1  Installation and Setup

1.1 Installation

• Install R and Rstudio (available from ECCC Software Centre)

  • Software Centre can be very slow to install, you can install R and RStudio without administrator permissions from the internet as well https://posit.co/download/rstudio-desktop/

• Install Git https://gitforwindows.org/ (does not require admin permissions)

  • NOTE: When asked about “Adjusting your PATH environment”, make sure to select “Git from the command line and also from 3rd-party software”. Otherwise, accept the defaults.

• Create a GitHub account https://github.com/

• Install R packages: Open RStudio and run in the console:

  • install.packages("usethis")
  • install.packages("gitcreds")

1.2 Set username and email for git

• usethis::use_git_config(user.name = "Jane Doe", user.email = "jane@example.org")
  • user.name is the name associated with your git commits so just make it informative for your collaborators (ie: actual name, github username)
  • user.email must match your GitHub account email

1.3 Let git talk to GitHub

• usethis::create_github_token()
  • Opens GitHub webpage: select “repo” (always selected so it is greyed out), “user”, and “workflow” scopes.
  • Copy the token
• gitcreds::gitcreds_set()
  • Should prompt you to paste your token and it will store it in the git credential manager.

1.4 Start a new project with GitHub

Step 1: Make a new repo on GitHub

• Go to https://github.com and make sure you are logged in.

• Near “Repositories”, click the big green “New” button.

  • How to fill this in:
    • Repository template: No template.
    • Repository name: myrepo . Like a variable name, in code: descriptive but brief, no whitespace. Letters, digits, - , . , or _ are allowed.
    • Description: any short description of the project
    • Public.
    • Initialize this repository with: Add a README file.
    • Click the big green button that says “Create repository”.

Step 2: Copy repo URL

• Now click the big green button that says “<> Code”.

• Copy a clone URL to your clipboard. Use the HTTPS URL.

Step 3: Clone into a new project in RStudio

• File > New Project > Version Control > Git. In the “repository URL” paste the URL of your new GitHub repository.
  • Be intentional about where you create this Project. Don’t put it inside another git repository.
  • I suggest you “Open in new session”.
• Click “Create Project” to create a new directory,
• This should download the README.md file that we created on GitHub in the previous step. Look in RStudio’s file browser pane for the README.md file.
• Behind the scenes, RStudio has done this for you: git clone https://github.com/see24/myrepo.git

1.5 Work on a project

• Edit the README.md file, e.g., by adding the line “This is a line from RStudio”.
• Save the file locally
• On the Git pane click commit

• In the pop-up review the changes at the bottom
• Check the “Staged” box and type a commit message and click “Commit”

1.5.1 Sync changes to GitHub: Push

• Click “Push” in the Rstudio Git pane
• Look at the repo on GitHub so see the new line is there

1.5.2 Sync local copy from GitHub: Pull

• In the GitHub repo main page
  
• In the upper right corner of the Readme, click on the pencil
• Add a line eg : “Line added from GitHub.”
• Click “Commit changes.”
• In RStudio click Pull on the Git pane
• You should see the new line in the Readme

1.6 Add an existing project to GitHub

1.6.1 Simplest way

• Create a new repo and Rstudio project in the same way as above
• Simply copy all files into the newly created folder on your local computer
• Stage and commit all files that you want to store on GitHub
  • Nothing sensitive ie passwords, keys etc (you can have a private repo if you are not ready to share code with the world)
  • Probably not large datasets
  • Use . gitignore to avoid git tracking things (more on this later)

1.6.2 Using usethis

This requires that your PAT is properly set up.

• If the project is not already an Rstudio project, call usethis::create_project("path/to/your/project")
• If the project is not already using Git call usethis::use_git()
• Stage and commit files (see above for caveats)
• Call usethis::use_github() which will create a new repo in your GitHub account with the folder name as the repo name.

These are the simplest way to do it but there are more advanced, more traditional git ways to do it: https://happygitwithr.com/existing-github-last.html

1.7 Issues with installation

If RStudio is not finding a git installation:

• Restart RStudio and try again
• If still not working, run this in the windows command line: git --exec-path
• Copy the path, then in RStudio click Tools > Global Options > Git/SVN and set the Git executable by clicking browse, pasting the path in the address bar and selecting the git.exe file.
• Restart RStudio again

See https://happygitwithr.com/rstudio-see-git.html for more instructions on troubleshooting

1.8 Git terminology summary 1

• Repository (repo): Folder that contains a hidden .git file that tracks changes made to files in that folder. The folder can “live” on your local computer or a server like GitHub’s. On GitHub the repository is also the web page where all the files are stored among other things
• Push: Copy changes from your local version of the repo to the GitHub version
• Pull: Copy changes from the GitHub version of the repo to your local version
• Clone: make a copy of a git repository. By default in R studio this is connected to the GitHub version (called the remote or origin)
• Commit: A marker that is kept in the git history and helps to incrementally track changes. Made useful by descriptive commit messages