R packages

This page describes basic steps for package installation from a CRAN mirror site and how to update installed packages following installation of a new version of R. See at the end of this page for a list of packages described in Mike’s Biostatistics Book.

Adding packages to base R installation

Installing R packages is straightforward, assuming the package is part of CRAN. Select a CRAN mirror site, e.g., 0-Cloud, RStudio’s mirror site.

chooseCRANmirror()

To find out what CRAN mirror was set for the current session use

findCRANmirror()

A list of mirror sites is stored on your computer once R is installed, see CRAN_mirrors.csv in the doc folder, e.g., ~/R-4.3.1/doc.

Once the CRAN mirror is selected, and assuming you have the name of the package, e.g., package.name, then

install.packages("package.name")

will work.

Useful additional command options include

install.packages("package.name", dependencies=TRUE)

which will also download and install any additional packages required. And

install.packages("package.name", quiet=TRUE)

which cuts down on the amount of screen output during installation.

If you receive the warning message

Warning: package 'package.name' is not available (for R version 4.3.2)

While it is possible the package has not yet become available, first double-check for typos.

Another warning message may be that a binary version is available, but a more recent source version is available, prompted by the question, Do you want to install from sources the package which needs compilation? In most cases, no is the answer. R will install a previous binary version. In order to install from source, RTools must be installed.

Update R packages after installing new R version

After updating to new version of R you’ll need to download and update the user installed packages again. If you are running RStudio, see instructions here. For Win11 users you can download and run a package called installr, for macOS users download and install updateR, which will assist you to update R packages.

I prefer to run a script, modified from R-Bloggers.com. This script works on any operating system, but updates only CRAN packages (e.g., not github or Bioconductor).

Before installing the new version of base R, start up your current R installation and set your working directory, setwd(). Enter the following script to gather and save all installed R packages. Select CRAN mirror when prompted.

tmp <- installed.packages()
installedpkgs <- as.vector(tmp[is.na(tmp[,"Priority"]), 1])
save(installedpkgs, file="installed_old.rda")

Shutdown R, then install and start the new version of R (see Install R for help).

In the new version of R, set your working directory as above. Enter the following script

load(file="installed_old.rda")
tmp <- installed.packages()
installedpkgs.new <- as.vector(tmp[is.na(tmp[,"Priority"]), 1])
missing <- setdiff(installedpkgs, installedpkgs.new)
install.packages(missing)
update.packages(ask=FALSE)

Should be good to go. You can remove old R version installation.

R packages used in Mike’s Biostatistics Book