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README.md

EpiModelHIV

Build Status

An R package for simulating HIV transmission dynamics among men who have sex with men and heterosexual populations, developed as an extension to our general network-based epidemic modeling platform, EpiModel.

EpiModel and EpiModelHIV use the statistical framework of temporal exponential-family random graph models to fit and simulate models of dynamic networks. These statistical methods have been developed and implemented as open-source software, building on the extensive efforts of the Statnet research group to build software tools for the representation, analysis, and visualization of complex network data.

These packages combine these Statnet methods with an agent-based epidemic modeling engine to simulate HIV transmission over networks, allowing for complex dependencies between the network, epidemiological, and demographic changes in the simulated populations. Readers new to these methods are recommended to consult our EpiModel resources, including our main Vignette describe the theory and implementation.

Installation

You can install EpiModelHIV in R using devtools:

install.packages("EpiModel", dependencies = TRUE)
devtools::install_github("statnet/tergmLite", subdir = "tergmLite")
devtools::install_github("statnet/EpiModelHIV")

Documentation on using this software package is forthcoming, although limited function documentation is provided within the package and available with the help(package = "EpiModelHIV") command.

Note on Repository and Package Name

This Github repository EpiModelHIV and the R package within it were previously named EpiModelHIVmsm. On 6/24/2016, we merged that MSM package with our EpiModelHIVhet (HIV models for heterosexuals) into this combined repository and package. All scripts from those separate packages should still function with this current version after changing the input to library.

Software Development Team

Author Department Institution
Samuel M. Jenness Department of Epidemiology Emory University
Steven M. Goodreau Department of Anthropology University of Washington

Literature

EpiModelHIV 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. DOI: 10.1136/sextrans-2015-052476.

  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. DOI: 10.1093/infdis/jiw223.

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