Setting Up and Customizing R
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For the longest time I resisted customizing R for my particular environment. My philosophy has been that each R script for each separate analysis I do should be self contained such that I can rerun the script from top to bottom on any machine and get the same results. This being said, I have now encountered a situation where there are multiple researchers using multiple R instances on multiple platforms. Briefly, our setup involves a shared network drive that is accessed using Rstudio on Windows as well as Rstudio Server running on Linux. I have created a setup R script file that sets the library location to the shared drive (using the oDrive variable also set globally), install the collection of R packages we regularly use, or update them, and setup the .Rprofile script appropriately for the platform the script is running on. I have also included the Rprofile script we are using.
Please provide comments about how you customize R for your needs.
My setup R script.
#List of most used R packages that we wish to install.libraries = c('cacheSweave', 'Deducer', 'devtools', 'doBy', 'foreign', 'gdata', 'ggplot2', 'Hmisc', 'JGR', 'maps', 'mapdata', 'mapproj', 'maptools', 'proto', 'psych', 'R2wd', 'RCurl', 'reshape', 'RODBC', 'roxygen2', 'seqinr', 'sm', 'sp', 'sqldf', 'survey', 'WriteXLS', 'XML', 'xtable')
#We will install packages from the main CRAN siterepos = 'http://cran.r-project.org'#Site provides some prebuilt binaries for Windowsrepos.win = 'http://www.stats.ox.ac.uk/pub/RWin'#URL for the R-Forge repository. repos.rforge = 'http://r-forge.r-project.org'
#Type of download for install.packages. Default to source.type = 'source'
if(Sys.info()['sysname'] == 'Windows') { oDrive = 'o:/' memory.limit(size=4095) #Set to 4GB (for 64-bit Windows, this can be much larger) #Set the R_LIBS environment varaible. This assumes the Setx program is installed #(this is included with the Service Pack 2 Support Tools) system(paste('Setx R_LIBS ', oDrive, 'R/library/Windows', sep='')) #We will manually add to libPaths since the system variable will not take #effect until R is restarted. .libPaths(paste(oDrive, 'R/library/Windows', sep='')) repos = c(repos, repos.win) #Add the Windows repos for use below # Set system environment varaible R_PROFILE system(paste('Setx R_PROFILE ', oDrive, 'R/Rprofile', sep='')) .type = 'win.binary'} else if(Sys.info()['sysname'] == 'Linux') { oDrive = '/n01/OutcomesAssessment/' file.copy(paste(oDrive, 'R/Rprofile', sep=''), '~/.Rprofile', overwrite=TRUE) .libPaths(paste(oDrive, 'R/library/Linux', sep=''))} else { stop('Unsupported operating system!')}
#Only load packages that are not already installed.for(l in libraries) { i = require(l, character.only=TRUE, lib.loc=.libPaths()[1], quietly=TRUE) if(!i) { install.packages(l, repos=repos, dep=TRUE, lib=.libPaths()[1], type=.type, destdir=paste(oDrive, 'R/library/download', sep='')) } else { detach(paste('package:', l, sep=''), character.only=TRUE) }}
#Make sure we have the latest versions of the packagesupdate.packages(repos=repos, ask=FALSE, lib.loc=.libPaths()[1], destdir=paste(oDrive, 'R/library/download', sep=''))
#Load some packages from Github. We won't bother checking if they are already#installed since these tend to change more often.library(devtools)install_github('irutils', 'jbryer', lib.loc=.libPaths()[1])install_github('ruca', 'jbryer', lib.loc=.libPaths()[1])install_github('ipeds', 'jbryer', lib.loc=.libPaths()[1])install_github('makeR', 'jbryer', lib.loc=.libPaths()[1])install_github('qualtrics', 'jbryer', lib.loc=.libPaths()[1])
#Install ecir packageinstall(paste(oDrive, 'R/ecir', sep=''), lib.loc=.libPaths()[1])
message("Installation of R packages complete. Please restart R now...")
My custom .Rprofile file.
# .Rprofile -- commands in this file will be executed at the beginning of# each R session. On Windows, the R_PROFILE environment variable must have value# with the full path to this file. On Linux (or other Unix like systems) this file# must be in the user's home directory.
# Set the default repository to the main CRAN siteoptions(repos=c(CRAN='http://cran.r-project.org'))
# Set the oDrive varaible and library pathif(Sys.info()['sysname'] == 'Windows') { oDrive = 'o:/' .libPaths(paste(oDrive, 'R/library/Windows', sep='')) require(utils, quietly=TRUE) print("Setting memory limit for R to 4GB...") memory.limit(size=4095) #Set to 4GB (for 64-bit Windows, this can be much larger) message(paste('R_LIBS: ', Sys.getenv('R_LIBS'), sep='')) message(paste('R_PROFILE: ', Sys.getenv('R_PROFILE'), sep=''))} else if(Sys.info()['sysname'] == 'Linux') { oDrive = '/n01/OutcomesAssessment/' .libPaths(paste(oDrive, 'R/library/Linux', sep=''))} else if(Sys.info()['sysname'] == 'Darwin') { oDrive = NULL}
# Customize the default look and feel of ggplot2if(require(ggplot2, quietly=TRUE)) { theme_update(panel.background=theme_blank(), panel.grid.major=theme_blank(), panel.border=theme_blank())}
# On Linux we will alter the default behavior of the makeR package.if(Sys.info()['sysname'] == 'Linux') { if(require(makeR, quietly=TRUE)) { setAutoOpen(FALSE) setDefaultBuilder(builder.rnw.native) }}
# Change the location of the SQL repositoryif(require(irutils, quietly=TRUE)) { setSQLRepos(paste(oDrive, 'R/ecir/data', sep=''))}
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