2 Software Setup

2.1 Setting up R and RStudio

R and RStudio are separate downloads and installations. R is the underlying statistical computing environment. 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.

2.1.1 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 XP/Vista/7/8 (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.

2.1.2 macOS / Mac OS X

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.

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
• It is also a good idea to install XQuartz (needed by some packages)
• 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.

2.1.3 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 are usually out of date. In any case, make sure you have the most recent version of R.
• 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.

These setup instructions are adapted from those written for Data Carpentry: R for Data Analysis and Visualization of Ecological Data.

2.2 Install tlverse

The tlverse ecosystem of packages are currently hosted at https://github.com/tlverse, not yet on CRAN. You can use the usethis package to install them:

install.packages("devtools")
devtools::install_github("tlverse/tlverse")

The tlverse depends on a large number of other packages that are also hosted on GitHub. Because of this, you may see the following error:

Error: HTTP error 403.
  API rate limit exceeded for 71.204.135.82. (But here's the good news:
  Authenticated requests get a higher rate limit. Check out the documentation
  for more details.)

  Rate limit remaining: 0/60
  Rate limit reset at: 2019-03-04 19:39:05 UTC

  To increase your GitHub API rate limit
  - Use `usethis::browse_github_pat()` to create a Personal Access Token.
  - Use `usethis::edit_r_environ()` and add the token as `GITHUB_PAT`.

This just means that R tried to install too many packages from GitHub in too short of a window. To fix this, you need to tell R how to use GitHub as your user (you’ll need a GitHub user account). Follow these two steps:

1. Type usethis::browse_github_pat() in your R console, which will direct you to GitHub’s page to create a New Personal Access Token (PAT).

2. Create a PAT simply by clicking “Generate token” at the bottom of the page.

3. Copy your PAT, a long string of lowercase letters and numbers.

4. Type usethis::edit_r_environ() in your R console, which will open your .Renviron file in the source window of RStudio.

   1. If your .Renviron file does not pop-up after calling usethis::edit_r_environ(); then try inputting Sys.setenv(GITHUB_PAT = "yourPAT"), replacing your PAT with inside the quotes. If this does not error, then skip to step 8.

5. In your .Renviron file, type GITHUB_PAT= and then paste your PAT after the equals symbol with no space.

6. In your .Renviron file, press the enter key to ensure that your .Renviron ends with a new line.

7. Save your .Renviron file. The example below shows how this syntax should look.

GITHUB_PAT=yourPAT

8. Restart R. You can restart R via the drop-down menu on RStudio’s “Session” tab, which is located at the top of the RStudio interface. You have to restart R for the changes to take effect!

After following these steps, you should be able to successfully install the package which threw the error above.