creates Objective functions from ingredients

the returned objective function has only one argument: the ABC variables that shall be mapped to ODE-model parameters.

Usage

makeObjective(experiments, simulate, distance = defaultDistance)

Arguments

experiments

a list of simulation experiments

simulate

closure that simulates the model

distance

a function that calculates ABC scores (distance between data and simulations)

Value

an objective function

Details

The user supplied distance function should accept three arguments: distance(SIM, DATA, STDV), all three matrices. SIM is the model output (simulation), DATA is the measured data, while STDV represents the standard error of that measurement. All three have the same size: N×M, where N is the number of observables (outputs), and M is th enumber of measurement time-points (length of the time-series).

Examples

# \donttest{
  f <- uqsa_example("AKAR4")
  m <- model_from_tsv(f)
  o <- as_ode(m)
  ex <- experiments(m,o)
  C <- generate_code(o)
  c_path(o) <- write_c_code(C)
#> Writing file: /tmp/RtmphJ6fjy/adf9204aaf2748b8/AKAR4.c
  so_path(o) <- shlib(o)
  s <- simulator.c(ex,o)
  objFunc <- makeObjective(ex,s)
  print(objFunc(values(m$Parameter)))
#> Warning: In 'Ops' : non-'errors' operand automatically coerced to an 'errors' object with no uncertainty
#>             [,1]
#> 400nM 0.16439580
#> 100nM 0.13721115
#> 25nM  0.09171478
# }