Reproducibility repository

This is a sample repository used for courses on reproducibility detailing how how to use RStudio with GitHub for version control and reproducibility.

Setup GitHub/RStudio

1. RStudio

• "Global Options" > Git/SVN
  • Check "Enable version control interfrace for RStudio projects"
  • specify "Git executable" path
  • Generate SSH RSA key ("Create RSA key") and copy public SSH RSA key ("View public key")

2. GitHub

• sign in and go to "Settings" > "SSH and GPG keys"

• Add a "New SSH key" (Title should refer to your RStudio, paste key from RStudio)

• also see this link for a tutorial for version control with Git in RStudio

Setup Project

• Create new repository on GitHub
• Copy repository URL
• In Rstudio, "File" > "New Project" > "Version Control" > "Git"
• Paste repository URL and set path (potentially also fill in "Project directory name" although this should be filled in from the repository)
• Click "Create Project"
• In RStudio, "File" > "New File" > "R Script", work on your code and save as desired (e.g. as "Reproducibility.R"); you can also add subfolders and (data) files to the directory.
• In RStudio, you should see a tab "Git" in one of the panes; click "Commit" (i.e. save the changes)
• In the window "RSStudio: Review Changes", select all files and paths you wish to commit, include a commit message and click "Commit" (and close the windows afterwards), and "Push" (i.e. synchronize the GitHub repository with the local versions)
• If you change your repository
  • on GitHub, you can "Pull" the changes to your local project
  • on RStudio, you can "Push" the changes to GitHub (best "Pull" first to avoid error messages)
    both from within RStudio's "Git* pane