leaspy.io.data.data
.Data
- class Data
Bases:
object
Main data container, initialized from a csv file or a
pandas.DataFrame
.Methods
from_csv_file
(path, **kws)Create a Data object from a CSV file.
from_dataframe
(df, **kws)Create a Data object from a
pandas.DataFrame
.from_individuals
(indices, timepoints, ...)Create a Data class object from lists of ID, timepoints and the corresponding values.
get_by_idx
(idx)Get the
IndividualData
of a an individual identified by its ID.load_cofactors
(df, *[, cofactors])Load cofactors from a pandas.DataFrame to the Data object
to_dataframe
(*[, cofactors])Return the subjects' observations in a
pandas.DataFrame
along their ID and ages at all visits.- static from_csv_file(path: str, **kws)
Create a Data object from a CSV file.
- Parameters
- pathstr
Path to the CSV file to load (with extension)
- **kws
Keyword arguments that are sent to
CSVDataReader
- Returns
- static from_dataframe(df: DataFrame, **kws)
Create a Data object from a
pandas.DataFrame
.- Parameters
- df
pandas.DataFrame
Dataframe containing ID, TIME and features.
- **kws
Keyword arguments that are sent to
DataframeDataReader
- df
- Returns
- Data
- static from_individuals(indices: List[str], timepoints: List[List], values: List[List], headers: List[str])
Create a Data class object from lists of ID, timepoints and the corresponding values.
- Parameters
- indiceslist[str]
Contains the individuals’ ID.
- timepointslist[array-like 1D]
For each individual
i
, list of ages at visits. Number of timepoints is referred below asn_timepoints_i
- valueslist[array-like 2D]
For each individual
i
, all values at visits. Shape is(n_timepoints_i, n_features)
.- headerslist[str]
Contains the features’ names.
- Returns
- Data
Data class object with all ID, timepoints, values and features’ names.
- get_by_idx(idx: str)
Get the
IndividualData
of a an individual identified by its ID.- Parameters
- idxIDType
The identifier of the patient you want to get the individual data.
- Returns
- load_cofactors(df: DataFrame, *, cofactors: Optional[List[str]] = None)
Load cofactors from a pandas.DataFrame to the Data object
- Parameters
- df
pandas.DataFrame
The dataframe where the cofactors are stored. Its index should be ID, the identifier of subjects and it should uniquely index the dataframe (i.e. one row per individual).
- cofactorslist[str] or None (default)
Names of the column(s) of df which shall be loaded as cofactors. If None, all the columns from the input dataframe will be loaded as cofactors.
- df
- Raises
- to_dataframe(*, cofactors=None)
Return the subjects’ observations in a
pandas.DataFrame
along their ID and ages at all visits.- Parameters
- cofactorslist[str], ‘all’, or None (default None)
Contains the cofactors’ names to be included in the DataFrame. If None (default), no cofactors are returned. If “all”, all the available cofactors are returned.
- Returns
pandas.DataFrame
Contains the subjects’ ID, age and scores (optional - and cofactors) for each timepoint.
- Raises