GitHub + RStudio

Happy Git and GitHub for the useR is a great resource for connecting Git/GitHub and RStudio.

This Markdown Cheatsheet is a quick reference for basic Markdown commands.

Lab Specific Git + RStudio Communication

On the GitHub Website

Generate token

  • Log into https://github.com/
  • Go to https://github.com/settings/tokens
  • Press Generate new token
  • Select Generate New Token (Fine-grained, repo-scoped) from the dropdown menu
  • Create token name
  • No description
  • Select expiration
  • Keep public repositories
  • Don’t add any permissions
  • Click generate token

Copy token

Copy this token to your computer (notes, word, password organizer, etc…) temporarily until after this process is completed.

In RStudio

Enter GitHub Token into R

  • Check if the “gitcreds” package is installed
    • at the prompt in the Console type ‘gitcreds()’
      • if an Error is received, please install package
install.packages("gitcreds")
  • Add your token to R
    • in the console at the prompt > run the command below
gitcreds::gitcreds_set()

  • Paste token when prompted

  • To check if this worked run “gitcreds::gitcreds_get()”

Note

Ensure you have packages rmarkdown and knitr installed by searching in the Packages tab.

UPDATE BEGINNING HERE

Test if all is working

Ready to go to town

Create a New Project in RStudio from an existing project on GitHub

Clone existing repo on GitHub

  • Navigate to the GitHub project page
    • e.g. https://github.com/gilmore-lab/student-testbed
  • Press the button Code
  • Copy the HTTPS link of the project by clicking the little icon to the right of the URL. The link will be something like https://github.com/gilmore-lab/student-testbed.git Clone with HTTPS

Create New Existing Project in RStudio

How to work on your own branch

Continue to update these instructions

Create a branch in GitHub

For each GitHub repository you will be working on in the lab that is shared among others, you will need to create your own Branch.

Please create your own branch directly in the repository on the GitHub site

Make changes to branch on repository

  • Ensure the branch name is listed in the Git window in R

Git Window in R

Create Pull Request, for review, on GitHub

  • Always run ‘Git Pull’ before changes are made

  • Make Changes to File

  • Commit changes

  • Run ‘Git Push’ to Your Branch on Github

  • Go to github.com/gilmorelab/<repository name> and create a Pull request