Function that creates the objective function
makeObjectiveSSA.RdGiven a parameter set, this function computes the distance between experimental data and simulated data (coresponding to the parameter in input).
Usage
makeObjectiveSSA(
experiments,
model.tab,
parNames,
distance,
parMap = identity,
outputFunction = identity,
vol = 4e-16,
unit = 1e-06,
reactions,
nStochSim = 1
)Arguments
- experiments
a list of experiments.
- model.tab
an SBtab model.
- 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 measurement noise (e.g. standard deviation), if needed by the function.
- 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).
- reactions
a list of GillespieSSA2 reactions
- nStochSim
number of stochastic simulations to average over.