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Installing R Packages

Jeffrey Leek
Johns Hopkins Bloomberg School of Public Health

R Packages

  • When you download R from the Comprehensive R Archive Network (CRAN), you get that ``base" R system

  • The base R system comes with basic functionality; implements the R language

  • One reason R is so useful is the large collection of packages that extend the basic functionality of R

  • R packages are developed and published by the larger R community

Obtaining R Packages

  • The primary location for obtaining R packages is CRAN

  • For biological applications, many packages are available from the Bioconductor Project

  • You can obtain information about the available packages on CRAN with the available.packages() function

              a <- available.packages() head(rownames(a), 3)  ## Show the names of the first few packages                          
              ## [1] "A3"       "abc"      "abcdeFBA"

  • There are approximately 5200 packages on CRAN covering a wide range of topics

  • A list of some topics is available through the Task Views link, which groups together many R packages related to a given topic

Installing an R Package

  • Packages can be installed with the install.packages() function in R

  • To install a single package, pass the name of the lecture to the install.packages() function as the first argument

  • The following the code installs the slidify package from CRAN

              install.packages("slidify")

  • This command downloads the slidify package from CRAN and installs it on your computer

  • Any packages on which this package depends will also be downloaded and installed

Installing an R Package

  • You can install multiple R packages at once with a single call to install.packages()

  • Place the names of the R packages in a character vector

              install.packages(c("slidify", "ggplot2", "devtools"))

Installing an R Package in RStudio

Installing an R Package in RStudio

Installing an R Package from Bioconductor

  • To get the basic installer and basic set of R packages (warning, will install multiple packages)
              source("http://bioconductor.org/biocLite.R") biocLite()
  • Place the names of the R packages in a character vector
              biocLite(c("GenomicFeatures", "AnnotationDbi"))

http://www.bioconductor.org/install/

Loading R Packages

  • Installing a package does not make it immediately available to you in R; you must load the package

  • The library() function is used to load packages into R

  • The following code is used to load the ggplot2 package into R

              library(ggplot2)

  • Any packages that need to be loaded as dependencies will be loaded first, before the named package is loaded

  • NOTE: Do not put the package name in quotes!

  • Some packages produce messages when they are loaded (but some don't)

Loading R Packages

After loading a package, the functions exported by that package will be attached to the top of the search() list (after the workspace)

              library(ggplot2) search()                          
              ##  [1] ".GlobalEnv"         "package:kernlab"    "package:caret"      ##  [4] "package:lattice"    "package:ggplot2"    "package:makeslides" ##  [7] "package:knitr"      "package:slidify"    "tools:rstudio"      ## [10] "package:stats"      "package:graphics"   "package:grDevices"  ## [13] "package:utils"      "package:datasets"   "package:methods"    ## [16] "Autoloads"          "package:base"

Summary

  • R packages provide a powerful mechanism for extending the functionality of R

  • R packages can be obtained from CRAN or other repositories

  • The install.packages() can be used to install packages at the R console

  • The library() function loads packages that have been installed so that you may access the functionality in the package

Posted by: tagselement.blogspot.com

Source: https://jtleek.com/modules/01_DataScientistToolbox/02_09_installingRPackages/