18.2 Create / clone a Github repository

RStudio provides the possibility to work with version-control projects that enable multiple users (e.g., collaborators or supervisor-student) to access and contribute to a project. In order to do so, one needs to first create a code repository in Github, or access an already existing repository, and create a version-control project in RStudio.

Install git in you local computer

The connection between RStudio and Github is done through the version control system Git. Instructions to download and install the software are available here: https://git-scm.com/downloads.

Create a Github repository

If you want to work on a new project, create a new repository in your Github dashboard of repositories or in any of the organisational accounts you belong to. When creating the repository, accept the option for generating a README.md document to serve as index.

Create a version-control project

Once your repository is created, you need to create a version-control R project linked to that repository in your local computer. Follow the following instructions to do so:

  1. Open RStudio.
  2. Click New Project
  3. Select the Version Control option in the first pop-up window, and the option Git in the second page.
  4. Go to your repository page at Github and copy the git url after clicking the < > Code green button. The link should look something like this: https://github.com/holo-omics/example.git
  5. Paste the repository URL you just copied in the Repository URL field. Leave the Project directory name empty, and select the local directory (folder) where you want to create a local copy of the Github repository.
  6. Click Create Project.

This procedure will generate an R project in the a folder with the name of the Github repository within the desired directory. The main difference of such a version-control project and a regular R project is the connection with Github through Git. If you open the project in RStudio, you will find a new tab called Git, which you can use to communicate with Github.

Set-up RStudio-Github connection

In order to be able to commit and push changes to Github, you need to configure git and RStudio.

Set-up git config

First, set-up git config using the following commands. Make sure you modify ‘Your Name’ and ‘’ before running the scripts below in your terminal.

git config --global user.name 'Your Name'
git config --global user.email 'your@email.com'

Generate a Github access token

Second, you need to generate a personal access token you will need to use when first pushing changes to Github. To generate the token, access your personal Github account and navigate through Settings (you will find it by clicking your avatar) > Developer settings (you will find it at the very bottom of the left menu) > Personal access tokens > Generate new token.

Connect RStudio to Github

Finally, you will need to modify something in your project to push the first change to Github and configure the connection between RStudio and Github.

  1. In RStudio open the README.md file, make any change you wish and save it.
  2. Any file within the project that has been edited will appear in the Git tab with a M - Modified status.
  3. Click the checkboxes of the files you want to commit (in this case the README.md file) to stage the file and click Commit.
  4. In the pop-up window, add a descriptive short message to the commit, and click Commit.
  5. Click Push to upload the changes to Github. The first time you push, RStudio will request your Github username and password. Note that instead of your Github access password, you need to use the access token instead.

These actions should enable you to connect RStudio to Github and to push changes from your local version of the repository to Github.

Work with version control

Once the initial commit is pushed, then you are ready to work with your version-control R project. Keep in mind that in a version-control project, the same project might contain multiple versions, including the one in Github and the ones in the local computers of the collaborators.

  • To access the latest version available in Github use the Pull button.
  • To update the Github version, use Commit followed by Push.

To learn more about Git and version control, check the many great tutorials available on the internet, for example: - https://ourcodingclub.github.io/tutorials/git/ - https://www.freecodecamp.org/news/git-and-github-the-basics/