amici.pandas

Pandas Wrappers

This module contains convenience wrappers that allow for easy interconversion between C++ objects from amici.amici and pandas DataFrames

Functions

construct_edata_from_data_frame(df, model, ...)	Constructs an ExpData instance according to the provided Model and DataFrame.
get_data_observables_as_data_frame(model, ...)	Write Observables from experimental data as DataFrame.
get_edata_from_data_frame(model, df[, by_id])	Constructs a ExpData instances according to the provided Model and DataFrame.
get_expressions_as_dataframe(model, ...[, by_id])	Get values of model expressions from lists of ReturnData as DataFrame.
get_residuals_as_data_frame(model, ...[, by_id])	Convert a list of ReturnData and ExpData to pandas DataFrame with residuals.
get_simulation_observables_as_data_frame(...)	Write Observables from simulation results as DataFrame.
get_simulation_states_as_data_frame(model, ...)	Get model state according to lists of ReturnData and ExpData.

amici.pandas.get_data_observables_as_data_frame(model, edata_list, by_id=False)

Write Observables from experimental data as DataFrame.

Parameters:

• model (amici.amici.ModelPtr | amici.amici.Model) – Model instance.

• edata_list (list[amici.amici.ExpData] | list[amici.amici.ExpDataPtr] | amici.amici.ExpData | amici.amici.ExpDataPtr) – list of ExpData instances with experimental data. May also be a single ExpData instance.

• by_id (bool | None) – If True, uses observable ids as column names in the generated DataFrame, otherwise the possibly more descriptive observable names are used.

Return type:

pandas.core.frame.DataFrame

Returns:

pandas DataFrame with conditions/timepoints as rows and observables as columns.

amici.pandas.get_edata_from_data_frame(model, df, by_id=False)

Constructs a ExpData instances according to the provided Model and DataFrame.

Parameters:

• df (pandas.core.frame.DataFrame) – dataframe with Observable Names/Ids, FixedParameter Names/Ids and time as columns. Standard deviations may be specified by appending ‘_std’ as suffix. Preequilibration fixedParameters may be specified by appending ‘_preeq’ as suffix. Presimulation fixedParameters may be specified by appending ‘_presim’ as suffix. Presimulation time may be specified as ‘t_presim’ column.

• model (amici.amici.ModelPtr | amici.amici.Model) – Model instance.

• by_id (bool | None) – Whether the column names in df are based on ids or names, corresponding to how the dataframe was created in the first place.

Return type:

list[amici.amici.ExpData]

Returns:

list of ExpData instances.

amici.pandas.get_expressions_as_dataframe(model, edata_list, rdata_list, by_id=False)

Get values of model expressions from lists of ReturnData as DataFrame.

Parameters:

• model (amici.amici.Model) – Model instance.

• edata_list (list[amici.amici.ExpData] | list[amici.amici.ExpDataPtr] | amici.amici.ExpData | amici.amici.ExpDataPtr) – list of ExpData instances with experimental data. May also be a single ExpData instance.

• rdata_list (list[amici.numpy.ReturnDataView] | amici.numpy.ReturnDataView) – list of ReturnData instances corresponding to ExpData. May also be a single ReturnData instance.

• by_id (bool | None) – If True, ids are used as identifiers, otherwise the possibly more descriptive names.

Return type:

pandas.core.frame.DataFrame

Returns:

pandas DataFrame with conditions/timepoints as rows and model expressions as columns.

amici.pandas.get_residuals_as_data_frame(model, edata_list, rdata_list, by_id=False)

Convert a list of ReturnData and ExpData to pandas DataFrame with residuals.

Parameters:

• model (amici.amici.Model) – Model instance.

• edata_list (list[amici.amici.ExpData] | list[amici.amici.ExpDataPtr] | amici.amici.ExpData | amici.amici.ExpDataPtr) – list of ExpData instances with experimental data. May also be a single ExpData instance.

• rdata_list (list[amici.numpy.ReturnDataView] | amici.numpy.ReturnDataView) – list of ReturnData instances corresponding to ExpData. May also be a single ReturnData instance.

• by_id (bool | None) – bool, optional (default = False) If True, ids are used as identifiers, otherwise the possibly more descriptive names.

Return type:

pandas.core.frame.DataFrame

Returns:

pandas DataFrame with conditions and residuals.

amici.pandas.get_simulation_observables_as_data_frame(model, edata_list, rdata_list, by_id=False)

Write Observables from simulation results as DataFrame.

Parameters:

• model (amici.amici.Model) – Model instance.

• edata_list (list[amici.amici.ExpData] | list[amici.amici.ExpDataPtr] | amici.amici.ExpData | amici.amici.ExpDataPtr) – list of ExpData instances with experimental data. May also be a single ExpData instance.

• rdata_list (list[amici.numpy.ReturnDataView] | amici.numpy.ReturnDataView) – list of ReturnData instances corresponding to ExpData. May also be a single ReturnData instance.

• by_id (bool | None) – If True, ids are used as identifiers, otherwise the possibly more descriptive names.

Return type:

pandas.core.frame.DataFrame

Returns:

pandas DataFrame with conditions/timepoints as rows and observables as columns.

amici.pandas.get_simulation_states_as_data_frame(model, edata_list, rdata_list, by_id=False)

Get model state according to lists of ReturnData and ExpData.

Parameters:

• model (amici.amici.Model) – Model instance.

• edata_list (list[amici.amici.ExpData] | list[amici.amici.ExpDataPtr] | amici.amici.ExpData | amici.amici.ExpDataPtr) – list of ExpData instances with experimental data. May also be a single ExpData instance.

• rdata_list (list[amici.numpy.ReturnDataView] | amici.numpy.ReturnDataView) – list of ReturnData instances corresponding to ExpData. May also be a single ReturnData instance.

• by_id (bool | None) – If True, ids are used as identifiers, otherwise the possibly more descriptive names.

Return type:

pandas.core.frame.DataFrame

Returns:

pandas DataFrame with conditions/timepoints as rows and state variables as columns.