ItsOyondi/activity01-course-tools

Activity 01 - Course Tools

This activity is intended to be completed in over three class sessions, including outside of class preparation work and three class meetings.

In this repository/directory, you should see six items:

• README-img - a folder containing images that I am embedding within this README.md file. You do not need to do anything with this.
• .gitignore - a file that is used to specify what Git can ignore when pushing to GitHub. You do not need to do anything with this.
• README.md - the document you are currently reading.
• day01-github-markdown - a folder that contains items for you to complete during the first class meeting.
• day02-rstudio-rmarkdown - a folder that contains items for you to complete during the second class meeting.
• day03-rstudio-r - a folder that contains items for you to complete during the third class meeting.

We will explore most of these items over these next class sessions. Before doing that, you will first make your own copy of this repository. Note that I will refer to “repositories” as “repos” (or a single “repository” as a “repo”) for the rest of the semester.

Day 1

Do not proceed in this document until you have minimally:

1. Completed this short (5-10 minutes) interactive Markdown tutorial.
2. Created a free GitHub account if you do not already have one.

Task 1: Forking the Repository

Read these directions first, then work through them. In this GitHub repo (i.e., my repo):

1. Click on the Fork icon near the upper-right-hand corner. You will be taken to a Create a new fork screen.
2. Verify that your GitHub username is selected under Owner and that the Repository name is activity01-course-tools with a green check mark (this verifies that you do not already have a GitHub repository with this name).
3. You may provide a Description if you would like. This is a way to provide some additional, more descriptive, meta information related to the things you did. I like to provide a brief description of what happened.
4. Verify that Copy the main branch only is selected.
5. Click on the green Create fork button at the bottom of this page.

You should be taken a copy of this repo that is in your GitHub account. That is, your page title should be username/activity01-course-tools, where username is replaced with your GitHub username. Directly below this, you will see the following message:

forked from gvsu-sta631/activity01-course-tools

You will complete the rest of this activity in your forked copy of the activity01-course-tools repo.

Check in

Take a moment to reflect on what this process is like compared to other methods you have used for sharing documents with others. Talk through these with your group members.

• Can you sketch out a diagram that relates that previous method/process to this GitHub method?
• What was easier about this GitHub method?
• What was more difficult about this GitHub method?

Task 2: Exploring a GitHub Repository

The last time that I taught STA 518 I had students complete this Preparation that includes videos that provide more details on what Git and GitHub are. You may find this preparation helpful to complete outside of class. Note that these videos are somewhat old and things in current GitHub are different. For our work this semester, we will not worry about Branches or Issues.

When you view repos on github.com, most will have a similar set up. There are a lot of icons, text, regions, etc. in every repo and it can be confusing what exactly you need to do. Whenever we will use a new feature on GitHub, I will provide you with details of what to do and what is happening. For the time being, you can focus on two regions of your new repo.

First, if you are currently reading this text that means that you are viewing the README.md file. Folks use this file for various reasons, but I will use it to describe what is in the repo and provide getting started directions for how you should interact with it. Here is an example of information the Posit (formerly RStudio) team provides in their README files: {ggplot2} repo README files take information written in Markdown (.md files) and formats it to look nice on a webpage.

Second, directly above the displayed README.md document is an area that looks similar to a folder/directory that you would interact with on your computer. In fact, once we start to work between RStudio and GitHub, your directory will be identical to your repo! I like to think of a GitHub repo as a folder system that others can view/copy/edit (with permission) rather than needing to zip up a folder on my computer and then email it to another person to work with. Repos can contain multiple types of files that use various syntax/text and also include subfolders, sub-subfolders, etc. Read these directions first, then work through them.

1. In your activity01-course-tools repo folder/directory, locate and click into the day01-github-markdown subfolder.
2. In the day01-github-markdown subfolder, you will be greeted by a new README.md file. Do your best to complete the tasks/directions provide in this subfolder by 11:59 pm (EST) on Tue, Jan 17.
3. In our Teams workspace (linked on Blackboard), find the General channel and post what was muddiest from these tasks. If someone else already posted what you though was muddy, add any clarification to their post and give them a “+ 1” 👍. Remember that this space is for conversations as well as posting questions. Read through your peers’ muddy posts and do your best to provide help.

The rest of this README document will contain tasks/directions for the next class meetings.

Day 2

Do not proceed in this document until you have minimally:

1. Verified that you can login to GVSU’s RStudio Workbench. Or (more advanced and I note that I may not be able to assist you with problem solving on your machine), you have installed R, RStudio, and Git on your computer and enabled RStudio and GitHub to communicate. If you choose have R, RStudio, and GitHub setup on your personal computer, I recommend following the directions from Dr. Jenny Bryan et al.
2. Completed this preparation to connect your RStudio Workbench instance and GitHub so they communicate with one another. Note that this is a preparation that I created for STA 418/518 and am reusing here - the process is the same so why create multiple copies of the same document.

Task 1: Updating your forked GitHub repo

You will need to start reading these directions back at my gvsu-sta631/activity01-course-tools GitHub repo and have your forked username/activity01-course-tools GitHub repo handy. I recommend that you have my repo opened on one half of your screen and your repo opened on the other half. Read these directions first, then work through them.

