Quick set up of GitHub in R

After many emails sharing my tutorial to set up GitHub on Windows 11 for RStudio, I’m publishing it online. There are other ways to do this, but this has always worked for me (and I still need it every time I try to set it up again).

Note: This is based on the Happy Git and GitHub for the useR guide, but includes only the steps I follow.

Create a GitHub Account

If you don’t have one yet, create a free account at github.com. Choose a professional, timeless name, it is hard to change it later.

Update R and RStudio

Check your current R version in the R console:

R.version.string

If you’re using a version older than R 4.0.0 (April 2020), you must update. Anyways, I would recomend updating R to the newest version from time to time (una vez al año no hace daño).

Download latest R and Rstudio versions: Posit RStudio Desktop Download

Install Git

Download Git for Windows from git-scm.com/download/win

Accept all default options during installation. You likely won’t ever need to open Git directly, RStudio will interface with it.

Configure Git with Your GitHub Account

Open a Terminal in RStudio (not the Console):

Go to Tools > Global Options > Terminal
Set “New terminals open with” to Git Bash
Open a new terminal in Tools > Terminal > New Terminal

Run these commands in the terminal (replace with your information):

git config --global user.name ‘yourname’
git config --global user.email ‘yourmail@example.com’
git config --global --list

⚠️ Note: In Git Bash, you cannot use Ctrl+C/Ctrl+V. Instead, right-click to copy and paste.

Create a GitHub Repository

Log into GitHub
Click New repository
Configure:
- Name: Choose a descriptive name
- Visibility: Private (recommended for work projects, you can make it public later!)
- Initialize with: Check “Add a README file”
- .gitignore template: None (for now)
View your new repository

Decide how are you going to access Github

For security, I use my GitHub account on my personal desktop and a 30-day Personal Access Token (PAT) on shared computers or laptops I carry around. If you’re using your GitHub login, you can skip to the next step.

To generate a token:

Go to github.com/settings/tokens
Click Generate new token (classic)
Give it a descriptive name
Set expiration (30 days, 60 days, or custom)
Select scopes: repo, user, gist, workflow
Click Generate token
Copy the token immediately—you won’t see it again

Create an R Project with Version Control

In RStudio:

File > New Project > Version Control > Git
In your GitHub repository (browser), click Code > Local > HTTPS and copy the URL
Paste into Repository URL
Choose a local directory for your project

⚠️ Important: Do NOT create your project in OneDrive, Google Drive, or other cloud sync folders. This can cause conflicts with Git. Create a dedicated local folder for Git repositories.

Choose whether to use GitHub login credentials or a PAT token (see previous section).

The Git Workflow (Commit, Push, Pull)

Once your project is set up, you’ll see a Git pane in RStudio.

Make this workflow part of your routine each time you work with RStudio, especially if you work from different computers:

1. Pull (download changes from GitHub):

Click the blue Pull arrow before starting work
Ensures you have the latest version

2. Work on your scripts and files as usual

3. Pull again (always pull before committing or pushing)

4. Commit (save changes locally):

Click Commit in the Git pane
Check files you want to include
Write a commit message: Be descriptive (“Add data cleaning script” not “update”). Future you will thank current you.
Click Commit

5. Push (upload changes to GitHub):

Click the green Push arrow
Your changes are now on GitHub

We did it!

And we’re done! Now you just need to keep pulling, committing, and pushing every day. Maybe one day I’ll write another blog post about more advanced Git features, like branching and merging (which might be obvious for software developers, but wasn’t for a veterinarian). I hope you found this useful. Here are some other helpful resources:

Learning Git and GitHub:

RStudio and Git:

Push the button and let me know before I
Get the wrong idea and go, you’re gonna
Miss the freak that I control

Sugababes, “Push The Button” (2005)

Last updated: November 2025