About EpiModel Gallery

What is EpiModel Gallery?

Templates for extending the EpiModel platform to model infectious disease dynamics over networks. Each example demonstrates how to build custom modules for stochastic network models using exponential random graph models (ERGMs).

EpiModel provides built-in SIS/SIR models out of the box, but its module API supports arbitrarily complex epidemic systems. These examples teach by example — from adding a single compartment to multi-stage disease models with interventions and cost-effectiveness analysis.

Getting Started

Prerequisites

R >= 4.5
EpiModel >= 2.6.0

Install EpiModel from CRAN:

install.packages("EpiModel")

Running an Example

Clone the repository, then run any example from the project root:

source("examples/si-vital-dynamics/model.R")

Or from the command line:

Rscript examples/si-vital-dynamics/model.R

Running All Examples

bash test.sh

Contributing

Contributions of new gallery examples are welcome! To contribute:

Fork the repository on GitHub.
Create a new subdirectory under examples/ containing:
- model.R — main script for network estimation and simulation
- module-fx.R — custom module functions
- index.qmd — annotated Quarto document
Include the standard unit test lines near the top of model.R (see existing examples).
Verify your example passes: bash test.sh
Submit a Pull Request.

Requesting New Examples

If you’d like to ask “how would you build a network model in EpiModel that does X?”, file a GitHub Issue with a detailed description.

Build Environment

The examples on this site are built and tested against the environment below, pinned with renv for reproducibility. The complete pinned set for all packages is recorded in renv.lock.

R environment
Field	Value
R version	R version 4.6.1 (2026-06-24)
Platform	aarch64-apple-darwin23
Operating system	macOS Tahoe 26.5.1

Core package versions
Package	Version
dampack	1.0.2.1000
deSolve	1.42
dplyr	1.2.1
EpiModel	2.6.1
ergm	4.12.0
ergm.multi	0.3.0
network	1.20.0
networkDynamic	0.12.0
networkDynamicData	0.3.0
networkLite	1.1.0
renv	1.2.3
statnet.common	4.13.0
tergm	4.2.2

Citation

If using EpiModel for teaching or research, please include a citation:

Jenness SM, Goodreau SM and Morris M. EpiModel: An R Package for Mathematical Modeling of Infectious Disease over Networks. Journal of Statistical Software. 2018; 84(8): 1-47. doi: 10.18637/jss.v084.i08

License

MIT

--- title: "About EpiModel Gallery" toc: true --- ## What is EpiModel Gallery? Templates for extending the [EpiModel](https://github.com/statnet/EpiModel) platform to model infectious disease dynamics over networks. Each example demonstrates how to build custom modules for stochastic network models using exponential random graph models (ERGMs). EpiModel provides built-in SIS/SIR models out of the box, but its module API supports arbitrarily complex epidemic systems. These examples teach by example --- from adding a single compartment to multi-stage disease models with interventions and cost-effectiveness analysis. ## Getting Started ### Prerequisites - **R** >= 4.5 - **EpiModel** >= 2.6.0 Install EpiModel from CRAN: ```r install.packages("EpiModel") ``` ### Running an Example Clone the [repository](https://github.com/EpiModel/EpiModel-Gallery), then run any example from the project root: ```r source("examples/si-vital-dynamics/model.R") ``` Or from the command line: ```bash Rscript examples/si-vital-dynamics/model.R ``` ### Running All Examples ```bash bash test.sh ``` ## Contributing Contributions of new gallery examples are welcome! To contribute: 1. Fork the [repository](https://github.com/EpiModel/EpiModel-Gallery) on GitHub. 2. Create a new subdirectory under `examples/` containing: - `model.R` --- main script for network estimation and simulation - `module-fx.R` --- custom module functions - `index.qmd` --- annotated Quarto document 3. Include the standard unit test lines near the top of `model.R` (see existing examples). 4. Verify your example passes: `bash test.sh` 5. Submit a Pull Request. ### Requesting New Examples If you'd like to ask "how would you build a network model in EpiModel that does X?", file a [GitHub Issue](https://github.com/EpiModel/EpiModel-Gallery/issues) with a detailed description. ## Build Environment The examples on this site are built and tested against the environment below, pinned with [renv](https://rstudio.github.io/renv/) for reproducibility. The complete pinned set for all packages is recorded in [`renv.lock`](https://github.com/EpiModel/EpiModel-Gallery/blob/main/renv.lock). ```{r} #| label: build-env #| echo: false #| message: false #| warning: false si <- sessionInfo() running <- if (is.null(si$running)) "Unknown" else si$running knitr::kable( data.frame( Field = c("R version", "Platform", "Operating system"), Value = c(si$R.version$version.string, si$platform, running), check.names = FALSE ), caption = "R environment" ) ``` ```{r} #| label: build-pkgs #| echo: false #| message: false #| warning: false core <- c("EpiModel", "ergm", "ergm.multi", "tergm", "tergmLite", "network", "networkLite", "networkDynamic", "statnet.common", "deSolve", "dplyr", "networkDynamicData", "dampack", "renv") core <- core[vapply(core, function(p) nzchar(system.file(package = p)), logical(1))] core <- core[order(tolower(core))] knitr::kable( data.frame( Package = core, Version = vapply(core, function(p) as.character(packageVersion(p)), character(1)), check.names = FALSE ), row.names = FALSE, caption = "Core package versions" ) ``` ## Citation If using EpiModel for teaching or research, please include a citation: > Jenness SM, Goodreau SM and Morris M. EpiModel: An R Package for Mathematical Modeling of Infectious Disease over Networks. *Journal of Statistical Software.* 2018; 84(8): 1-47. doi: 10.18637/jss.v084.i08 ## License [MIT](https://github.com/EpiModel/EpiModel-Gallery/blob/main/LICENSE)