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Function that creates the objective function

makeObjectiveSSA.Rd

Given a parameter set, this function computes the distance between experimental data and simulated data (coresponding to the parameter in input).

Usage

makeObjectiveSSA(
  experiments,
  model,
  parNames,
  distance,
  parMap = identity,
  Phi,
  reactions,
  nStochSim = 1,
  parameters_from_expressions = NULL
)

Arguments

experiments

a list of experiments

parNames

the names of the (biological) parameters of the model

distance

a user supplied function that calculates a distance between simulation and data with an interface of distance(simulation, data, errVal), where errVal is an estimate of the measuremnet noise (e.g. standard deviation), if needed by the function.

parMap

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

Phi

Volume

reactions

a list that encodes the reactions for GillespieSSA2

nStochSim

number of stochastic simulations to average over

Value

a closure for the objective function that implicitly depends on all of the arguments to this function but explicitly only on the ABC parameters parABC.