The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.

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 ORCID iD [aut, cre], Robin Eriksson ORCID iD [aut], Stefan Engblom ORCID iD [aut], Pavol Bauer ORCID iD [aut], Thomas Rosendal ORCID iD [ctb], Ivana Rodriguez Ewerlöf ORCID iD [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.pdf
Vignettes: SimInf: An R Package for Data-Driven Stochastic Disease Spread Simulations
Post-process data in a trajectory
Scheduled events

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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.