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GillespieSSA: Gillespie's Stochastic Simulation Algorithm (SSA)

Provides a simple to use, intuitive, and extensible interface to several stochastic simulation algorithms for generating simulated trajectories of finite population continuous-time model. Currently it implements Gillespie's exact stochastic simulation algorithm (Direct method) and several approximate methods (Explicit tau-leap, Binomial tau-leap, and Optimized tau-leap). The package also contains a library of template models that can be run as demo models and can easily be customized and extended. Currently the following models are included, 'Decaying-Dimerization' reaction set, linear chain system, logistic growth model, 'Lotka' predator-prey model, Rosenzweig-MacArthur predator-prey model, 'Kermack-McKendrick' SIR model, and a 'metapopulation' SIRS model. Pineda-Krch et al. (2008) <doi:10.18637/jss.v025.i12>.

Version: 0.6.2
Depends: R (≥ 2.0.0)
Imports: grDevices, graphics, methods, stats, utils
Suggests: knitr, rmarkdown, testthat
Published: 2022-03-10
DOI: 10.32614/CRAN.package.GillespieSSA
Author: Mario Pineda-Krch [aut], Robrecht Cannoodt ORCID iD [aut, cre]
Maintainer: Robrecht Cannoodt <rcannood at gmail.com>
License: GPL (≥ 3)
URL: https://github.com/rcannood/GillespieSSA
NeedsCompilation: no
Materials: README NEWS
In views: DifferentialEquations
CRAN checks: GillespieSSA results

Documentation:

Reference manual: GillespieSSA.pdf
Vignettes: Decaying-Dimerization Reaction Set (Gillespie, 2001)
SIRS metapopulation model (Pineda-Krch, 2008)
Linear Chain System (Cao et al., 2004)
Pearl-Verhulst Logistic growth model (Kot, 2001)
Lotka predator-prey model (Gillespie, 1977; Kot, 2001)
Radioactive decay model (Gillespie, 1977)
Rosenzweig-MacArthur predator-prey model (Pineda-Krch et al., 2007)
Kermack-McKendrick SIR model (Brown & Rothery, 1993)

Downloads:

Package source: GillespieSSA_0.6.2.tar.gz
Windows binaries: r-devel: GillespieSSA_0.6.2.zip, r-release: GillespieSSA_0.6.2.zip, r-oldrel: GillespieSSA_0.6.2.zip
macOS binaries: r-release (arm64): GillespieSSA_0.6.2.tgz, r-oldrel (arm64): GillespieSSA_0.6.2.tgz, r-release (x86_64): GillespieSSA_0.6.2.tgz, r-oldrel (x86_64): GillespieSSA_0.6.2.tgz
Old sources: GillespieSSA archive

Reverse dependencies:

Reverse imports: hybridModels
Reverse suggests: GillespieSSA2

Linking:

Please use the canonical form https://CRAN.R-project.org/package=GillespieSSA 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.