Fast and principled simulations of the SIR model on temporal networks

PLoS One. 2021 Feb 12;16(2):e0246961. doi: 10.1371/journal.pone.0246961. eCollection 2021.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Communicable Diseases / epidemiology*
  • Communicable Diseases / immunology
  • Computer Simulation
  • Humans
  • Immunity
  • Models, Biological
  • Software

Grants and funding

P.H. was supported by JSPS KAKENHI Grant Number JP 18H01655. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.