petab.v1.observables
Functions for working with the PEtab observables table
Functions
Create empty observable dataframe |
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Get placeholder variables in noise or observable definition for the given observable ID. |
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Read the provided observable file into a |
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Get output parameters |
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Get all placeholder parameters from observable table observableFormulas and noiseFormulas |
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Write PEtab observable table |
- petab.v1.observables.create_observable_df() DataFrame [source]
Create empty observable dataframe
- Returns:
Created DataFrame
- petab.v1.observables.get_formula_placeholders(formula_string: str, observable_id: str, override_type: Literal['observable', 'noise']) list[str] [source]
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 whetherformula
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.v1.observables.get_observable_df(observable_file: str | DataFrame | Path | None) DataFrame | None [source]
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.v1.observables.get_output_parameters(observable_df: DataFrame, model: Model, observables: bool = True, noise: bool = True, mapping_df: DataFrame | None = None) list[str] [source]
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.v1.observables.get_placeholders(observable_df: DataFrame, observables: bool = True, noise: bool = True) list[str] [source]
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.