SimInf: A Framework for Data-Driven Stochastic Disease SpreadSimulations
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> or the Particle Markov Chain Monte Carlo ('PMCMC') algorithm of 'Andrieu' and others (2010) <doi:10.1111/j.1467-9868.2009.00736.x>.
| Version: | 10.1.0 |
| Depends: | R (≥ 4.0) |
| Imports: | digest, graphics, grDevices,MASS, methods, stats, utils,Matrix (≥ 1.3-0) |
| Suggests: | knitr,rmarkdown |
| Published: | 2025-11-17 |
| DOI: | 10.32614/CRAN.package.SimInf |
| Author: | Stefan Widgren [aut, cre], Robin Eriksson [aut], Stefan Engblom [aut], Pavol Bauer [aut], Thomas Rosendal [ctb], Ivana Rodriguez Ewerlöf [ctb], Attractive Chaos [cph] (Author of 'kvec.h'.) |
| Maintainer: | Stefan Widgren <stefan.widgren at gmail.com> |
| BugReports: | https://github.com/stewid/SimInf/issues |
| License: | GPL-3 |
| URL: | https://github.com/stewid/SimInf,http://stewid.github.io/SimInf/ |
| NeedsCompilation: | yes |
| SystemRequirements: | GNU Scientific Library (GSL) |
| Citation: | SimInf citation info |
| Materials: | README,NEWS |
| In views: | Epidemiology |
| CRAN checks: | SimInf results |
Documentation:
Downloads:
| Package source: | SimInf_10.1.0.tar.gz |
| Windows binaries: | r-devel:SimInf_10.1.0.zip, r-release:SimInf_10.1.0.zip, r-oldrel:SimInf_10.1.0.zip |
| macOS binaries: | r-release (arm64):SimInf_10.1.0.tgz, r-oldrel (arm64):SimInf_10.1.0.tgz, r-release (x86_64):SimInf_10.1.0.tgz, r-oldrel (x86_64):SimInf_10.1.0.tgz |
| Old sources: | SimInf archive |
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