Exercise 02

Practice Reproducible Research Workflows

Learning Objectives

  • Integrating an RStudio project, a local git repository, and a GitHub remote repository

Challenge 1

Begin with a remote repo…

Follow the instructions outlined as Method 1 in Module 6 to do the following:

Step 1

  • Set up a new GitHub repo in your GitHub workspace named “exercise-02a” (be sure to use this name and capitalization EXACTLY).

Step 2

  • Add me as a collaborator on the repo by going to “Settings”, choosing “Collaborators”, then “Add People”, and searching for my GitHub username (“difiore”).

Step 3

  • Clone your repo to your local computer.

Step 4

  • Create a new Quarto or RMarkdown document locally with notes you take in class this week – call it “notes.qmd” or “notes.Rmd” – including at least some expository text written in Markdown and at least one R code block. If you make a “.qmd” document, I recommend unchecking “Use visual markdown editor”, though that is your choice.

… OR …

Step 5

  • Use Render (for “.qmd”) or Knit (for “.Rmd”) to publish your document as HTML.

… OR …

Step 6

  • Stage (or “add”) and “commit” the changes to your repo locally and then “push” those up to GitHub.

Step 7

  • Visit your repo on GitHub to confirm that you have done the above steps successfully.

Step 8

  • Submit the URL for your repo in Canvas

Challenge 2

Begin with a local repo…

This is an alternative workflow to that described above, which also works well. It is outlined in more detail in Module 6 as “Option 3” under Connecting a Local Repo to GitHub.

Step 1

  • From within RStudio, create a new project called “exercise-2b” in a brand new directory also called “exercise-2b” (be sure to use this name and capitalization EXACTLY).

NOTE: Be sure to check the box marked “Create a git repository” before pressing the “Create Project” button.

After making the repository, you will need to make a first commit to get git to begin tracking changes.

Step 2

  • Configure a GitHub Personal Access Token (PAT) as described in Module 5 and Module 6, making sure that R and RStudio can access your cached credentials.

Step 3

  • As outlined in Module 6 Connecting a Local Repo to GitHub Option 1, open your project locally and run usethis::use_github(protocol="https") from the R console within your project’s working directory.

Step 4

  • Answer the question about whether the suggested name for the remote repository is adequate and hit . [This question may not always appear.]

This will create a new remote repository on GitHub, add it as a remote origin/main, and open the GitHub page for the repository in your browser. Switch back to RStudio and continue with Steps 4 to 8 from above.