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

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

Usage

simulator.stoch(
  experiment,
  model.tab = model.tab,
  reactions = NULL,
  parMap = identity,
  vol = 4e-16,
  unit = 1e-06,
  nStochSim = 3
)

Arguments

experiment

an experiment

model.tab

an SBtab model

reactions

a list that encodes the reactions for GillespieSSA2

parMap

a function that translates ABC variables (parABC) into something the model will accept.

vol

Volume in which the reactions take place

unit

unit of measure (1e-6 corresponds to micrometer)

nStochSim

number of stochastic simulations to average over

Value

a function that given a parameter returns a simulated trajectory obrained via the Gillespie algorithm