GillespieSSA

What is GillespieSSA?
GillespieSSA is a package for the statistical computing and graphics language and environment R. GillespieSSA provides a simple to use 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.

GillespieSSA can be downloaded from CRAN or, preferably, installed directly from the internet from the R command prompt:

R> install.packages("GillespieSSA")

and then one can do, for example,

R> ?GillespieSSA # for the main manual page

R> demo("GillespieSSA") # for the full suite of demos

Documentation

• Pineda-Krch, M. 2007. GillespieSSA: A user-friendly stochastic simulation package for R. Poster presented at the !useR 2007 meeting at the Iowa State University. [PDF], [PNG]
• Pineda-Krch, M. 2008. Implementing the Stochastic Simulation Algorithm in R Using the GillespieSSA Package. Journal of Statistical Software 25(12): 1-18. [PDF]

Author and maintainer: Mario Pineda-Krch (contact info)

License

• GillespieSSA, like R, is free open source software licensed under the GNU Public License (GPL 3.0 or above)
• According to this license the software is provided as is and comes WITHOUT WARRANTY.

Development

• Development of GillespieSSA is taking place at its github site.