A.10: R packages
- Page ID
- 45304
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)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)
cuts down on the amount of screen output during installation.
If you receive the following warning message,
Warning: package 'package.name' is not available (for R version 4.3.2)
it may be possible that the package has not yet become available, but 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, the answer is no. 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.
To check installed packages, just view the object installedpkgs created earlier.
R packages used in Mike’s Biostatistics Book
list updated 12 August 2024