EpiModel

Mathematical Modeling of Infectious Disease Dynamics

An R package for simulating mathematical models of infectious disease dynamics using network-based, individual-based, and compartmental modeling frameworks. 

install.packages("EpiModel")

CRAN Version Downloads

Animated network epidemic simulation

Resources

Stylized EpiModel R code on a dark background

Package Documentation

Full function reference, vignettes, and getting started guides on the EpiModel pkgdown site.

SEIR vs SEIRS prevalence time series comparison plot

Training Materials

Materials from our Network Modeling for Epidemics (NME) course at SISMID.

SEIR and SIS compartmental model flow diagrams

EpiModel Gallery

Worked examples and templates for extending EpiModel to build custom epidemic models.

Get Started

EpiModel supports several modeling classes, but its unique contribution is stochastic network models built on the statistical framework of temporal exponential random graph models (ERGMs). The learning pathway below is designed for those looking to build network-based epidemic models with EpiModel.

1
Beginning
2
Intermediate
3
Advanced
Beginning
Intermediate
Advanced

Ecosystem

EpiModel builds on the Statnet suite of R packages for statistical network analysis, extending them into a platform for infectious disease modeling, applied research tools, and high-performance computing.

Statnet Foundation

network Classes and methods for relational data storage and manipulation

ergm Exponential-family random graph models for cross-sectional network analysis

tergm Temporal ERGMs for modeling dynamic network evolution over time

networkDynamic Dynamic network data structures for temporal relational data

Extensions & Tools

EpiModelHIV Network models of HIV transmission dynamics among MSM and heterosexual populations

ARTnet Network and epidemic parameterization from the ARTnet study (MSM in the US)

EpiModelCOVID Network-based epidemic modeling of SARS-CoV-2 transmission

EpiModelHIV-Template Template repository for building new EpiModelHIV-based projects

HPC & Infrastructure

EpiModelHPC Parallel simulation with checkpointing on Slurm clusters and multi-core desktops

slurmworkflow Define and run inter-dependent jobs on Slurm HPC without persistent SSH

swfcalib Automated multi-parameter model calibration on Slurm HPC

networkLite Lightweight network data structure for faster simulation performance

Community

EpiModel has been used in 125+ published studies across HIV/STI epidemiology, COVID-19 modeling, veterinary epidemiology, and more. See the full list.

Need help? File an issue on GitHub.