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1. Raue, Bioinformatics 31(21), 2015↩︎

2. Kaschek, dMod, 2016 (https://cran.r-project.org/package=dMod)↩︎

Simulate IQRsysModel

sim_IQRsysModel.Rd

Allow the simulation of an IQRsysModel for user defined settings. Note that the IQRsysModel object is optimized for parameter estimation purposes. As such it is not intended to simulate user desired dosing schedules - but only the dosing schedules that are defined in the dataset to be used for estimation. As such the main model settings that can be accessed in sim_IQRsysModel() are the model parameters to allow the user to play with parameter values - for a sensitivity analysis or to manually modify parameters in the search for reasonable initial guesses. The output of sim_IQRsysModel() is an IQRsysModel with updated parameters (if changed) and updated predictions list field that contains the simulations. Results can be displayed using plot_IQRsysModel().

sim_IQRsysModel(
  sysModel,
  simtime = NULL,
  parameters = NULL,
  FLAGoutputsOnly = TRUE,
  FLAGverbose = FALSE,
  SIMOPT.method = NULL,
  SIMOPT.atol = NULL,
  SIMOPT.rtol = NULL,
  SIMOPT.hmin = NULL,
  SIMOPT.hmax = NULL,
  SIMOPT.hini = NULL,
  SIMOPT.maxsteps = NULL,
  SIMOPT.nauxtimes = NULL
)

Arguments

sysModel

IQRsysModel object.

simtime

numeric vector of desired simulation times.

parameters

named vector of parameter values. Any parameter which is not explicitly provided is set according to the model parameters (see output of getPars_IQRsysModel).

FLAGoutputsOnly

by default, only outputs are returned. If FALSE, ODE states and outputs are returned.

FLAGverbose

Logical. Print parameters table to console?

SIMOPT.method

character denoting the integration method, e.g. "lsodes" (default), "lsoda" See the deSolve package for a list of available integrators

SIMOPT.atol

numeric, absolute error tolerance

SIMOPT.rtol

numeric, relative error tolerance

SIMOPT.hmin

numeric, minimal integration step size

SIMOPT.hmax

numeric, maximal integration step size

SIMOPT.hini

numeric, initial integration step size

SIMOPT.maxsteps

numeric, maximum number of integration steps

SIMOPT.nauxtimes

additional times to simulate the prediction function

Value

The simulation is added to sysModel as list entry prediction and sysModel is returned.

See also

Other QSP: IQRsysEst(), IQRsysModel(), IQRsysProject(), addOutputs_IQRmodel(), addRelations_IQRmodel(), as_IQRsysEst(), as_IQRsysProjectMulti(), as_IQRsysProject(), comparePars_IQRsysModel(), duplicate_IQRsysProject(), exportVariant_IQRmodel(), exportVirtualSubjects_IQRnlmeProject(), export_IQRsysData(), getDosing_IQRsysModel(), getEmpiricalETACovarianceMatrix_IQRsysProject(), getOptTrace_IQRsysProject(), getPars_IQRoptTrace(), getPars_IQRsysModel(), getPrediction_IQRsysModel(), hasrun_IQRsysProject(), importVariant_IQRmodel(), import_IQRsysData(), is_IQRsysEst(), is_IQRsysModel(), is_IQRsysProjectMulti(), is_IQRsysProject(), load_IQRsysProject(), modelSpec_IQRsysEst(), model_IQRsysModel(), offsetTIME_IQRsysData(), plotDVPRED_IQRsysModel(), plotFit_IQRsysModel(), plotPars_IQRsysModel(), plotPred_IQRsysModel(), plotProfile_IQRsysModel(), plotWRES_IQRsysModel(), plotWaterfall_IQRsysModel(), plot_IQRoptTrace(), plot_IQRsysModel(), print.IQRsensitivity(), print.IQRsysProject(), profile_IQRsysModel(), replaceTerms_IQRmodel(), run_IQRsysProjectMulti(), run_IQRsysProject(), sample_IQRsysModel(), sensitivity_IQRmodel(), setPars_IQRsysModel(), sim_IQRvirtualSubjects(), simbio_CSV2namedVector(), simbio_updateParamIC_IQRmodel(), spmIIV_IQRsysProject(), spm_IQRsysProject(), switchOpt_IQRsysModel(), tablePars_IQRsysModel()

Author

Daniel Kaschek, IntiQuan GmbH