GillespieSSA2: Gillespie's Stochastic Simulation Algorithm for Impatient People

A fast, scalable, and versatile framework for simulating large systems with Gillespie's Stochastic Simulation Algorithm ('SSA'). This package is the spiritual successor to the 'GillespieSSA' package originally written by Mario Pineda-Krch. Benefits of this package include major speed improvements (>100x), easier to understand documentation, and many unit tests that try to ensure the package works as intended. Cannoodt and Saelens et al. (2020) <doi:10.1101/2020.02.06.936971>.

Version: 0.2.8
Depends: R (≥ 3.3)
Imports: assertthat, dplyr, dynutils, Matrix, methods, purrr, Rcpp (≥ 0.12.3), RcppXPtrUtils, readr, rlang, stringr, tidyr
LinkingTo: Rcpp
Suggests: covr, ggplot2, GillespieSSA, knitr, rmarkdown, testthat (≥ 2.1.0)
Published: 2021-05-18
Author: Robrecht Cannoodt ORCID iD [aut, cre], Wouter Saelens ORCID iD [aut]
Maintainer: Robrecht Cannoodt <rcannood at>
License: GPL (≥ 3)
NeedsCompilation: yes
Citation: GillespieSSA2 citation info
Materials: README NEWS
CRAN checks: GillespieSSA2 results


Reference manual: GillespieSSA2.pdf
Vignettes: Introduction to GillespieSSA2
Converting from GillespieSSA to GillespieSSA2
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)


Package source: GillespieSSA2_0.2.8.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): GillespieSSA2_0.2.8.tgz, r-release (x86_64): GillespieSSA2_0.2.8.tgz, r-oldrel: GillespieSSA2_0.2.8.tgz
Old sources: GillespieSSA2 archive

Reverse dependencies:

Reverse imports: dyngen


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