
mpi.close.Rslaves()
mpi.quit()
```