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Fast and principled simulations of the SIR model on temporal networks

The Susceptible–Infectious–Recovered (SIR) model is the canonical model of epidemics of infections that make people immune upon recovery. Many of the open questions in computational epidemiology concern the underlying contact structure’s impact on models like the SIR model. Temporal networks constit...

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Autor principal: Holme, Petter
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7880429/
https://www.ncbi.nlm.nih.gov/pubmed/33577564
http://dx.doi.org/10.1371/journal.pone.0246961
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author Holme, Petter
author_facet Holme, Petter
author_sort Holme, Petter
collection PubMed
description The Susceptible–Infectious–Recovered (SIR) model is the canonical model of epidemics of infections that make people immune upon recovery. Many of the open questions in computational epidemiology concern the underlying contact structure’s impact on models like the SIR model. Temporal networks constitute a theoretical framework capable of encoding structures both in the networks of who could infect whom and when these contacts happen. In this article, we discuss the detailed assumptions behind such simulations—how to make them comparable with analytically tractable formulations of the SIR model, and at the same time, as realistic as possible. We also present a highly optimized, open-source code for this purpose and discuss all steps needed to make the program as fast as possible.
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spelling pubmed-78804292021-02-19 Fast and principled simulations of the SIR model on temporal networks Holme, Petter PLoS One Research Article The Susceptible–Infectious–Recovered (SIR) model is the canonical model of epidemics of infections that make people immune upon recovery. Many of the open questions in computational epidemiology concern the underlying contact structure’s impact on models like the SIR model. Temporal networks constitute a theoretical framework capable of encoding structures both in the networks of who could infect whom and when these contacts happen. In this article, we discuss the detailed assumptions behind such simulations—how to make them comparable with analytically tractable formulations of the SIR model, and at the same time, as realistic as possible. We also present a highly optimized, open-source code for this purpose and discuss all steps needed to make the program as fast as possible. Public Library of Science 2021-02-12 /pmc/articles/PMC7880429/ /pubmed/33577564 http://dx.doi.org/10.1371/journal.pone.0246961 Text en © 2021 Petter Holme http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Holme, Petter
Fast and principled simulations of the SIR model on temporal networks
title Fast and principled simulations of the SIR model on temporal networks
title_full Fast and principled simulations of the SIR model on temporal networks
title_fullStr Fast and principled simulations of the SIR model on temporal networks
title_full_unstemmed Fast and principled simulations of the SIR model on temporal networks
title_short Fast and principled simulations of the SIR model on temporal networks
title_sort fast and principled simulations of the sir model on temporal networks
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7880429/
https://www.ncbi.nlm.nih.gov/pubmed/33577564
http://dx.doi.org/10.1371/journal.pone.0246961
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