scikit-survival 0.26.0__cp314-cp314-macosx_10_15_x86_64.whl

sksurv/datasets/base.py

@@ -0,0 +1,614 @@
+import warnings
+
+import numpy as np
+import pandas as pd
+from pandas.api.types import CategoricalDtype
+
+from ..column import categorical_to_numeric, standardize
+from ..io import loadarff
+from ..util import safe_concat
+
+__all__ = [
+    "get_x_y",
+    "load_arff_files_standardized",
+    "load_aids",
+    "load_bmt",
+    "load_cgvhd",
+    "load_breast_cancer",
+    "load_flchain",
+    "load_gbsg2",
+    "load_whas500",
+    "load_veterans_lung_cancer",
+]
+
+
+def _get_data_path(name):
+    from importlib.resources import files
+
+    return files(__package__) / "data" / name
+
+
+def _get_x_y_survival(dataset, col_event, col_time, val_outcome, competing_risks=False):
+    if col_event is None or col_time is None:
+        y = None
+        x_frame = dataset
+    else:
+        event_type = np.int64 if competing_risks else bool
+        y = np.empty(dtype=[(col_event, event_type), (col_time, np.float64)], shape=dataset.shape[0])
+        if competing_risks:
+            y[col_event] = dataset[col_event].to_numpy()
+        else:
+            y[col_event] = (dataset[col_event] == val_outcome).to_numpy()
+        y[col_time] = dataset[col_time].to_numpy()
+
+        x_frame = dataset.drop([col_event, col_time], axis=1)
+
+    return x_frame, y
+
+
+def _get_x_y_other(dataset, col_label):
+    if col_label is None:
+        y = None
+        x_frame = dataset
+    else:
+        y = dataset.loc[:, col_label]
+        x_frame = dataset.drop(col_label, axis=1)
+
+    return x_frame, y
+
+
+def get_x_y(data_frame, attr_labels, pos_label=None, survival=True, competing_risks=False):
+    """Split data frame into features and labels.
+
+    Parameters
+    ----------
+    data_frame : pandas.DataFrame, shape = (n_samples, n_columns)
+        A data frame.
+
+    attr_labels : sequence of str or None
+        A list of one or more columns that are considered the label.
+        If `survival` is `True`, then attr_labels has two elements:
+        1) the name of the column denoting the event indicator, and
+        2) the name of the column denoting the survival time.
+        If the sequence contains `None`, then labels are not retrieved
+        and only a data frame with features is returned.
+
+    pos_label : any, optional
+        Which value of the event indicator column denotes that a
+        patient experienced an event. This value is ignored if
+        `survival` is `False`.
+
+    survival : bool, optional, default: True
+        Whether to return `y` that can be used for survival analysis.
+
+    competing_risks : bool, optional, default: False
+        Whether `y` refers to competing risks situation. Only used if `survival` is `True`.
+
+    Returns
+    -------
+    X : pandas.DataFrame, shape = (n_samples, n_columns - len(attr_labels))
+        Data frame containing features.
+
+    y : structured array, shape = (n_samples,), or pandas.DataFrame, shape = (n_samples, len(attr_labels)), or None
+        If `survival` is `True`, a structured array with two fields.
+        The first field is a boolean where ``True`` indicates an event and ``False``
+        indicates right-censoring. The second field is a float with the time of
+        event or time of censoring.
+
+        If `survival` is `False` and `attr_labels` not `None`, a :class:`pandas.DataFrame`
+        with columns specified by `attr_labels`.
+
+        If `survival` is `False` and `attr_labels` is `None`, `y` is set to `None`.
