Make Poisson Time-Step (PTS) Sampler for a SPN Model — step_PTS

Make a function closure to implement a Poisson time-step (tau-leaping with fixed tau) sampler for a SPN.

Usage

step_PTS_decoupled(S, Sout, haz, dt = 0.01, maxhaz = 1e+06, human_ode = "SIS")

Arguments

S: a stoichiometry Matrix-class object
Sout: an optional matrix to track of event firings
haz: a list of hazard functions
dt: time-step for tau-leap method
maxhaz: maximum allowable hazard
human_ode: ode used for human states

Value

function closure for use in sim_trajectory_R or sim_trajectory_CSV

Details

This sampling algorithm is based on representing a SPN as a set of competing Poisson processes; it thus uses an integer valued state space but approximates the number of events over dt.

The design of step_PTS is from: Wilkinson, D. J. (2011). Stochastic modeling for systems biology. CRC press

Elements of the N list come from two places: The stoichiometry matrix (S) is generated in spn_S and the hazards (h) come from spn_hazards.

For other samplers, see: step_CLE, step_DM, step_ODE