Setup Instructions - Mac

If you want to edit this website locally on your Mac, here are the setup instructions:

  1. Create a free GitHub if you don’t have one already. Enabling 2fa is recommended (and may be required by your organization.)
  2. Follow the Quarto “Get Started” instructions to install Quarto on your system.
  3. Install R
  4. Install gfortran
  5. Install RStudio
  6. Install git
    • Verify install worked with git --version in your Terminal, which should produce a version number
  7. Install Python 3
    • Verify install worked with python --version in your Terminal, which should produce a version number
  8. Clone the relevant GitHub repository to your local computer
  9. Create a Python virtualenv:
    1. In your Terminal, run python3 -m venv python_env
    2. Then run source python_env/bin/activate to activate the virtualenv
    3. Run pip install -r requirements.txt to install dependencies
  10. Open RStudio, go to “File > Open Project…”, and navigate to the folder of your cloned repo. You should see a fhir-for-research.Rproj file in this folder – if you do, that’s the right folder.
  11. Run renv::restore() in the R Console to load all the R dependencies

Note: Running quarto check in your Terminal will return what components of Quarto have been installed properly and where there might be issues.