Function that creates a closure that simulates a stochastic trajectory with the Gillespie algorithm given certain experimental conditions and a parameter vector, and computes the distance between the simulation and the experimental data
simulator.stoch.RdFunction that creates a closure that simulates a stochastic trajectory with the Gillespie algorithm given certain experimental conditions and a parameter vector, and computes the distance between the simulation and the experimental data
Usage
simulator.stoch(
experiments,
model.tab = model.tab,
reactions = NULL,
parMap = identity,
outputFunction = function(t, state, param) {
state
},
vol = 4e-16,
unit = 1e-06,
nStochSim = 3,
distance = NULL
)Arguments
- experiments
a list of experiment.
- model.tab
an SBtab model.
- reactions
a list of GillespieSSA2 reactions.
- parMap
a function that translates ABC variables (parABC) into something the model will accept.
- outputFunction
a function that, given (t,state,param), outputs the quantity that is measured in the experiments (e.g., the outputFunction may output the concentration of one of the compounds in the system).
- vol
Volume in which the reactions take place.
- unit
unit of measure for the volume (it converts the volume into liters).
- nStochSim
number of stochastic simulations to average over.
- distance
(optional) function that computes the distance between experimental data and simulated data. Default value is NULL.