Pre-workshop instructions

Published

June 5, 2024

Software

R (Version 4.3.0 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 # Optional but recommended

  • 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 Git GUI (Version >= 2.40.0):

  • 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. As detailed on this page you will need to install git-gui using homebrew:

    /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
brew install git-gui

  • 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.

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 dataset need to be donwloaded:

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.

Getting scripts

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