Last chance! 50% off unlimited learning
Sale ends in
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.
The stochastic simulation algorithm (SSA) is a procedure for constructing
simulated trajectories of finite populations in continuous time.
If
Reactions are single instantaneous events changing at least one of the populations (e.g. birth, death, movement, collision, predation, infection, etc). These cause the state of the system to change over time.
The SSA procedure samples the time
Each reaction
ssa()
: The main entry point for running an SSA simulation.
plot_ssa()
: A standard visualisation for generating an overview plot fo the output.
ssa_exact()
, ssa_etl()
, ssa_btl()
: Different SSA algorithms.
ode_em()
: An ODE algorithm.
compile_reactions()
: A function for precompiling the reactions.
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()
).
ssa()
for more explanation on how to use GillespieSSA2