petab.core¶

PEtab core functions (or functions that don’t fit anywhere else)

Functions

`flatten_timepoint_specific_output_overrides`(…)	Flatten timepoint-specific output parameter overrides.
`get_notnull_columns`(df, candidates)	Return list of `df`-columns in `candidates` which are not all null/nan.
`get_observable_id`(parameter_id)	Get PEtab observable ID from PEtab-style sigma or observable AssignmentRule-target `parameter_id`.
`parameter_is_offset_parameter`(parameter, formula)	Check if is offset parameter.
`parameter_is_scaling_parameter`(parameter, …)	Check if is scaling parameter.

petab.core.flatten_timepoint_specific_output_overrides(petab_problem: petab.problem.Problem) → None¶

Flatten timepoint-specific output parameter overrides.

If the PEtab problem definition has timepoint-specific observableParameters or noiseParameters for the same observable, replace those by replicating the respective observable.

This is a helper function for some tools which may not support such timepoint-specific mappings. The measurement table is modified in place.

Parameters:	petab_problem – PEtab problem to work on

petab.core.get_notnull_columns(df: pandas.core.frame.DataFrame, candidates: Iterable[T_co])¶

Return list of df-columns in candidates which are not all null/nan.

The output can e.g. be used as input for pandas.DataFrame.groupby.

Parameters:	df – Dataframe candidates – Columns of `df` to consider

petab.core.get_observable_id(parameter_id: str) → str¶

Get PEtab observable ID from PEtab-style sigma or observable AssignmentRule-target parameter_id.

e.g. for ‘observable_obs1’ -> ‘obs1’, for ‘sigma_obs1’ -> ‘obs1’

Parameters:	parameter_id – Some parameter ID
Returns:	Observable ID

petab.core.parameter_is_offset_parameter(parameter: str, formula: str) → bool¶

Check if is offset parameter.

Parameters:	parameter – Some identifier. formula – Some sympy-compatible formula.
Returns:	`True` if parameter `parameter` is an offset parameter with positive sign in formula `formula`.

petab.core.parameter_is_scaling_parameter(parameter: str, formula: str) → bool¶

Check if is scaling parameter.

Parameters:

parameter – Some identifier.
formula – Some sympy-compatible formula.

Returns:

True if parameter parameter is a scaling parameter in formula: formula.