HW01: Test software setup and practice editing files

Overview

Due: Wednesday, July 2nd by 11:59 PM (Chicago Time)

This first homework assignment has two main goals: to verify your computer setup and to practice basic R syntax, Markdown, and R Markdown.

Accessing and Cloning Your hw01 Repository

Important

This will work only if you have submitted your GitHub username (see Lecture 1) and accepted the email invitation to join our GitHub organization (check the email linked to your GitHub account). Make sure you’ve completed the setup under Software Setup and confirmed everything is working properly.

Accessing the repo:

  1. Go at this link to accept the invitation and create your private hw01 repository on GitHub. Your repository will be named hw01-<USERNAME> and will be ready within a few seconds. If this does not work, see the note in red above.

  2. Once the repository has been created, click the link provided to access it.

Cloning the repo into your Workbench:

  1. Log into Workbench and start a new project:
    File > New Project > Version Control > Git

  2. In the Repository URL field:

    • Paste the URL of your GitHub repository. To find the URL, go to your hw01 repo on GitHub, click the green Code button, and copy the SSH or HTTPS link (use the method you configured during setup: Workbench users must select SSH).
    • The project name should auto-fill. If not, type hw01-<USERNAME> manually.

  3. Choose where to save the project directory locally.
    Tip: Use a dedicated folder such as homeworks to keep things organized and avoid moving folders after cloning them

  4. Check the box “Open in new session” (optional but recommended for keeping projects separate and organized)

  5. Click Create Project. This will:

    • Create a new folder on your machine
    • Initialize a Git repository linked to GitHub
    • Open an RStudio Project in a new session

You’ll use this same process to access and set up each homework assignment throughout the course.

General Homework Workflow

Your workflow for all homework assignments will follow these steps:

  1. Accept the GitHub repo invitation and clone the repo (see above)
  2. Edit the files included in the repo
  3. Save your changes locally in RStudio Workbench
  4. Pull – Stage – Commit – Push:
    • Pull from GitHub: this should not change anything if you’re the only one working on the repo, but it’s a good habit to always pull first
    • Stage and commit your changes to your local Git repository
    • Push your committed changes to your GitHub repository online

For this course, I assume you’ll be using the Git interface built into RStudio. If you haven’t yet, complete the Using Git within RStudio tutorial to get comfortable with the process.

Tip
  • Commit and push your work often—multiple times per session if possible. Don’t wait until you’ve finished the entire assignment.
  • Never edit files directly on GitHub. Always work in your local Git repository (e.g., on Workbench) and then push changes to GitHub. Think of your GitHub repo as a live online backup of your local project.

File Types Used for Homework Assigments

All assignments in this course will be completed and submitted using Markdown and R Markdown files:

  • Markdown (.md) is a lightweight formatting language used to structure text.
    • GitHub README files are typically written in Markdown (.md) or plain text (.txt).
    • In this course, we use Markdown files only for writing README files because GitHub renders them directly in the browser.
    • You can reference R code in Markdown, but you cannot run and execute it.
  • R Markdown (.Rmd) is a format that allows you to combine R code, output, and text in one file.
    • It’s an extension of Markdown designed for dynamic analysis and reproducible reports specifically for R.
    • You’ll use R Markdown to complete most homework assignments.

In short, for this course:

  • Use Markdown (.md) only for writing a short summary in the README.md file
  • Use R Markdown (.Rmd) for completing the bulk of your assignment, e.g., analysis and code-based work

Assignment Description

For this first assignment, you’ll edit and push the following two files to your GitHub repo: README.md and code.rmd

Edit the README.md file

You will see a file named README.md in your repository.

A README is usually a plain text (.txt) or Markdown (.md) file that provides important information about a project—such as a summary, installation steps, or example output. In this course, you’ll use it to document your work and reflect on your process.

Your Task: edit the README.md file by replacing the placeholder text with a short biography of yourself. To achieve a “pass”, your biography must include the following elements:

  • At least one header
  • Some emphasis (italic or bold text)
  • At least one list
  • An image (e.g., a photo of yourself or something meaningful to you)
    • Upload the image into your repo by importing it in Workbench
    • Embed it in the Markdown file using the correct syntax
  • At least one link (e.g., to a website or profile)

At the end of your README, add a short reflection that includes:

  • A brief summary of your Git/GitHub workflow for this homework
    (Bullet points or a short narrative are both fine.)
  • Your evaluation of the homework experience
    (E.g., something new you learned, what went well, what confused you, etc.)
  • A list of resources you consulted
    (Include links, tools, and names of any collaborators. If you used AI tools, briefly describe how.)

Edit the code.rmd file

You will see a file named code.rmd in your repository.

Your task: edit the code.rmd file by making the following changes (all must be included for a “pass”):

  • Add at least two new YAML header options:
    • Do not delete or modify the existing ones
    • Example additions: author:, subtitle:, toc: true, etc
    • Feel free to experiment, see readings and slides from Lecture 1 for ideas
  • Add at least two R code chunks with a short explanation in plain text (not as code comment):
    • Your code can be simple (think at the examples from lecture 1), but it must run and produce the correct output
    • Your final knitted .html file should show both code and output
    • If your code generates plots (not required, but possible), make sure the output images are also pushed to GitHub

Submit the Assignment

To submit your assignment on Canvas, follow these steps:

  1. Before the deadline, push the final version of your work to your GitHub repository. Tip: don’t wait until the end to make your first commit—commit, stage, and push your work regularly as you go.

    Your GitHub repository should include:

    • The updated README.md
    • The edited code.rmd
    • A knitted output file generated from code.rmd (this must be a .md document, not anything else)

  2. When you’re ready to submit:

    • Copy the URL of your GitHub repository. It will look something like: https://github.com/csp-summer25/hw01-yourusername
    • Submit that URL on Canvas under HW01. Do not upload any files to Canvas. We only need the repository link.

Assessment

This assignment is evaluated on a Pass/Fail basis. To earn a Pass:

Your README.md should include a clear introduction that meets all specified requirements. It should demonstrate your ability to use Markdown syntax, such as headers, emphasis, lists, links, and images. You should also include a short description of how you edited and committed your changes, along with reflections on your experience using Git/GitHub, Markdown, and R Markdown.

Your code.rmd file must knit successfully. It should contain at least two new YAML header fields and two R code chunks, each introduced with a brief explanation written as plain text (not as code comments).

All required files must be pushed to your GitHub repository.

For more details, see the Assessment section of the Syllabus.