amici.petab.petab_import
PEtab Import
Import a model in the petab
(https://github.com/PEtab-dev/PEtab) format
into AMICI.
Functions
|
Create an AMICI model for a PEtab problem. |
- amici.petab.petab_import.import_petab_problem(petab_problem, model_output_dir=None, model_name=None, compile_=None, non_estimated_parameters_as_constants=True, **kwargs)[source]
Create an AMICI model for a PEtab problem.
- Parameters:
petab_problem (
petab.v1.problem.Problem
) – A petab problem containing all relevant information on the model.model_output_dir (
str
|pathlib.Path
|None
) – Directory to write the model code to. It will be created if it doesn’t exist. Defaults to current directory.model_name (
str
) – Name of the generated model module. Defaults to the ID of the model or the model file name without the extension.compile – If
True
, the model will be compiled. IfFalse
, the model will not be compiled. IfNone
, the model will be compiled if it cannot be imported.non_estimated_parameters_as_constants – Whether parameters marked as non-estimated in PEtab should be considered constant in AMICI. Setting this to
True
will reduce model size and simulation times. If sensitivities with respect to those parameters are required, this should be set toFalse
.kwargs – Additional keyword arguments to be passed to
amici.sbml_import.SbmlImporter.sbml2amici()
oramici.pysb_import.pysb2amici()
, depending on the model type.
- Return type:
- Returns:
The imported model.