amici.petab.simulator
PEtab Simulator
Functionality related to the use of AMICI for simulation with petab.Simulator
.
Use cases:
generate data for use with PEtab’s plotting methods
generate synthetic data
Classes
|
Implementation of the PEtab Simulator class that uses AMICI. |
- class amici.petab.simulator.PetabSimulator(*args, amici_model=None, **kwargs)[source]
Implementation of the PEtab Simulator class that uses AMICI.
- __init__(*args, amici_model=None, **kwargs)[source]
Initialize the simulator.
Initialize the simulator with sufficient information to perform a simulation. If no working directory is specified, a temporary one is created.
- Parameters:
petab_problem – A PEtab problem.
working_dir – All simulator-specific output files will be saved here. This directory and its contents may be modified and deleted, and should be considered ephemeral.
- add_noise(simulation_df, noise_scaling_factor=1, **kwargs)
Add noise to simulated data.
- Parameters:
simulation_df (
pandas.core.frame.DataFrame
) – A PEtab measurements table that contains simulated data.noise_scaling_factor (
float
) – A multiplier of the scale of the noise distribution.**kwargs – Additional keyword arguments are passed to
sample_noise()
.
- Return type:
- Returns:
Simulated data with noise, as a PEtab measurements table.
- remove_working_dir(force=False, **kwargs)
Remove the simulator working directory, and all files within.
See the
petab.simulate.Simulator.__init__()
method arguments.- Parameters:
force (
bool
) – IfTrue
, the working directory is removed regardless of whether it is a temporary directory.**kwargs – Additional keyword arguments are passed to
shutil.rmtree()
.
- Return type:
- simulate(noise=False, noise_scaling_factor=1, as_measurement=False, **kwargs)
Simulate a PEtab problem, optionally with noise.
- Parameters:
noise (
bool
) – If True, noise is added to simulated data.noise_scaling_factor (
float
) – A multiplier of the scale of the noise distribution.as_measurement (
bool
) – Whether the data column is namedpetab.C.MEASUREMENT
(True) orpetab.C.SIMULATION
(False).**kwargs – Additional keyword arguments are passed to
petab.simulate.Simulator.simulate_without_noise()
.
- Return type:
- Returns:
Simulated data, as a PEtab measurements table.
- simulate_without_noise(**kwargs)[source]
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: