Package: GillespieSSA 0.6.2

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>.

Authors:Mario Pineda-Krch [aut], Robrecht Cannoodt [aut, cre]

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GillespieSSA.pdf |GillespieSSA.html✨
GillespieSSA/json (API)
NEWS

# Install 'GillespieSSA' in R:
install.packages('GillespieSSA', repos = c('https://rcannood.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/rcannood/gillespiessa/issues

On CRAN:

7.37 score 3 stars 1 packages 93 scripts 344 downloads 7 mentions 6 exports 0 dependencies

Last updated 3 years agofrom:b532ff9206. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winOKOct 31 2024
R-4.5-linuxOKOct 31 2024
R-4.4-winOKOct 31 2024
R-4.4-macOKOct 31 2024
R-4.3-winOKOct 31 2024
R-4.3-macOKOct 31 2024

Exports:ssassa.btlssa.dssa.etlssa.otlssa.plot

Dependencies:

Decaying-Dimerization Reaction Set (Gillespie, 2001)

Rendered fromdecaying_dimer.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2019-07-16
Started: 2019-07-13

Kermack-McKendrick SIR model (Brown & Rothery, 1993)

Rendered fromsir.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2019-07-16
Started: 2019-07-13

Linear Chain System (Cao et al., 2004)

Rendered fromlinear_chain.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2019-07-16
Started: 2019-07-13

Lotka predator-prey model (Gillespie, 1977; Kot, 2001)

Rendered fromlotka_predator_prey.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2019-07-16
Started: 2019-07-13

Pearl-Verhulst Logistic growth model (Kot, 2001)

Rendered fromlogistic_growth.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2019-07-16
Started: 2019-07-13

Radioactive decay model (Gillespie, 1977)

Rendered fromradioactive_decay.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2019-07-16
Started: 2019-07-13

Rosenzweig-MacArthur predator-prey model (Pineda-Krch et al., 2007)

Rendered fromrm_predator_prey.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2019-07-16
Started: 2019-07-13

SIRS metapopulation model (Pineda-Krch, 2008)

Rendered fromepi_chain.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2019-07-16
Started: 2019-07-13