Pre-workshop instructions

Published

February 3, 2026

Software

R (Version 4.5 or Later):

  • Windows: Download the R installer from the CRAN website. Follow the installation instructions.

  • Mac: Download the R installer from the CRAN website. Follow the installation procedure.

  • Linux: R is typically available through the package manager of your Linux distribution. On Ubuntu you can use the following command in your terminal:

     sudo apt-get install r-base r-base-dev

  • For help during the installation, refer to the R Installation and Administration documentation.

RStudio (Version 2023.03 or Later): - Windows, Mac, Linux:

Download the RStudio installer from the RStudio Download page. Choose the appropriate version for your operating system and follow the installation instructions provided.

For alternative IDEs like Visual Studio Code, download and install according to your preferences.

Git and Gitnuro (Version >= 2.40.0):

Git

  • Windows: Download the Git installer from the Git Downloads website. Follow the installation instructions provided. Ensure that the Git GUI component is selected during installation.

  • Mac: Download the installer from the Git Downloads page and follow the installation instructions.

  • Linux: Install Git using your package manager. On Ubuntu, use the following command:

    sudo apt-get install git git-gui

For detailed installation instructions, refer to the Git Installation documentation.

Graphic User Interface (GUI)

Git can be used directly as a command line program directly from a terminal. This is useful to automate stuff but not that user friendly. Therefore many software provide a nice graphic interface to manage and visualize your git repository.

For this workshop, we will use Gitnuro, a free and open-source GUI which is available on any OS. Go to this page https://gitnuro.com/, download and install it.

Tip

Note: Make sure that at least one GUI software is installed and working before the workshop.

R packages

  • Windows, Mac, Linux: All the packages can be installed with R package manager. Open RStudio and run the following command in the console:

    install.packages("quarto", "tidyverse", "styler", "gt", "here")

  • For Linux, some packages might required additional compilation steps, please refer to your distribution documentation.

Tip

Note: Ensure that all software versions meet or exceed the specified requirements for better experience during the workshop.

Data

Data used in the workshop is a sample of the NHANES study in particular 2007 and 2009 waves, including demographic, medical and various exposure variables. Two datasets need to be downloaded:

If you wish to recreate the data by yourself, please have a look at the script in data-raw/nhanes.R in the GitHub repository.

Scripts

Please download the initial script of the workshop: starting_script.R

Set up the project

Go through the first section of the hand-on exercise 1 where you can setup the course folder and populate it with a RStudio project and a git repository.

Hands-On Activity 1 - Set up you project