amici.pandas

Pandas Wrappers

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

Functions Summary

constructEdataFromDataFrame(df, model, condition)

Constructs an ExpData instance according to the provided Model and DataFrame.

getDataObservablesAsDataFrame(model, edata_list)

Write Observables from experimental data as DataFrame.

getEdataFromDataFrame(model, df[, by_id])

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

getResidualsAsDataFrame(model, edata_list, …)

Convert a list of ExpData to pandas DataFrame.

getSimulationObservablesAsDataFrame(model, …)

Write Observables from simulation results as DataFrame.

getSimulationStatesAsDataFrame(model, …[, …])

Compute model residuals according to lists of ReturnData and ExpData.

Functions

amici.pandas.constructEdataFromDataFrame(df, model, condition, by_id=False)[source]

Constructs an ExpData instance according to the provided Model and DataFrame.

Parameters
  • df (pandas.core.frame.DataFrame) – pd.DataFrame with Observable Names/Ids as columns. Standard deviations may be specified by appending ‘_std’ as suffix.

  • model (typing.Union[amici.amici.ModelPtr, amici.amici.Model]) – Model instance.

  • condition (pandas.core.series.Series) – pd.Series with FixedParameter Names/Ids as columns. Preequilibration conditions may be specified by appending ‘_preeq’ as suffix. Presimulation conditions may be specified by appending ‘_presim’ as suffix.

  • by_id (typing.Optional[bool]) –

    Indicate whether in the arguments, column headers are based on ids or

    names. This should correspond to the way df and condition was created in the first place.

Return type

amici.amici.ExpData

Returns

ExpData instance.

amici.pandas.getDataObservablesAsDataFrame(model, edata_list, by_id=False)[source]

Write Observables from experimental data as DataFrame.

Parameters
Return type

pandas.core.frame.DataFrame

Returns

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

amici.pandas.getEdataFromDataFrame(model, df, by_id=False)[source]

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 (typing.Union[amici.amici.ModelPtr, amici.amici.Model]) – Model instance.

  • by_id (typing.Optional[bool]) – 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

typing.List[amici.amici.ExpData]

Returns

list of ExpData instances.

amici.pandas.getResidualsAsDataFrame(model, edata_list, rdata_list, by_id=False)[source]

Convert a list of ExpData to pandas DataFrame.

Parameters
Return type

pandas.core.frame.DataFrame

Returns

pandas DataFrame with conditions and observables.

amici.pandas.getSimulationObservablesAsDataFrame(model, edata_list, rdata_list, by_id=False)[source]

Write Observables from simulation results as DataFrame.

Parameters
Return type

pandas.core.frame.DataFrame

Returns

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

amici.pandas.getSimulationStatesAsDataFrame(model, edata_list, rdata_list, by_id=False)[source]

Compute model residuals according to lists of ReturnData and ExpData.

Parameters
Return type

pandas.core.frame.DataFrame

Returns

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