Lab 04: Scaffolding reproducible research

Preparation

• Read/ annotate: Recipe #4. You can refer back to this document to help you at any point during this lab activity.

Objectives

• Review using Git and Github to clone a repository
• Apply new Git and Github skills to fork, clone, commit, and push changes to a repository
• Establish a workflow for reproducible research using Quarto and Git

Instructions

Getting started

In this, and subsequent labs, you will be using Git and Github to fork, clone, commit, and push changes to lab repositories. The steps necessary include the following:

1. Fork the repository to your own Github account

2. Clone the repository to your local machine

3. Open the README file and complete the lab activity

4. Commit and push your changes to your forked repository

The submission process is also distinct. Instead of submitting a PDF or Word document, you will submit a link to your updated GitHub repository. Feedback will be provided through the repository through commenting features and pull requests.

Furthermore, if you have questions about the lab, or you have technical issues, you can post your question or link to the GitHub repository in the Discussions section of the lin-380-s24 organization on GitHub.

Scaffolding your research

1. For this lab, you will create a new Quarto document in the repository named lab-04.qmd. Title this document "Lab 04: Scaffolding reproducible research".

2. Create the following sections in your .qmd document:

• Reproducible research
• Project management

3. In the section "Repoducible research", describe what reproducible research is and why it is an important component of modern science. Include the following information:

   • When we say "reproducible research", what do we mean?
   • What is the difference between the 'computing environment' and the 'project structure'?
   • How does Git and GitHub support reproducible research practices?

4. In the section "Project management", describe the process of forking, cloning, editing, committing, and pushing changes to a repository (Scenario A). Create a step-by-step guide that you can use to refer back to in the future. Include bullet points, useful links, screenshots, and/ or code snippets to help illustrate your process.

Assessing your progress

1. Add a section which describes your learning in this lab.

Some questions to consider:

• What did you learn?
• What did you find most/ least challenging?
• What resources did you consult?
  • Instructor? R or Quarto documentation, Websites (provide links)?
• What more would you like to know about reproducible research and/ or Git and GitHub?
  • Find potential resources you might consult to continue your learning. Provide links and a brief description of the resource.

Submission for feedback

• Commit and push your changes to your forked repository
• Provide a link to your GitHub repository through Canvas

License

This work is licensed under a Creative Commons Attribution 4.0 International License.