Published by the Foundation for Open Access Statistics Editors-in-chief: Bettina Grün, Torsten Hothorn, Edzer Pebesma, Achim Zeileis    ISSN 1548-7660; CODEN JSSOBK
Authors: Fernando S. Marques, José H. H. Grisi-Filho, Marcos Amaku, Jean C. R. Silva, Erivânia C. Almeida, José L. Silva Júnior
Title: hybridModels: An R Package for the Stochastic Simulation of Disease Spreading in Dynamic Networks
Abstract: Disease spreading simulations are traditionally performed using coupled differential equations. However, in the setting of metapopulations, most of the solutions provided by this method do not account for the dynamic topography of subpopulations. Conversely, the alternative approach of individual-based modeling (IBM) may add computational cost and complexity. Hybrid models allow for the study of disease spreading because they combine both aforementioned approaches by separating them across different scales: a local scale that addresses subpopulation dynamics using coupled differential equations and a global scale that addresses the contact between these subpopulations using IBM. We present a simple way of simulating the spread of disease in dynamic networks using the high-level statistical computational language R and the hybridModels package. We built four examples using disease spread models at the local scale in several different networks: an animal movement network; a three-node network, whose model solution using a stochastic simulation algorithm is compared with the ordinary differential equations approach; the commuting of individuals between patches, which we compare with the permanent migration of individuals; and the commuting of individuals within the metropolitan area of São Paulo.

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Paper: hybridModels: An R Package for the Stochastic Simulation of Disease Spreading in Dynamic Networks     Download PDF (Downloads: 268)
hybridModels_0.3.7.tar.gz: R source package Download (Downloads: 23; 27KB)
v94i06.R: R replication code Download (Downloads: 27; 19KB)
daily_commuting_from_residence.csv: Supplementary data (CSV format) Download (Downloads: 24; 224KB)
zones.csv: Supplementary data (CSV format) Download (Downloads: 25; 12KB)

DOI: 10.18637/jss.v094.i06

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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.