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: 8.4.0
Depends: R (≥ 4.0)
Imports: digest, graphics, grDevices, MASS, methods, stats, utils, Matrix
Suggests: knitr, rmarkdown
Published: 2021-09-19
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], 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
CRAN checks: SimInf results

Documentation:

Reference manual: SimInf.pdf
Vignettes: SimInf: An R Package for Data-Driven Stochastic Disease Spread Simulations
Scheduled events

Downloads:

Package source: SimInf_8.4.0.tar.gz
Windows binaries: r-devel: SimInf_8.4.0.zip, r-devel-UCRT: SimInf_8.4.0.zip, r-release: SimInf_8.4.0.zip, r-oldrel: SimInf_8.4.0.zip
macOS binaries: r-release (arm64): SimInf_8.4.0.tgz, r-release (x86_64): SimInf_8.4.0.tgz, r-oldrel: SimInf_8.4.0.tgz
Old sources: SimInf archive

Reverse dependencies:

Reverse imports: SPOTMisc

Linking:

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