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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
Converting from GillespieSSA to GillespieSSA2
Decaying-Dimerization Reaction Set
SIRS metapopulation model
Linear Chain System
Pearl-Verhulst Logistic Growth model
Lotka Predator-Prey model
Radioactive Decay model
Rosenzweig-MacArthur Predator-Prey model
Kermack-McKendrick SIR model

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-release (arm64): GillespieSSA2_0.3.0.tgz, r-oldrel (arm64): 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:

Please use the canonical form https://CRAN.R-project.org/package=GillespieSSA2 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.