Installing and Using R Packages
- What is R packages?
- Installing R packages
- Load and use an R package
- View loaded R packages
- Remove installed packages
- Update installed packages
- Related articles
In our previous articles, we published i) guides for installing and launching R/RStudio, ii) the basics of R programming, and ii) guides for finding help in R.
Here, we’ll describe:
- what is an R package
- and how to install and use R packages
What is R packages?
An R package is an extension of R containing data sets and specific functions to solve specific questions.
R comes with standard (or base) packages, which contain the basic functions and data sets as well as standard statistical and graphical functions that allow R to work.
There are also thousands other R packages available for download and installation from CRAN, Bioconductor and GitHub repositories.
After installation, you must first load the package for using the functions in the package.
Installing R packages
Packages can be installed either from CRAN (for general packages), from Bioconductor (for biology-related packages) or from Github (developing versions of packages).
Install a package from CRAN
The function install.packages() is used to install a package from CRAN. The syntax is as follow:
For example, to install the package named readr, type this:
Note that, every time you install an R package, R may ask you to specify a CRAN mirror (or server). Choose one that’s close to your location, and R will connect to that server to download and install the package files.
It’s also possible to install multiple packages at the same time, as follow:
Install a package from Bioconductor
Bioconductor contains packages for analyzing biological related data. In the following R code, we want to install the R/Bioconductor package limma, which is dedicated to analyse genomic data.
To install a package from Bioconductor, use this:
Install a package from Github
GitHub is a repository useful for all software development and data analysis, including R packages. It makes sharing your package easy. You can read more about GitHub here: Git and GitHub, by Hadley Wickham.
To install a package from GitHub, the R package devtools (by Hadley Wickham) can be used. You should first install devtools if you don’t have it installed on your computer.
For example, the following R code installs the latest version of survminer R package developed by A. Kassambara (https://github.com/kassambara/survminer).
View the list of installed packages
To view the list of the already installed packages on your computer, type :
Note that, in RStudio, the list of installed packages are available in the lower right window under Packages tab (see the image below).
Folder containing installed packages
R packages are installed in a directory called library. The R function .libPaths() can be used to get the path to the library.
Load and use an R package
To use a specific function available in an R package, you have to load the R package using the function library().
In the following R code, we want to import a file (“http://www.sthda.com/upload/decathlon.txt”) into R using the R package readr, which has been installed in the previous section.
The function read_tsv() [in readr] can be used to import a tab separated .txt file:
# Import my data library("readr") my_data <- read_tsv("http://www.sthda.com/upload/decathlon.txt") # View the first 6 rows and tge first 6 columns # syntax: my_data[row, column] my_data[1:6, 1:6]
name 100m Long.jump Shot.put High.jump 400m 1 SEBRLE 11.04 7.58 14.83 2.07 49.81 2 CLAY 10.76 7.40 14.26 1.86 49.37 3 KARPOV 11.02 7.30 14.77 2.04 48.37 4 BERNARD 11.02 7.23 14.25 1.92 48.93 5 YURKOV 11.34 7.09 15.19 2.10 50.42 6 WARNERS 11.11 7.60 14.31 1.98 48.68
View loaded R packages
To view the list of loaded (or attached) packages during an R session, use the function search():
 ".GlobalEnv" "package:readr" "package:stats" "package:graphics"  "package:grDevices" "package:utils" "package:datasets" "package:methods"  "Autoloads" "package:base"
If you’re done with the package readr and you want to unload it, use the function detach():
detach("readr", unload = TRUE)
Remove installed packages
To remove an installed R package, use the function remove.packages() as follow:
Update installed packages
If you want to update all installed R packages, type this:
To update specific installed packages, say readr and ggplot2, use this:
update.packages(oldPkgs = c("readr", "ggplot2"))
install.packages(“package_name”): Install a package
library(“package_name”): Load and use a package
detach(“package_name”, unload = TRUE): Unload a package
remove.packages(“package_name”): Remove an installed package from your computer
- update.packages(oldPkgs = “package_name”): Update a package
This analysis has been performed using R software (ver. 3.2.3).
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