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 [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.html , GillespieSSA.pdf

Vignettes:

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

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:

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