1. Getting Started

Getting Started

To use the FoodNet enhanced model pipeline, you will need:

• R (version 4.3.2) with the brms and tidybayes packages.
• Nextflow (version 24.04.2) for running the pipeline.
• Access to the FoodNet surveillance dataset.
• Singularity or Docker for containerization (Singularity is used in the examples).

For a detailed list of software and dependencies, please refer to the GitHub repository.

We highly recommend using Docker or Singularity containers for full pipeline reproducibility. If these are not possible, Conda is also supported. See the -profile section for more information.