parpe.hdf5_pe_input¶

Functions for generating parPE parameter estimation HDF5 input files

Functions

`main`()	Generate HDF5 file based on CLI options
`parse_cli_args`()	Parse command line arguments
`requires_preequilibration`(measurement_df)	rtype: `bool`
`write_optimization_options`(f)	Create groups and write some default optimization settings
`write_parameter_map`(f, mapping_matrix, ...)	Write parameter mapping

Classes

HDF5DataGenerator(petab_problem, amici_model)

Generate HDF5 file with fixed parameters and measurements for an AMICI-imported SBML model based on a PEtab problem.

Functions

parpe.hdf5_pe_input.main()[source]¶: Generate HDF5 file based on CLI options

parpe.hdf5_pe_input.requires_preequilibration(measurement_df)[source]¶

parpe.hdf5_pe_input.write_optimization_options(f)[source]¶

Create groups and write some default optimization settings

parpe.hdf5_pe_input.write_parameter_map(f, mapping_matrix, override_matrix, num_model_parameters, compression=None)[source]¶

Write parameter mapping

parPE