amici.pandas

Pandas Wrappers

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

Functions

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 ReturnData and ExpData to pandas DataFrame with residuals.

getSimulationObservablesAsDataFrame(model, ...)

Write Observables from simulation results as DataFrame.

getSimulationStatesAsDataFrame(model, ...[, ...])

Get model state according to lists of ReturnData and ExpData.

get_expressions_as_dataframe(model, ...[, by_id])

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

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:

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 ReturnData and ExpData to pandas DataFrame with residuals.

Parameters:
Return type:

pandas.core.frame.DataFrame

Returns:

pandas DataFrame with conditions and residuals.

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 observables as columns.

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

Get model state according to lists of ReturnData and ExpData.

Parameters:
Return type:

pandas.core.frame.DataFrame

Returns:

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

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

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

Parameters:
Return type:

pandas.core.frame.DataFrame

Returns:

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