+    """
+    if survival:
+        if len(attr_labels) != 2:
+            raise ValueError(f"expected sequence of length two for attr_labels, but got {len(attr_labels)}")
+        if pos_label is None and not competing_risks:
+            raise ValueError("pos_label needs to be specified if survival=True")
+        return _get_x_y_survival(data_frame, attr_labels[0], attr_labels[1], pos_label, competing_risks)
+
+    return _get_x_y_other(data_frame, attr_labels)
+
+
+def _loadarff_with_index(filename):
+    dataset = loadarff(filename)
+    if "index" in dataset.columns:
+        if isinstance(dataset["index"].dtype, CategoricalDtype):
+            # concatenating categorical index may raise TypeError
+            # see https://github.com/pandas-dev/pandas/issues/14586
+            dataset = dataset.astype({"index": "str"})
+        dataset.set_index("index", inplace=True)
+    return dataset
+
+
+def load_arff_files_standardized(
+    path_training,
+    attr_labels,
+    pos_label=None,
+    path_testing=None,
+    survival=True,
+    standardize_numeric=True,
+    to_numeric=True,
+):
+    """Load dataset in ARFF format.
+
+    Parameters
+    ----------
+    path_training : str
+        Path to ARFF file containing data.
+
+    attr_labels : sequence of str
+        Names of attributes denoting dependent variables.
+        If ``survival`` is set, it must be a sequence with two items:
+        the name of the event indicator and the name of the survival/censoring time.
+
+    pos_label : any type, optional
+        Value corresponding to an event in survival analysis.
+        Only considered if ``survival`` is ``True``.
+
+    path_testing : str, optional
+        Path to ARFF file containing hold-out data. Only columns that are available in both
+        training and testing are considered (excluding dependent variables).
+        If ``standardize_numeric`` is set, data is normalized by considering both training
+        and testing data.
+
+    survival : bool, optional, default: True
+        Whether the dependent variables denote event indicator and survival/censoring time.
+
+    standardize_numeric : bool, optional, default: True
+        Whether to standardize data to zero mean and unit variance.
+        See :func:`sksurv.column.standardize`.
+
+    to_numeric : bool, optional, default: True
+        Whether to convert categorical variables to numeric values.
+        See :func:`sksurv.column.categorical_to_numeric`.
+
+    Returns
+    -------
+    x_train : pandas.DataFrame, shape = (n_train, n_features)
+        Training data.
+
+    y_train : structured array, shape = (n_train,), or pandas.DataFrame, shape = (n_train, len(attr_labels))
+        Dependent variables of training data.
+
+        If `survival` is `True`, a structured array with two fields.
+        The first field is a boolean where ``True`` indicates an event and ``False``
+        indicates right-censoring. The second field is a float with the time of
+        event or time of censoring.
+
+        If `survival` is `False` and `attr_labels` not `None`, a :class:`pandas.DataFrame`
+        with columns specified by `attr_labels`.
+
+        If `survival` is `False` and `attr_labels` is `None`, `y_train` is set to `None`.
+
+    x_test : None or pandas.DataFrame, shape = (n_test, n_features)
+        Testing data if `path_testing` was provided.
+
+    y_test : None or structured array, shape = (n_test,)
+        Dependent variables of testing data if `path_testing` was provided.
+
+        If `survival` is `True`, a structured array with two fields.
+        The first field is a boolean where ``True`` indicates an event and ``False``
+        indicates right-censoring. The second field is a float with the time of
+        event or time of censoring.
+
+        If `survival` is `False` and `attr_labels` not `None`, a :class:`pandas.DataFrame`
+        with columns specified by `attr_labels`.
+
+        If `survival` is `False` and `attr_labels` is `None`, `y_test` is set to `None`.
