petab.observables

Functions for working with the PEtab observables table

Functions

create_observable_df()	Create empty observable dataframe
get_formula_placeholders(formula_string, ...)	Get placeholder variables in noise or observable definition for the given observable ID.
get_observable_df(observable_file)	Read the provided observable file into a pandas.Dataframe.
get_output_parameters(observable_df, model)	Get output parameters
get_placeholders(observable_df[, ...])	Get all placeholder parameters from observable table observableFormulas and noiseFormulas
write_observable_df(df, filename)	Write PEtab observable table

petab.observables.create_observable_df() → DataFrame

Create empty observable dataframe

Returns:

Created DataFrame

petab.observables.get_formula_placeholders(formula_string: str, observable_id: str, override_type: Literal['observable', 'noise']) → List[str]

Get placeholder variables in noise or observable definition for the given observable ID.

Parameters:

• formula_string – observable formula

• observable_id – ID of current observable

• override_type – 'observable' or 'noise', depending on whether formula is for observable or for noise model

Returns:

List of placeholder parameter IDs in the order expected in the observableParameter column of the measurement table.

petab.observables.get_observable_df(observable_file: str | DataFrame | Path | None) → DataFrame | None

Read the provided observable file into a pandas.Dataframe.

Parameters:

observable_file – Name of the file to read from or pandas.Dataframe.

Returns:

Observable DataFrame

petab.observables.get_output_parameters(observable_df: DataFrame, model: Model, observables: bool = True, noise: bool = True, mapping_df: DataFrame | None = None) → List[str]

Get output parameters

Returns IDs of parameters used in observable and noise formulas that are not defined in the model.

Parameters:

• observable_df – PEtab observable table

• model – The underlying model

• observables – Include parameters from observableFormulas

• noise – Include parameters from noiseFormulas

• mapping_df – PEtab mapping table

Returns:

List of output parameter IDs

petab.observables.get_placeholders(observable_df: DataFrame, observables: bool = True, noise: bool = True) → List[str]

Get all placeholder parameters from observable table observableFormulas and noiseFormulas

Parameters:

• observable_df – PEtab observable table

• observables – Include parameters from observableFormulas

• noise – Include parameters from noiseFormulas

Returns:

List of placeholder parameters from observable table observableFormulas and noiseFormulas.

petab.observables.write_observable_df(df: DataFrame, filename: str | Path) → None

Write PEtab observable table

Parameters:

• df – PEtab observable table

• filename – Destination file name