Getting started

What is NFIDD?

NFIDD (Nowcasting and Forecasting Infectious Disease Dynamics) is an MIT-licensed library of sessions for learning about nowcasting and forecasting of infectious disease surveillance data. This course is a living resource designed to help epidemiologists, public health professionals, and researchers understand and apply real-time analysis methods to infectious disease surveillance data.

Set up

Each session in this course uses R code for demonstration. All the content is self-contained within a software package designed for the course.

You have three options for using this course:

  1. Web-only: View sessions on the website
  2. Local setup: Install R, packages, and download course materials for the full interactive experience
  3. Hybrid: Install just the packages but use the website for viewing content
Important

Installation Issues? If you’re having trouble with any installation steps, ask for help early! Don’t skip ahead - each step builds on the previous ones. On the day of the course, we have a small number of web clients available as backup if installation issues persist.

Summary of Installation Steps

If you choose the local setup option, here’s what you’ll need to do:

  1. Install R and RStudio (use the Visual Editor for best notebook experience)
  2. Install the nfidd R package
  3. Install cmdstan
  4. Download course materials (if using the hybrid approach you may not need to do this)

Don’t skip any steps - they all work together to provide the full course experience.

Installing R

  • R is used as the main programming language. You can check which version you have by typing R.version in your R session. We recommend installing the latest R version 4.5.1 (2025-06-13).
  • RStudio is a popular graphic user interface (GUI). Its Visual Editor provides the best experience of going through this course. Please make sure you update RStudio to the latest version.

Installing additional requirements

Before you get started with the course, you will first need to install the following software.

Installation of the nfidd package

To install the packages needed in the course, including the nfidd package that contains data files and helper functions used throughout:

options(repos = c(
  "CRAN" = "https://cloud.r-project.org",
  "stan-dev" = "https://stan-dev.r-universe.dev",
  "epiforecasts" = "https://epiforecasts.r-universe.dev"
))
install.packages("nfidd", dependencies = TRUE)

Then you can check that the installation completed successfully by loading the package into your R session:

library("nfidd")

Installing cmdstan

The course relies on running stan through the cmdstanr R package, which itself uses the cmdstan software. This requires a separate installation step:

cmdstanr::install_cmdstan()
Note

This may take a few minutes. Also you’re likely to see lots of warnings and other messages printed to your screen - don’t worry, this is normal and doesn’t mean there is a problem.

If there are any problems with this, you can try (on Windows) to fix them using

cmdstanr::check_cmdstan_toolchain(fix = TRUE)

You can test that you have a working cmdstanr setup using

cmdstanr::cmdstan_version()
[1] "2.36.0"

For more details, and for links to resources in case something goes wrong, see the Getting Started with CmdStanr vignette of the package.

Accessing the course

If you want to use the local workflow, you will need a local copy of the course material.

  • Directly download the course material:

    Tip

    Download

  • Alternatively, if you are familiar with git you can clone the repo.

  • If you prefer to use the hybrid workflow, you can view each session on the website, and copy-paste the code into your own R script. In that case you don’t need to download the material.

    • Tip: if you hover over each code chunk on the website you can use a “Copy” button at the top right corner.

Interacting with a local copy of the course material

A benefit of downloading or cloning all the material is that you can interact with the session files directly.

In this course, all content is written using Quarto notebooks (.qmd files). This means that we can combine text with code and see the output directly. The notebooks are then directly reproduced on the course website (for example, this page).

Recommended approach: Work with the notebooks using RStudio’s visual editor mode. See guidance on this below.

Using RStudio’s Visual Editor (Recommended for Notebooks)
  1. Open a session notebook: Each session is saved as a .qmd file in nfidd/sessions/
  2. Switch to Visual mode: Look for the “Visual” button in the top-left of the editor pane (next to “Source”)
  3. Execute code: Use the green “play” button at the top-right corner of each code chunk, or Ctrl/Cmd + Enter for line-by-line execution
  4. Visual mode benefits: Easier to read formatted text and equations, better experience with code chunks and outputs

Alternative approaches that also work:

Other editors: Use VS Code or other editors that support Quarto notebooks. The .qmd files will work in any Quarto-compatible environment.

Tip

The Quarto extension for VS Code also supports a visual editor mode. You can find it in the command palette.

Day-of-Course Updates

If you’re returning to the course after some time or joining a live session, you may want to update your setup to ensure you have the latest content and package versions.