amici.petab_simulate

PEtab Simulate

Functionality related to the use of AMICI for simulation with PEtab’s Simulator class.

Use cases:

• generate data for use with PEtab’s plotting methods

• generate synthetic data

Classes

PetabSimulator(*args[, amici_model])

Implementation of the PEtab Simulator class that uses AMICI.

class amici.petab_simulate.PetabSimulator(*args, amici_model=None, **kwargs)

Implementation of the PEtab Simulator class that uses AMICI.

simulate_without_noise(**kwargs)

See petab.simulate.Simulator.simulate() docstring.

Additional keyword arguments can be supplied to specify arguments for the AMICI PEtab import, simulate, and export methods. See the docstrings for the respective methods for argument options: - amici.petab_import.import_petab_problem(), and - amici.petab_objective.simulate_petab().

Note that some arguments are expected to have already been specified in the Simulator constructor (including the PEtab problem).

Return type

pandas.core.frame.DataFrame