GillespieSSA2: Gillespie’s Stochastic Simulation Algorithm for impatient people.

GillespieSSA2 is 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.

GillespieSSA2 has the following added benefits:

• The whole algorithm is run in Rcpp which results in major speed improvements (>100x). Even your propensity functions (reactions) are being compiled to Rcpp!
• Parameters and variables have been renamed to make them easier to understand.
• Many unit tests try to ensure that the code works as intended.

The SSA methods currently implemented are: Exact (ssa_exact()), Explicit tau-leaping (ssa_etl()), and the Binomial tau-leaping (ssa_btl()).

Install

You can install:

• the latest released version from CRAN with

  install.packages("GillespieSSA2")

• the latest development version from github with

  devtools::install_github("rcannood/GillespieSSA2", build_vignettes = TRUE)

If you encounter a bug, please file a minimal reproducible example on the issues page.

Examples

The following example models are available:

• Introduction to GillespieSSA2:
  vignette("an_introduction", package="GillespieSSA2")
• Converting from GillespieSSA to GillespieSSA2:
  vignette("converting_from_GillespieSSA", package="GillespieSSA2")
• Decaying-Dimerization Reaction Set (Gillespie, 2001):
  vignette("decaying_dimer", package="GillespieSSA2")
• SIRS metapopulation model (Pineda-Krch, 2008):
  vignette("epi_chain", package="GillespieSSA2")
• Linear Chain System (Cao et al., 2004):
  vignette("linear_chain", package="GillespieSSA2")
• Pearl-Verhulst Logistic Growth model (Kot, 2001):
  vignette("logistic_growth", package="GillespieSSA2")
• Lotka Predator-Prey model (Gillespie, 1977; Kot, 2001):
  vignette("lotka_predator_prey", package="GillespieSSA2")
• Radioactive Decay model (Gillespie, 1977):
  vignette("radioactive_decay", package="GillespieSSA2")
• Rosenzweig-MacArthur Predator-Prey model (Pineda-Krch et al., 2007):
  vignette("rm_predator_prey", package="GillespieSSA2")
• Kermack-McKendrick SIR model (Brown & Rothery, 1993):
  vignette("sir", package="GillespieSSA2")

Latest changes

Check out news(package = "GillespieSSA2") or NEWS.md for a full list of changes.

Recent changes in GillespieSSA2 0.2.7 (14-07-2020)

• BUG FIX: Renamed autoplot.ssa() to plot_ssa() for compatibility with R 4.0.

Recent changes in GillespieSSA2 0.2.6 (14-03-2020)

• BUG FIX: Zap small negative propensity and state values.

• FEATURE autoplot.ssa(): Allow plotting the firings.

• DEBUG FEATURE ssa(): Allow returning the GillespieSSA2 instead of running it.