1. At the top of your username/activity01-course-tools repo (above the repo contents section), verify that you see a message that looks something like:

This branch is X commits behind gvsu-sta631:main.

2. Click on the hyperlinked “X commits behind” portion of that message to be taken to a Comparing changes page.
3. Verify that your drop-down menu options specify:
   • base repository: username/activity01-course-tools
   • base: main
   • head repository: gvsu-sta631/activity01-course-tools
   • compare: main
4. Also verify that you have a message directly below this that says:

✓ Able to merge. These branches can be automatically merged.

Flag me if you see something different.

5. Click on the green Create pull request button under this previous message. Note you can look at the changes that I made, if you so desire, by scrolling down. However, this is not necessary.
6. On the next page, provide a short descriptive message in the “Title” box (e.g., “Adding Day 2 materials”). You can also provide a more detailed message in the “Leave a comment” box if you choose.
7. Click on the green Create pull request button.
8. On the next screen which is titled the same thing as what you provided in the “Title” box on the previous screen, you will be presented with a bunch of information. If you scroll down a little, you should see a green check mark with a message that specifies:

This branch has no conflicts with the base branch

And you can click on the green Merge pull request.

9. You will be provided with with an opportunity to provide another meaningful message (or accept the default message). Finally, click on the green Confirm merge button. You can now work directly from your username/activity01-course-tools repo.

In summary, what you just did is pulled my changes into your repository. Git and GitHub refer to this as a “pull request” because you are asking to pull items into your repo.

Task 2: Authoring in RStudio

In your username/activity01-course-tools repo, go into the day02-rstudio-rmarkdown subfolder and follow the tasks listed in the README. You will follow these directions for today’s activity of building your own Distill website!

Day 3

Do not proceed in this document until you have affirmed these items:

• What the main uses for each region/pane in RStudio: https://r4ds.had.co.nz/introduction.html#rstudio.
• What an Rmarkdown file is, how to run code in an Rmarkdown file or Console, and how RStudio helps notify you of potential problems in your code: https://r4ds.had.co.nz/workflow-scripts.html and https://r4ds.had.co.nz/r-markdown.html.
• What RStudio Projects are, determining where things “live” in RStudio, and the benefits of beginning each R session from a “vanilla” (sessions that do not retain information from previous sessions): https://r4ds.had.co.nz/workflow-projects.html.

I think it incredibly important that you force RStudio to start from a clean session everytime that you start it up, that I kindly ask that you follow the recommendations in Section 8.1 of R for Data Science by updating your Global Options.

Check in

Verify that you can access GVSU’s RStudio Workbench. Then, see if you can affirm each of these questions:

• I can create an RMarkdown document.
• I can run a simple calculation (e.g., 2 + 2) in an R Script, an RMarkdown document, and the R Console.
• I can load an R package in an R Script, an RMarkdown document, and the R Console (e.g., like {ggplot2})
• I can create a simple data visualization using {ggplot2} in an R Script, an RMarkdown document, and the R Console (e.g., like a scatterplot using the msleep dataset).

Updating your forked GitHub repo again

These are the same directions that you used to update your forked GitHub for Day 2 - practice, practice, practice.

You will need to start reading these directions back at my gvsu-sta631/activity01-course-tools GitHub repo and have your forked username/activity01-course-tools GitHub repo handy. I recommend that you have my repo opened on one half of your screen and your repo opened on the other half. Read these directions first, then work through them.

1. At the top of your username/activity01-course-tools repo (above the repo contents section), verify that you see a message that looks something like:

This branch is X commits behind gvsu-sta631:main.

2. Click on the hyperlinked “X commits behind” portion of that message to be taken to a Comparing changes page.
3. Verify that your drop-down menu options specify:
   • base repository: username/activity01-course-tools
   • base: main
   • head repository: gvsu-sta631/activity01-course-tools
   • compare: main
4. Also verify that you have a message directly below this that says:

✓ Able to merge. These branches can be automatically merged.

Flag me if you see something different.

5. Click on the green Create pull request button under this previous message. Note you can look at the changes that I made, if you so desire, by scrolling down. However, this is not necessary.
6. On the next page, provide a short descriptive message in the “Title” box (e.g., “Adding Day 2 materials”). You can also provide a more detailed message in the “Leave a comment” box if you choose.
7. Click on the green Create pull request button.
8. On the next screen which is titled the same thing as what you provided in the “Title” box on the previous screen, you will be presented with a bunch of information. If you scroll down a little, you should see a green check mark with a message that specifies:

This branch has no conflicts with the base branch

And you can click on the green Merge pull request.

9. You will be provided with with an opportunity to provide another meaningful message (or accept the default message). Finally, click on the green Confirm merge button. You can now work directly from your username/activity01-course-tools repo.

In summary, what you just did is pulled my changes into your repository. Git and GitHub refer to this as a “pull request” because you are asking to pull items into your repo.

Task 2: Authoring in RStudio

In your username/activity01-course-tools repo, go into the day03-rstudio-r subfolder and follow the tasks listed in the README. You will follow these directions for today’s activity of working through a simple linear regression analysis.

Attribution

This document is based on David Keyes’ tutorial at R for the Rest of Us and Happy Git with R by Jenny Bryan et al.