Introduction

In this module, we will learn about R packages. There are ~12000 packages available on CRAN or the Comprehensive R Archive Network. Packages are available for different topics and you should always look for a package before writing code from scratch. In case you have written your own codes for a new analysis or topic, do share it with the R community by converting the R scripts into a package. You can learn more about building R packages from R Packages, a book written by Hadley Wickham.

Agenda

In this post, we will learn to:

• install R packages from
  • CRAN
  • GitHub
  • BitBucket
  • Bioconductor
  • rForge
• install different versions of a package
• load, update & remove installed packages
• access package documentation

CRAN

Packages from CRAN can be installed using install.packages(). The name of the package must be enclosed in single or double quotes.

install.packages('ggplot2')

GitHub

Some R packages are made available on GitHub before releasing them on CRAN. Such packages can be installed using install_github() from devtools or remotes package. You need to specify the name of the repository and the package. For example, to download ggplot2 or dplyr, below is the code:

devtools::install_github("tidyverse/ggplot2")
remotes::install_github("tidyverse/dplyr")

BitBucket

Bitbucket is similar to GitHub. You can install packages from Bitbucket using install_bitbucket() from devtools or remotes pacakge.

devtools::install_bitbucket("dannavarro/lsr-package")
remotes::install_bitbucket("dannavarro/lsr-package")

Bioconductor

Bioconductor provides tools for analysis and comprehension of high throughput genomic data. Packages hosted on Bioconductor can be installed in multiple ways:

devtools

Use install_bioc() from devtools.

install_bioc("SummarizedExperiment")

biocLite

Use biocLite() function.

source('http://bioconductor.org/biocLite.R')
biocLite('GenomicFeatures')

rForge

Many R packages are hosted at R-Forge, a platform for development of R packages.

install.packages('quantstrat', repos = 'https://r-forge.r-project.org/')

Install Different Versions

Now that we have learnt how to install packages, let us look at installing different versions of the same package.

remotes::install_version('dplyr', version = 0.5.0)

If you want to install the latest release from GitHub, append @*release to the repository name. For example, to install the latest release of dplyr:

remotes::install_github('tidyverse/dplyr@*release')

Installed Packages

Library Paths

Library is a directory that contains all installed packages. Usually there will be more than one R library in your systme. You can find the location of the libraries using .libPaths().

.libPaths()

## [1] "C:/Users/HP/Documents/R/win-library"
## [2] "C:/Program Files/R/R-3.5.0/library"

You can use lib.loc when you want to install, load, update and remove packages from a particular library.

Load

To use the functionalities offered by a package, we must load it into the current R session. Use library() to load a R package and specify the location of the package using the lib.loc argument.

library(lubridate, lib.loc = "C:/Program Files/R/R-3.4.1/library")