1. Make sure git is installed on your computer. If not, you can download and install git HERE for free.

2. Ensure Global Options in RStudio are configured.

   • Select Tools at the top of RStudio
   • Select Global Options (a pop up will open)
   • Select Git/SVN from the left side panel
   • Under “Git Executable:” select Browse and navigate to your git executable file. When you are done the path will probably look something like this “C:/Program Files/Git/bin/git.exe”
   • Select Terminal from the left side panel.
   • Use the drop down menu so that “New terminals open with:” Git Bash
   • Select Apply followed by Ok at the bottom of the global options page.
   • Select the Terminal (next to the console). You should see a blinking cursor next to a $. If not, select Terminal 1 (below the terminal tab) and select New Terminal.

In the console run the following code:

• library(usethis)
• use_git_config(user.name = "Jane Doe", user.email = "jane@example.org")
  • Replace “Jane Doe” with your GitHub id and “jane@example.org” with the email tied to your GitHub account.

1. Go to the repo you created on the GitHub website.
2. Select the copy button to the right of the URL in the blue “Quick Setup” box.
3. In RStudio select Project (None) in the very top right corner.
4. Select New Project
5. In the pop-up window select Version Control.
6. Select Git
7. Paste the URL you copied from your GitHub repo into the top box under “Repository URL:”
8. Select Browse to navigate to the folder you would like this project to be in.
   
9. Select Create Project.

Yaml

• Metadata for your document
• allows for setting the output and other key document setting
• Begins and ends with a line of three dashes (---)

White space

• Plain text field
• Allows for your analysis to be presented with the code and output

Code Chuncks

• Grey sections that begin and end with three ```
• Can support R, Python, Bash, D3, Rcpp, SQL, Stan, …

Headers can help keep your document organized and create and easy way to jump between sections of your document.

• Each header is denoted with a using pound signs with # being the largest header and ###### being the smallest.
• You can also add a horizontal line in your document to separate sections by adding 3 asterisks (***)

• “|” is used to separate columns, i.e “|column 1|Column 2|”.
• A set of dashes are used to separate the header from the body of the table i.e. “|- - -|- - -|”
• “:” is used to justify the column: left justified = “|:- - -|”, right justified = “|- - -:|”, centered = “|:- - -:|”

Code:

Output:

If you are more comfortable using Microsoft Word than R the visual editor in R Studio can be a great resource. The visual editor provides a word-like interface to edit your markdown document and will add the markdown or html code to your source document.

To access the visual editor select the compass button in the top right corner of the source panel shown below.

This will render your document and provide a word-like toolbar below the standard R Studio toolbar.

After you are finished in the visual editor, selecting the compass button again will bring you back to your code and any changes you made in the visual editor will be coded for you.

• All code needs to be in a code chunk to be evaluated.
• Each chunk starts and ends with three (```) (the accent mark by your esc key)
• The beginning will also have {r} to indicate that it is an r code chunk
• Additional options can be added inside the curly braces to change how the chunk is evaluated or how output is displayed. A full list of options can be found HERE
• Comments can be added to your code chunk with the # just like in an R script.
• It is good practice to name your code chunks. Two philosophies on this are to name each chunk based on what that chunk is doing or what the main output of the chunk is.

Updating lines 5-7 of the YAML header as shown below allows for your code to be folded into your document. This will hide your code initially and add a show code button at the location of each code chunk.

A code button will also be added at the top right of the knitted document that will that allow you to show or hide all code chunks in the document.

The klippy package adds a button to each of your code chunks in the knitted document that allows for easy copying of the code. Klippy can be installed by running:

install.packages("remotes")
remotes::install_github(("rlesur/klippy"))

Next, just add the following code chunk anywhere in your document.

You will then see a blue clipboard button in the top left of each code chunk in your knitted document. (Note: klippy only works with Html output)

The next few slides will walk you though how to push your files to your github repo.

Since we created this project as a for version control with GitHub you will notice that you now have a Git Tab in the same panel as your environment. In this tab you will see all the files that have changed since your last commit.

Before we can push our files to GitHub we need to commit. Committing creates a permanent snapshot of your changes with an informative description of what you changed that you can then push to GitHub.

• To commit we will first select check box of the file we want to commit.

• Next select Commit below the history tab. This will open a new pop-up window.

Next you will add an informative message into the commit message box outlining what you changed in the file. (Similar to commenting your code, future you and your collaborators will thank you for this.)

After adding your commit message select the commit button.

Pulling files is a much simpler process than pushing. Pulling updates your local copy of the repo with the remote copy located on GitHub. This will download any new files or changes to old files that you do not have on your machine.

You can pull by selecting the blue down arrow under the connections tab.