SimInf: A Framework for Data-Driven Stochastic Disease Spread Simulations
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>.
| Version: | 9.8.1 |
| Depends: | R (≥ 4.0) |
| Imports: | digest, graphics, grDevices, MASS, methods, stats, utils, Matrix (≥ 1.3-0) |
| Suggests: | knitr, rmarkdown |
| Published: | 2024-06-21 |
| 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 |
| NeedsCompilation: | yes |
| SystemRequirements: | GNU Scientific Library (GSL) |
| Citation: | SimInf citation info |
| Materials: | README, NEWS |
| In views: | Epidemiology |
| CRAN checks: | SimInf results |
Documentation:
| Reference manual: | SimInf.html , SimInf.pdf |
| Vignettes: |
SimInf: An R Package for Data-Driven Stochastic Disease Spread Simulations (source, R code) Post-process data in a trajectory (source, R code) Scheduled events (source, R code) |
Downloads:
| Package source: | SimInf_9.8.1.tar.gz |
| Windows binaries: | r-devel: SimInf_9.8.1.zip, r-release: SimInf_9.8.1.zip, r-oldrel: SimInf_9.8.1.zip |
| macOS binaries: | r-release (arm64): SimInf_9.8.1.tgz, r-oldrel (arm64): SimInf_9.8.1.tgz, r-release (x86_64): SimInf_9.8.1.tgz, r-oldrel (x86_64): SimInf_9.8.1.tgz |
| Old sources: | SimInf archive |
Linking:
Please use the canonical form https://CRAN.R-project.org/package=SimInf to link to this page.