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.

Author
Mario Pineda-Krch <mpineda@math.ualbeta.ca>
Date of publication
2012-01-15 12:32:46
Maintainer
ORPHANED
License
GPL (>= 3)
Version
0.5-4
URLs

View on CRAN

Man pages

GillespieSSA-package
Gillespie Stochastic Simulation Algorithm package
ssa
Invoking the stochastic simulation algorithm
ssa.btl
Binomial tau-leap method (BTL)
ssa.btl.diag
Binomial tau-leap method (BTL) for nu-diagonalized systems
ssa.check.args
Validates the arguments for the ssa wrapper function
ssa.check.method
Validates consistency of the system definition
ssa.d
Direct method (D)
ssa.d.diag
Direct method (D) for nu-diagonalized systems
ssa.etl
Explicit tau-leap method (ETL)
ssa.etl.diag
Explicit tau-leap method (ETL) for nu-diagonalized systems
ssa.nutiling
Direct method nu-diagonalization mapping
ssa.otl
Optimized tau-leap method (OTL)
ssa.otl.diag
Optimized tau-leap method (OTL) for nu-diagonalized systems
ssa.plot
Simple plotting of ssa output
ssa.run
Higher-level interface to the method functions
ssa.terminate
Terminates a simulation that was invoked using ssa

Files in this package

GillespieSSA
GillespieSSA/COPYING
GillespieSSA/inst
GillespieSSA/inst/doc
GillespieSSA/inst/doc/index.html
GillespieSSA/inst/doc/pineda-krch2008.pdf
GillespieSSA/NAMESPACE
GillespieSSA/demo
GillespieSSA/demo/GillespieSSA.R
GillespieSSA/demo/lotka.R
GillespieSSA/demo/logisticGrowth.R
GillespieSSA/demo/sir.R
GillespieSSA/demo/decayingDimer.R
GillespieSSA/demo/linearChain.R
GillespieSSA/demo/radioactiveDecay.R
GillespieSSA/demo/00Index
GillespieSSA/demo/epiChain.R
GillespieSSA/demo/rma.R
GillespieSSA/R
GillespieSSA/R/ssa.etl.diag.R
GillespieSSA/R/ssa.terminate.R
GillespieSSA/R/ssa.d.diag.R
GillespieSSA/R/ssa.btl.diag.R
GillespieSSA/R/ssa.run.R
GillespieSSA/R/ssa.R
GillespieSSA/R/ssa.check.method.R
GillespieSSA/R/ssa.otl.diag.R
GillespieSSA/R/ssa.etl.R
GillespieSSA/R/ssa.plot.R
GillespieSSA/R/ssa.d.R
GillespieSSA/R/ssa.check.args.R
GillespieSSA/R/ssa.otl.R
GillespieSSA/R/ssa.btl.R
GillespieSSA/R/ssa.nutiling.R
GillespieSSA/MD5
GillespieSSA/DESCRIPTION
GillespieSSA/man
GillespieSSA/man/ssa.plot.Rd
GillespieSSA/man/ssa.d.diag.Rd
GillespieSSA/man/ssa.Rd
GillespieSSA/man/ssa.etl.Rd
GillespieSSA/man/ssa.check.args.Rd
GillespieSSA/man/ssa.nutiling.Rd
GillespieSSA/man/ssa.d.Rd
GillespieSSA/man/ssa.btl.diag.Rd
GillespieSSA/man/ssa.run.Rd
GillespieSSA/man/ssa.terminate.Rd
GillespieSSA/man/ssa.btl.Rd
GillespieSSA/man/ssa.otl.diag.Rd
GillespieSSA/man/ssa.check.method.Rd
GillespieSSA/man/ssa.otl.Rd
GillespieSSA/man/ssa.etl.diag.Rd
GillespieSSA/man/GillespieSSA-package.Rd