Update README with description of the project

README.md

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 # SISMID Module 2 Materials (2025)
+
+**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 2: Mathematical Models of Infectious Diseases](https://sph.emory.edu/SISMID/modules/math-models/index.html). The materials are presented as an interactive Quarto book website with lecture notes, hands-on R exercises, and comprehensive tutorials for epidemiological modeling.
+
 ## About This Project
 
+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.
+
+### Content Overview
+
+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
+
 ### Who Is This For & Pre-Requisite Knowledge?
 
+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](https://sismid2025.callumarnold.com/just-enough-r) if you're new to R)
+- Working installation of R and RStudio
+- Approximately 30-60 minutes for setup and prerequisite review
+
+## Getting Started
+
+### Download and Build the Website
+
+1. **Clone the repository:**
+   ```bash
+   git clone https://github.com/arnold-c/SISMID-Module-02_2025.git
+   cd SISMID-Module-02_2025
+   ```
+
+2. **Install R dependencies:**
+   This project uses `renv` for reproducible package management. In R:
+   ```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/](https://quarto.org/docs/get-started/)
+
+4. **Build the website:**
+   ```bash
+   # 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`
+
+### Development Workflow
+
+- **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
 
 ## Built With
 
-- [Quarto](https://quarto.org)
+- [Quarto](https://quarto.org) - Scientific and technical publishing system
+- [R](https://www.r-project.org/) - Statistical computing and graphics
+- [renv](https://rstudio.github.io/renv/) - Reproducible R package management
+- Key R packages: `{tidyverse}`, `{deSolve`}, `{ggplot2`}, `{gt`}, and more (see `renv.lock`)
 
 ## Contact
 
-You can contact me via my email: "callum *at* callumarnold *dot* com".
+You can contact me via my email: "contact *at* callumarnold *dot* com".
 
 ## Contributing
 
-If you see any issues, please open an Issue or Discussion on the book's GitHub page.
-Or, if you know Git, you can open a Pull Request to fix the issue directly, which is even better!
+We welcome contributions to improve these educational materials! Here are several ways you can help:
+
+### Reporting Issues
+- **Found a bug or error?** Open an [Issue](https://github.com/arnold-c/SISMID-Module-02_2025/issues) describing the problem
+- **Have a suggestion?** Start a [Discussion](https://github.com/arnold-c/SISMID-Module-02_2025/discussions) to share your ideas
+- **Unclear instructions?** Let us know what could be explained better (open a [Discussion](https://github.com/arnold-c/SISMID-Module-02_2025/discussions))
+
+### Contributing Code or Content
+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](https://posit-dev.github.io/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
+
+### Content Guidelines
+- 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
+
+### Development Setup for Contributors
+- 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
 
-If you are interested in contributing text, please email me and we can make it happen!
+**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.
 
 ## Acknowledgements
 

_book/r-session-04.html

@@ -2179,7 +2179,7 @@
 <span id="cb24-278"><a href="#cb24-278"></a>R <span class="ot">&lt;-</span> <span class="dv">1</span> <span class="co"># number recovered</span></span>
 <span id="cb24-279"><a href="#cb24-279"></a>time <span class="ot">&lt;-</span> <span class="dv">0</span></span>
 <span id="cb24-280"><a href="#cb24-280"></a></span>
-<span id="cb24-281"><a href="#cb24-281"></a>beta <span class="ot">&lt;-</span> .<span class="dv">5</span> <span class="co"># transmission rate</span></span>
+<span id="cb24-281"><a href="#cb24-281"></a>beta <span class="ot">&lt;-</span> <span class="fl">0.5</span> <span class="co"># transmission rate</span></span>
 <span id="cb24-282"><a href="#cb24-282"></a>gamma <span class="ot">&lt;-</span> <span class="dv">1</span> <span class="sc">/</span> <span class="dv">7</span> <span class="co"># recovery rate</span></span>
 <span id="cb24-283"><a href="#cb24-283"></a><span class="in">```</span></span>
 <span id="cb24-284"><a href="#cb24-284"></a></span>