EpiModel is an R package for simulating mathematical models of infectious disease dynamics. Epidemic model classes include deterministic compartmental models, stochastic individual-contact models, and stochastic network models. Network models use the robust statistical methods of exponential-family random graph models (ERGMs) from the Statnet suite of R packages. Standard templates for epidemic modeling include SI, SIR, and SIS disease types. EpiModel features an API for extending these templates to address novel research aims.
EpiModel is part of a broader platform for infectious disease modeling. Visit epimodel.org for the full ecosystem, learning pathway, team, and project information.
Installation
The current release version can be found on CRAN and installed with:
install.packages("EpiModel", dependencies = TRUE)To install the development version, use the remotes package:
if (!require("remotes")) install.packages("remotes")
remotes::install_github("EpiModel/EpiModel")Documentation
Package Documentation. Full function reference, vignettes, and getting started guides are on the pkgdown site.
Methods Paper. The main methods paper in the Journal of Statistical Software describes the modeling framework and software design: doi:10.18637/jss.v084.i08.
Training Course. Network Modeling for Epidemics (NME) is our course at the Summer Institute in Statistics and Modeling in Infectious Diseases (SISMID). Materials are open-source and updated annually.
EpiModel Gallery. The EpiModel Gallery provides worked examples and templates for extending EpiModel’s stochastic network models with custom epidemic modules.
Getting Help
Users are encouraged to use GitHub Issues to ask questions (both technical coding questions and conceptual modeling questions), report bugs, and request new features.
Citation
If using EpiModel for teaching or research, please include a citation to our main methods paper:
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
Please also send us an email if you have used EpiModel in your work so we can add it to our records.
Authors
EpiModel is developed by Samuel Jenness, Steven Goodreau, Martina Morris, and Adrien Le Guillou. Additional contributors are listed on the contributors page. See the full team at epimodel.org/team.
Funding and Literature
The development of EpiModel has been supported by grants from the National Institutes of Health (NIH) and the Centers for Disease Control and Prevention (CDC). Details are available on the project page.
EpiModel and its extension packages have been used in 125+ published studies. See the full list.
Copyright
These materials are distributed under the GPL-3 license, with the copyright and attribution requirements listed in the LICENSE.