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GillespieSSA2: Gillespie's Stochastic Simulation Algorithm for Impatient People (original) (raw)

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
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.html , <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)

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Reverse dependencies:

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