EpiModel: tools for simulating mathematical models of infectious disease. Epidemic model classes include deterministic compartmental models, stochastic individual contact models, and stochastic network models. Disease types include SI, SIR, and SIS epidemics with and without demography, with tools available for expansion to model complex epidemic processes.

The current release version can be found on CRAN and installed with:

install.packages("EpiModel", dependencies = TRUE)

To install this development version, use the devtools package:

if (!require("devtools")) install.packages("devtools")
devtools::install_github("statnet/EpiModel")

The main website for EpiModel, with tutorials and other supporting files is http://epimodel.org/. Users are encouraged to join the email list for EpiModel as a place to ask questions, report bugs, and tell us about your research using these tools.

A good place to start learning about EpiModel is the main vignette, currently under review, but currently available in pre-press form here!

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

Jenness SM, Goodreau SM, Morris M (2017). EpiModel: Mathematical Modeling of Infectious Disease. R Package Version 1.5.0. URL: http://epimodel.org/. DOI: 10.5281/zenodo.16767.

Please also send us an email if you have used EpiModel in your work.

EpiModel has been used in the following scientific articles.

1. Jenness SM, Goodreau SM, Morris M, Cassels S. Effectiveness of Combination Packages for HIV-1 Prevention in Sub-Saharan Africa Depends on Partnership Network Structure. Sexually Transmitted Infections. 2016; 92(8): 619-624. LINK

2. Jenness SM, Goodreau SM, Rosenberg E, Beylerian EN, Hoover KW, Smith DK, Sullivan P. Impact of CDC’s HIV Preexposure Prophylaxis Guidelines among MSM in the United States. Journal of Infectious Diseases. 2016; 214(12): 1800-1807. LINK

3. Jenness SM, Sharma A, Goodreau SM, Rosenberg ES, Weiss KM, Hoover KW, Smith DK, Sullivan P. Individual HIV Risk versus Population Impact of Risk Compensation after HIV Preexposure Prophylaxis Initiation among Men Who Have Sex with Men. PLoS One. 2017; 12(1): e0169484. LINK

4. Goodreau SM, Rosenberg ES, Jenness SM, Luisi N, Stansfield SE, Millett G, Sullivan P. Sources of Racial Disparities in HIV Prevalence among Men Who Have Sex with Men in Atlanta, GA: A Modeling Study. Lancet HIV. Epub ahead of print. DOI: 10.1016/ S2352-3018(17)30067. LINK

5. Jenness SM, Weiss KM, Goodreau SM, Rosenberg E, Gift T, Chesson H, Hoover KW, Smith DK, Liu AY, Sullivan P. Incidence of Gonorrhea and Chlamydia Following HIV Preexposure Prophylaxis among Men Who Have Sex with Men: A Modeling Study. Clinical Infectious Diseases. Epub ahead of print. DOI: 10.1093/cid/cix439. LINK

1. Ezenwa VO, Archie EA, Craft ME, Hawley DM, Martin LB, Moore J, White L. Host behaviour-parasite feedback: an essential link between animal behaviour and disease ecology. Proc Biol Sci. 2016; 283(1828). LINK

2. Goldstein ND, Eppes SC, Mackley A, Tuttle D, Paul DA. A Network Model of Hand Hygiene: How Good Is Good Enough to Stop the Spread of MRSA? Infect Control Hosp Epidemiol. 2017:1-8. LINK

Development of this software has been supported by the following grants from the National Institutes of Health (NIH) and Centers for Disease Control and Prevention (CDC):

• NIH R01HD68395: Statistical Methods for Network Epidemiology (PI: Martina Morris)
• NIH R21HD075662: Using Sexual Network Transmission Models to Explain HIV Disparities Between Black and White MSM (PI: Steven Goodreau)
• NIH R01AI108490: Integrated Bio-Social Models for HIV Epidemiology (MPIs: Steven Goodreau, Joshua Herbeck, and John Mittler)
• NIH R21MH112449: Modeling Antiretroviral-Based Prevention among MSM in the US (PI: Samuel Jenness)
• NIH P30AI050409: Center for AIDS Research at Emory University (MPIs: Carlos del Rio and James Curran)
• NIH P30AI027757: Center for AIDS Research at the University of Washington (PI: King Holmes)
• CDC U38PS004646: Enhancing Models of HIV, Viral Hepatitis, STIs, and Tuberculosis to Inform and Improve Public Health Impact (PI: Patrick Sullivan)
• NIH P30DA027828: Center for Prevention Implementation Methodology for Drug Abuse and HIV (Ce-PIM) (PI: Henricks Brown and Brian Mustanski)

These materials are distributed under the GPL-3 license, with the following copyright and attribution requirements listed here.