Here’s my submitted abstract for the poster I will be presenting at the useR! 2007 meeting in August.
GillespieSSA: A stochastic simulation package for R
Center for Animal Disease Modeling and Surveillance
University of California, Davis
Stochastic simulation models are invaluable tools for studying the inherent randomness in biological and physical systems. It is well know that stochasticity in finite populations, particularly where key species or events may occur at low frequencies, can generate dynamics profoundly different from the predictions of the deterministic differential equations. Here I present the package GillespieSSA, a versatile and extensible framework for stochastic simulation in R. GillespieSSA provides a simple interface to several efficient stochastic simulation algorithms making them accessible to researchers and students with limited programming background. The first version of the package includes the classical Gillespie Stochastic Simulation Algorithm (SSA), optimized SSA, and several tau-leaping methods. To encourage the use of efficient stochastic simulation algorithms in the biological sciences the package includes model templates for basic ecological, epidemiological, and evolutionary models.
So I finally spilled the beans! I have been working on this package for the last while and finally it is coming together, just in time for the R meeting. There is still lots to do, however, before the big day. So many lines of code and so little time…