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Authoring scientific publications with R Markdown: Setup

Setup instructions

R and RStudio are separate downloads and installations. R is the underlying statistical computing environment, but using R alone is no fun. RStudio is a graphical integrated development environment (IDE) that makes using R much easier and more interactive. You need to install R before you install RStudio. Once installed, because RStudio is an IDE, RStudio will run R in the background. You do not need to run it separately.

Windows

If you already have R and RStudio installed

  • Open RStudio, and click on “Help” > “Check for updates”. If a new version is available, quit RStudio, and download the latest version for RStudio.
  • To check which version of R you are using, start RStudio and the first thing that appears in the console indicates the version of R you are running. Alternatively, you can type sessionInfo(), which will also display which version of R you are running. Go on the CRAN website, and check whether a more recent version is available. If so, please download and install it. You can check here for more information on how to remove old versions from your system if you wish to do so.

    • If you don’t have R and RStudio installed

  • Download R from the CRAN website.
  • Run the .exe file that was just downloaded.
  • Go to the RStudio download page.
  • Under Installers select RStudio x.yy.zzz - Windows. Vista/7/8/10 (where x, y, and z represent version numbers).
  • Double click the file to install it.
  • Once it’s installed, open RStudio to make sure it works and you don't get any error messages.

    • macOS

    If you already have R and RStudio installed

    Open RStudio, and click on “Help” > “Check for updates”. If a new version is available, quit RStudio, and download the latest version for RStudio. To check the version of R you are using, start RStudio and the first thing that appears on the terminal indicates the version of R you are running. Alternatively, you can type sessionInfo(), which will also display which version of R you are running. Go on the CRAN website and check whether a more recent version is available. If so, please download and install it. In any case, make sure you have at least R 3.6.

    If you don’t have R and RStudio installed

  • Download R from the CRAN website.
  • Select the .pkg file for the latest R version. Double click on the downloaded file to install R.
  • Go to the Rstudio download page
  • Under Installers select RStudio x.yy.zzz - Mac OS X 10.6+ (64-bit) (where x, y, and z represent version numbers).
  • Double click the file to install RStudio.
  • Once it’s installed, open RStudio to make sure it works and you don’t get any error messages.

    • Linux

  • Follow the instructions for your distribution from CRAN, they provide information to get the most recent version of R for common distributions. For most distributions, you could use your package manager (e.g., for Debian/Ubuntu run sudo apt-get install r-base, and for Fedora sudo yum install R), but we don’t recommend this approach as the versions provided by this approach are usually out of date. In any case, make sure you have at least R 3.6.
  • Go to the RStudio download page.
  • Under *Installers* select the version that matches your distribution, and install it with your preferred method (e.g., with Debian/Ubuntu sudo dpkg -i rstudio-x.yy.zzz-amd64.deb at the terminal).
  • Once it’s installed, open RStudio to make sure it works and you don’t get any error messages.