GillespieSSA

R package 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.


References in zbMATH (referenced in 10 articles , 1 standard article )

Showing results 1 to 10 of 10.
Sorted by year (citations)

  1. Fernando S. Marques, José H. H. Grisi-Filho, Jean C. R. Silva, Erivânia C. Almeida, José L. Silva Júnior: hybridModels: An R Package for the Stochastic Simulation of Disease Spreading in Dynamic Networks (2020) not zbMATH
  2. Kamara, Abdul A.; Wang, Xiangjun; Mouanguissa, Lagès Nadège: Analytical solution for post-death transmission model of Ebola epidemics (2020)
  3. Alvarez, Robinson F.; Barbuto, José A. M.; Venegeroles, Roberto: A nonlinear mathematical model of cell-mediated immune response for tumor phenotypic heterogeneity (2019)
  4. Alfonso Landeros, Timothy Stutz, Kevin L. Keys, Alexander Alekseyenko, Janet S. Sinsheimer, Kenneth Lange, Mary Sehl: BioSimulator.jl: Stochastic simulation in Julia (2018) arXiv
  5. Simon DW Frost: Gillespie.jl: Stochastic Simulation Algorithm in Julia (2016) not zbMATH
  6. Stefan Widgren, Pavol Bauer, Stefan Engblom: SimInf: An R package for Data-driven Stochastic Disease Spread Simulations (2016) arXiv
  7. Karline Soetaert; Thomas Petzoldt: Inverse Modelling, Sensitivity and Monte Carlo Analysis in R Using Package FME (2010) not zbMATH
  8. zu Dohna, Heinrich; Pineda-Krch, Mario: Fitting parameters of stochastic birth-death models to metapopulation data (2010)
  9. zu Dohna, Heinrich; Pineda-Krch, Mario: Fitting parameters of stochastic birth-death models to metapopulation data (2010)
  10. Mario Pineda-Krch: GillespieSSA: Implementing the Gillespie Stochastic Simulation Algorithm in R (2008) not zbMATH