Exports a model structure with associated parameterization variant

exportVariant_IQRmodel.Rd

IQR Tools allows to store IQRmodels with a certain parameterization in a folder. Such a folder is allowed to contain the general structural model as model.txt file and several csv files that contain model parameterizations in terms of state initial conditions and parameter values. The format of these CSV files is: Column names: NAME, TYPE, INFO, VALUE NAME: Name of the parameter or state in the model. Note, not all parameters or states need to appear. This function here will export all though. But for import only selected elements can be present. TYPE: "State" or "Parameter" INFO: The comment in the IQRmodel for the respective element. "NA" is not present VALUE: The value of the respective element - always numeric A special case with more than one VALUE column is possible and will be used to handle multiple similar parameterizations - e.g. for virtual patients under a same condition.

exportVariant_IQRmodel(
  model,
  pathname,
  parameters = NULL,
  FLAGss = TRUE,
  comment = NULL,
  variantname = "default",
  timeSS = 10000,
  opt_abstol = 1e-06,
  opt_reltol = 1e-06
)

Arguments

model

An IQRmodel with a parameterization of interest

pathname

The pathname to which to export model and parameterization

parameters

Named numeric vector with parameter definitions that are applied to the model before exporting the parameterization variant.

FLAGss

Logical. If TRUE then the parameterization that is saved will correspond to the steady state of the model. Otherwise the models parameterization and ICs will be stored as defined in the model. Steady-state computation is conducted by simulation.

comment

A comment about the parameterization can be provided and will be stored in a separate file as the parameterization - using the same name but with .info attached. File will be only written if a comment is provided.

variantname

The name of the parameterization variant to be stored. The name will be used as a filename with special characters removed and .csv appended.

timeSS

The time to be used to simulate to steady-state (if desired by setting FLAGss to TRUE)

opt_abstol

The absolute integrator tolerance for ss stimulation

opt_reltol

The relative integrator tolerance for ss stimulation

See also

Other IQRmodel: IQRmodel(), addOutputs_IQRmodel(), addRelations_IQRmodel(), createSimIQRmodelSpec(), exportSBML_IQRmodel(), export_IQRmodel(), getPars_IQRmodel(), hasCcodeFunctions_IQRmodel(), hasInitialAssignments_IQRmodel(), importSBML_IQRmodel(), importVariant_IQRmodel(), is_IQRmodel(), new_IQRmodel(), print.IQRmodel(), print.IQRsensitivity(), regenerate_IQRmodel(), replaceTerms_IQRmodel(), sensitivity_IQRmodel(), setParameters_IQRmodel(), setPars_IQRmodel(), sim_IQRmodel(), sim_IQRmodel_strict(), simbio_CSV2namedVector(), simbio_updateParamIC_IQRmodel(), stoichiometry_IQRmodel(), strReplace_IQRmodel()

Other QSP: IQRsysEst(), IQRsysModel(), IQRsysProject(), addOutputs_IQRmodel(), addRelations_IQRmodel(), as_IQRsysEst(), as_IQRsysProject(), as_IQRsysProjectMulti(), comparePars_IQRsysModel(), duplicate_IQRsysProject(), 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_IQRsysProject(), is_IQRsysProjectMulti(), 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_IQRsysProject(), run_IQRsysProjectMulti(), sample_IQRsysModel(), sensitivity_IQRmodel(), setPars_IQRsysModel(), sim_IQRsysModel(), sim_IQRvirtualSubjects(), simbio_CSV2namedVector(), simbio_updateParamIC_IQRmodel(), spmIIV_IQRsysProject(), spm_IQRsysProject(), switchOpt_IQRsysModel(), tablePars_IQRsysModel()