Mathematical Models of Infectious Diseases

This repository contains the educational materials for the 2025 Summer Institute in Statistics and Modeling in Infectious Diseases (SISMID) Module 1: Mathematical Models of Infectious Diseases. The materials are presented as an interactive Quarto book website with lecture notes, hands-on R exercises, and comprehensive tutorials for epidemiological modeling.

This educational resource provides a comprehensive introduction to mathematical modeling of infectious diseases, covering fundamental concepts from basic SIR dynamics to advanced topics like stochastic models and parameter estimation. The materials are designed for a 3-day intensive workshop format but can also be used for self-paced learning.

The materials are organized into three main sections:

Pre-Requisites: Setup guides and foundational knowledge

• R and RStudio installation
• Essential R programming concepts
• Project organization best practices

Day 1: Introduction and Basic Models

• Introduction to modeling concepts
• Basic SIR dynamics
• Herd immunity and vaccination strategies

Day 2: Advanced Modeling Concepts

• Heterogeneity in models
• Age-structured models
• Parameter estimation techniques

Day 3: Stochastic Models and Applications

• Stochastic modeling approaches
• Advanced R exercises and applications

This material is designed for:

• Graduate students and researchers in epidemiology, public health, or related fields
• Practitioners working in infectious disease modeling
• Anyone interested in learning mathematical approaches to understanding disease transmission

Prerequisites:

• Basic understanding of calculus and differential equations
• Familiarity with R programming (see the "Just Enough R" section if you're new to R)
• Working installation of R and RStudio
• Approximately 30-60 minutes for setup and prerequisite review

1. Clone the repository:

   git clone https://github.com/arnold-c/SISMID-Module-02_2025.git
   cd SISMID-Module-01_2025

2. Install R dependencies: This project uses renv for reproducible package management. In R:

   # Install renv if you don't have it
   install.packages("renv")
   
   # Restore the project library
   renv::restore()

3. Install Quarto: Download and install Quarto from https://quarto.org/docs/get-started/

4. Build the website:

   # Render the entire book
   quarto render
   
   # Or preview with live reload during development
   quarto preview

5. View the website: Open _book/index.html in your browser, or use the local server from quarto preview

• Live preview: quarto preview - starts a local server with automatic reload
• Render single file: quarto render filename.qmd
• Check project: quarto check
• Update R packages: renv::snapshot() after adding new packages

• Quarto - Scientific and technical publishing system
• R - Statistical computing and graphics
• renv - Reproducible R package management
• Key R packages: {tidyverse}, {deSolve}, {ggplot2}, {gt}, and more (see renv.lock)

You can contact me via my email: "contact at callumarnold dot com".

We welcome contributions to improve these educational materials! Here are several ways you can help:

• Found a bug or error? Open an Issue describing the problem
• Have a suggestion? Start a Discussion to share your ideas
• Unclear instructions? Let us know what could be explained better (open a Discussion)

1. Fork the repository and create a feature branch
2. Make your changes following the existing style and structure
   • The R code uses the Air formatter for the R code chunks. Please follow the instructions on their website for the best way to employ the formatter in your development environment.
3. Test your changes by rendering the affected pages with quarto render
4. Submit a Pull Request with a clear description of your changes

• Follow the existing Quarto markdown format and callout patterns
• Test all R code chunks to ensure they execute correctly
• Maintain consistency with the educational tone and level
• Include appropriate citations for new references

• Ensure you can successfully run quarto preview and renv::restore()
• Check that your changes don't break existing functionality
• Follow the project's code style and organization patterns

Interested in contributing substantial content? Please reach out to me first by opening a discussion on this GitHub page (and @ me) so we can coordinate efforts and ensure your contributions align with the overall educational goals.

This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.