git clone https://github.com/username/repo-name.git
# creates a new folder "repo-name/" in the working directory

cd repo-name  # move into the repo directory

git status  # check to see if anything has changed
git pull    # get the latest version of the code

# make changes!

git add file1.R file2.csv  # mark these files as changed
git add .                  # alternative: mark all changed files
git commit -m "A description of what I changed"

git push  # push your changes to github