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GillespieSSA: Gillespie’s Stochastic Simulation Algorithm (SSA)

GillespieSSA 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.

Install

You can install GillespieSSA from CRAN using

install.packages("GillespieSSA")

Or, alternatively, you can install the development version of GillespieSSA from GitHub using

devtools::install_github("rcannood/GillespieSSA", build_vignettes = TRUE)

Examples

The following example models are available:

Latest changes

Check out news(package = "GillespieSSA") or NEWS.md for a full list of changes.

Recent changes in GillespieSSA 0.6.2

Recent changes in GillespieSSA 0.6.1

This release contains a major rewrite of the internal code, to make sure the code is readable and that the algorithm doesn’t continuously update the local environment.

References

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.