R/parEstimationLBodeWeighted.R

In saezlab/CellNOpt-Feeder: Integration of CellNOptR to add missing links

# $Id$

parEstimationLBodeWeighted<-function (cnolist, model, method="ga",
                                      ode_parameters = NULL, indices = NULL,
                                      paramsGA=NULL, paramsSSm=NULL)
{
  
  
  if (class(cnolist)=="CNOlist"){cnolist = compatCNOlist(cnolist)}
  if (method == "essm"){
    if (is.null(paramsSSm)){
      paramsSSm = defaultParametersSSm()
    }
    ode_parameters <- 
      parEstimationLBodeSSmWeighted(cnolist, model,
                                    ode_parameters=ode_parameters, 
                                    indices=indices,
                                    maxeval=paramsSSm$maxeval,
                                    maxtime=paramsSSm$maxtime,
                                    ndiverse=paramsSSm$ndiverse,
                                    dim_refset=paramsSSm$dim_refset,
                                    local_solver=paramsSSm$local_solver,
                                    time=paramsSSm$time,
                                    verbose=paramsSSm$verbose,
                                    transfer_function=paramsSSm$transfer_function,
                                    reltol=paramsSSm$reltol,
                                    atol=paramsSSm$atol,
                                    maxStepSize=paramsSSm$maxStepSize,
                                    maxNumSteps=paramsSSm$maxNumSteps,
                                    maxErrTestsFails=paramsSSm$maxErrTestsFails,
                                    nan_fac=paramsSSm$nan_fac,
                                                   
                                                   # added
                                    lambda_tau=paramsSSm$lambda_tau,
                                    lambda_k=paramsSSm$lambda_k,
                                    bootstrap=paramsSSm$bootstrap,
                                    SSpenalty_fac=paramsSSm$SSpenalty_fac,
                                    SScontrolPenalty_fac=paramsSSm$SScontrolPenalty_fac,
                                    boot_seed=paramsSSm$boot_seed
    )
    
    
  }
  else if(method=="ga"){
    if (is.null(paramsGA)){
      paramsGA <- defaultParametersGA()
    }
    ode_parameters < parEstimationLBodeGA(cnolist, model,
                                          ode_parameters=ode_parameters,
                                          indices=indices,
                                          mutationChance=paramsGA$mutationChance,
                                          popSize=paramsGA$popSize,
                                          iters=paramsGA$iters,
                                          elitism=paramsGA$elitism,
                                          time=paramsGA$time,
                                          monitor=paramsGA$monitor,
                                          verbose=paramsGA$verbose,
                                          transfer_function=paramsGA$transfer_function,
                                          reltol=paramsGA$reltol,
                                          atol=paramsGA$atol,
                                          maxStepSize=paramsGA$maxStepSize,
                                          maxNumSteps=paramsGA$maxNumSteps,
                                          maxErrTestsFails=paramsGA$maxErrTestsFails,
                                          nan_fac=paramsGA$nan_fac)
  }
  else{
    stop ("method argument must be either 'ga' or 'essm'." )
  }
  return(ode_parameters)
}