step_DM {MGDrivE2} | R Documentation |
Make Gillespie's Direct Method (DM) Sampler for a SPN model
Description
Make a function closure to implement Gillespie's Direct Method sampler for a SPN.
Usage
step_DM(S, Sout, haz, maxhaz = 1e+06)
Arguments
S |
a stoichiometry |
Sout |
an optional matrix to track of event firings |
haz |
a list of hazard functions |
maxhaz |
maximum allowable hazard |
Details
The direct method is an exact sampling algorithm; it simulates each event individually. Because of this it may be extremely slow for non-trivial population sizes, and thus should be used to debug and test rather than for serious Monte Carlo simulation.
The design of step_DM
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_PTS
, step_ODE
Value
function closure for use in sim_trajectory_R
or sim_trajectory_CSV