Published by the Foundation for Open Access Statistics Editors-in-chief: Bettina Grün, Torsten Hothorn, Rebecca Killick, Edzer Pebesma, Achim Zeileis    ISSN 1548-7660; CODEN JSSOBK
Authors: Chris Groendyke, David Welch
Title: epinet: An R Package to Analyze Epidemics Spread across Contact Networks
Abstract: We present the R package epinet, which provides tools for analyzing the spread of epidemics through populations. We assume that the relationships among individuals in a population are modeled by a contact network described by an exponential-family random graph model and that the disease being studied spreads across the edges of this network from infectious to susceptible individuals. We use a susceptible-exposed-infectiousremoved compartmental model to describe the progress of the disease within each host. We describe the functionality of the package, which consists of routines that perform simulation, plotting, and inference. The main inference routine utilizes a Bayesian approach and a Markov chain Monte Carlo algorithm. We demonstrate the use of the package through two examples, one involving simulated data and one using data from an actual measles outbreak.

Page views:: 2721. Submitted: 2015-11-22. Published: 2018-02-27.
Paper: epinet: An R Package to Analyze Epidemics Spread across Contact Networks     Download PDF (Downloads: 988)
epinet_2.1.8.tar.gz: R source package Download (Downloads: 105; 81KB)
v83i11.R: R replication code Download (Downloads: 135; 4KB)
SuppPlotData.RData: Supplementary data (R binary format) Download (Downloads: 125; 1KB)

DOI: 10.18637/jss.v083.i11

This work is licensed under the licenses
Paper: Creative Commons Attribution 3.0 Unported License
Code: GNU General Public License (at least one of version 2 or version 3) or a GPL-compatible license.