SimInf

A Framework for Data-Driven Stochastic Disease Spread Simulations

Stefan Engblom, Robin Eriksson, Stefan Widgren, Pavol Bauer

Last update: 20 December 2023

Copyright license: GNU General Public License, version 3.0

Software version identifier: 9.5.0, 1.0.0, 2.0.0, 3.0.0, 4.0.0, 5.0.0, 5.1.0, 6.0.0, 6.1.0, 6.2.0, 6.3.0, 6.4.0, 6.5.0, 6.5.1, 7.0.0, 7.0.1, 8.0.0, 8.1.0, 8.2.0, 8.3.0, 8.3.2, 8.4.0, 9.0.0, 9.1.0, 9.2.0, 9.3.1, 9.4.0, 9.6.0

Source code repository: https://github.com/cran/SimInf

Description

Provides an efficient and very flexible framework to conduct data-driven epidemiological modeling in realistic large scale disease spread simulations. The framework integrates infection dynamics in subpopulations as continuous-time Markov chains using the Gillespie stochastic simulation algorithm and incorporates available data such as births, deaths and movements as scheduled events at predefined time-points. Using C code for the numerical solvers and 'OpenMP' (if available) to divide work over multiple processors ensures high performance when simulating a sample outcome. One of our design goals was to make the package extendable and enable usage of the numerical solvers from other R extension packages in order to facilitate complex epidemiological research. The package contains template models and can be extended with user-defined models. For more details see the paper by Widgren, Bauer, Eriksson and Engblom (2019) <doi:10.18637/jss.v091.i12>. The package also provides functionality to fit models to time series data using the Approximate Bayesian Computation Sequential Monte Carlo ('ABC-SMC') algorithm of Toni and others (2009) <doi:10.1098/rsif.2008.0172>.

Cites work

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