amici.petab_simulate.PetabSimulator
- class amici.petab_simulate.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.
Methods Summary
__init__
(*args[, amici_model])Initialize the simulator.
add_noise
(simulation_df[, noise_scaling_factor])Add noise to simulated data.
remove_working_dir
([force])Remove the simulator working directory, and all files within.
simulate
([noise, noise_scaling_factor])Simulate a PEtab problem, optionally with noise.
simulate_without_noise
(**kwargs)See
petab.simulate.Simulator.simulate()
docstring.Methods
- __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 __init__ method arguments.
- simulate(noise=False, noise_scaling_factor=1, **kwargs)
Simulate a PEtab problem, optionally with noise.
- Parameters
- 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