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. (2021) <doi:10.1038/s41467-021-24152-2>.

Version: 0.3.0
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: 2023-01-23
DOI: 10.32614/CRAN.package.GillespieSSA2
Author: Robrecht Cannoodt ORCID iD [aut, cre], Wouter Saelens ORCID iD [aut]
Maintainer: Robrecht Cannoodt <rcannood at gmail.com>
BugReports: https://github.com/rcannood/GillespieSSA2/issues
License: GPL (≥ 3)
URL: https://rcannood.github.io/GillespieSSA2/, https://github.com/rcannood/GillespieSSA2
NeedsCompilation: yes
Citation: GillespieSSA2 citation info
Materials: README NEWS
CRAN checks: GillespieSSA2 results

Documentation:

Reference manual: GillespieSSA2.pdf
Vignettes: Introduction to GillespieSSA2 (source, R code)
Converting from GillespieSSA to GillespieSSA2 (source, R code)
Decaying-Dimerization Reaction Set (source, R code)
SIRS metapopulation model (source, R code)
Linear Chain System (source, R code)
Pearl-Verhulst Logistic Growth model (source, R code)
Lotka Predator-Prey model (source, R code)
Radioactive Decay model (source, R code)
Rosenzweig-MacArthur Predator-Prey model (source, R code)
Kermack-McKendrick SIR model (source, R code)

Downloads:

Package source: GillespieSSA2_0.3.0.tar.gz
Windows binaries: r-devel: GillespieSSA2_0.3.0.zip, r-release: GillespieSSA2_0.3.0.zip, r-oldrel: GillespieSSA2_0.3.0.zip
macOS binaries: r-devel (arm64): GillespieSSA2_0.3.0.tgz, r-release (arm64): GillespieSSA2_0.3.0.tgz, r-oldrel (arm64): GillespieSSA2_0.3.0.tgz, r-devel (x86_64): GillespieSSA2_0.3.0.tgz, r-release (x86_64): GillespieSSA2_0.3.0.tgz, r-oldrel (x86_64): GillespieSSA2_0.3.0.tgz
Old sources: GillespieSSA2 archive

Reverse dependencies:

Reverse imports: dyngen

Linking:

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