+    """
+    dataset = _loadarff_with_index(path_training)
+
+    x_train, y_train = get_x_y(dataset, attr_labels, pos_label, survival)
+
+    if path_testing is not None:
+        x_test, y_test = _load_arff_testing(path_testing, attr_labels, pos_label, survival)
+
+        if len(x_train.columns.symmetric_difference(x_test.columns)) > 0:
+            warnings.warn("Restricting columns to intersection between training and testing data", stacklevel=2)
+
+            cols = x_train.columns.intersection(x_test.columns)
+            if len(cols) == 0:
+                raise ValueError("columns of training and test data do not intersect")
+
+            x_train = x_train.loc[:, cols]
+            x_test = x_test.loc[:, cols]
+
+        x = safe_concat((x_train, x_test), axis=0)
+        if standardize_numeric:
+            x = standardize(x)
+        if to_numeric:
+            x = categorical_to_numeric(x)
+
+        n_train = x_train.shape[0]
+        x_train = x.iloc[:n_train, :]
+        x_test = x.iloc[n_train:, :]
+    else:
+        if standardize_numeric:
+            x_train = standardize(x_train)
+        if to_numeric:
+            x_train = categorical_to_numeric(x_train)
+
+        x_test = None
+        y_test = None
+
+    return x_train, y_train, x_test, y_test
+
+
+def _load_arff_testing(path_testing, attr_labels, pos_label, survival):
+    test_dataset = _loadarff_with_index(path_testing)
+
+    has_labels = pd.Index(attr_labels).isin(test_dataset.columns).all()
+    if not has_labels:
+        if survival:
+            attr_labels = [None, None]
+        else:
+            attr_labels = None
+    return get_x_y(test_dataset, attr_labels, pos_label, survival)
+
+
+def load_whas500():
+    """Load and return the Worcester Heart Attack Study dataset
+
+    The dataset has 500 samples and 14 features.
+    The endpoint is death, which occurred for 215 patients (43.0%).
+
+    See [1]_, [2]_ for further description.
+
+    Returns
+    -------
+    x : pandas.DataFrame
+        The measurements for each patient.
+
+    y : structured array with 2 fields
+        *fstat*: boolean indicating whether the endpoint has been reached
+        or the event time is right-censored.
+
+        *lenfol*: total length of follow-up (days from hospital admission date
+        to date of last follow-up)
+
+    References
+    ----------
+    .. [1] https://web.archive.org/web/20170114043458/http://www.umass.edu/statdata/statdata/data/
+
+    .. [2] Hosmer, D., Lemeshow, S., May, S.:
+        "Applied Survival Analysis: Regression Modeling of Time to Event Data."
+        John Wiley & Sons, Inc. (2008)
+    """
+    fn = _get_data_path("whas500.arff")
+    return get_x_y(loadarff(fn), attr_labels=["fstat", "lenfol"], pos_label="1")
+
+
+def load_gbsg2():
+    """Load and return the German Breast Cancer Study Group 2 dataset
+
+    The dataset has 686 samples and 8 features.
+    The endpoint is recurrence free survival, which occurred for 299 patients (43.6%).
+
+    See [1]_, [2]_ for further description.
+
+    Returns
+    -------
+    x : pandas.DataFrame
+        The measurements for each patient.
+
+    y : structured array with 2 fields
+        *cens*: boolean indicating whether the endpoint has been reached
+        or the event time is right-censored.
+
+        *time*: total length of follow-up
+
+    References
+    ----------
+    .. [1] http://ascopubs.org/doi/abs/10.1200/jco.1994.12.10.2086
+
+    .. [2] Schumacher, M., Basert, G., Bojar, H., et al.
+        "Randomized 2 × 2 trial evaluating hormonal treatment and the duration of chemotherapy
+        in node-positive breast cancer patients."
+        Journal of Clinical Oncology 12, 2086–2093. (1994)
+    """
+    fn = _get_data_path("GBSG2.arff")
+    return get_x_y(loadarff(fn), attr_labels=["cens", "time"], pos_label="1")
+
+
+def load_veterans_lung_cancer():
+    """Load and return data from the Veterans' Administration
+    Lung Cancer Trial
+
+    The dataset has 137 samples and 6 features.
+    The endpoint is death, which occurred for 128 patients (93.4%).
+
+    See [1]_ for further description.
+
+    Returns
+    -------
+    x : pandas.DataFrame
+        The measurements for each patient.
+
+    y : structured array with 2 fields
+        *Status*: boolean indicating whether the endpoint has been reached
+        or the event time is right-censored.
+
+        *Survival_in_days*: total length of follow-up
+
+    References
+    ----------
+    .. [1] Kalbfleisch, J.D., Prentice, R.L.:
+        "The Statistical Analysis of Failure Time Data." John Wiley & Sons, Inc. (2002)
+    """
+    fn = _get_data_path("veteran.arff")
+    return get_x_y(loadarff(fn), attr_labels=["Status", "Survival_in_days"], pos_label="dead")
+
+
+def load_aids(endpoint="aids"):
+    """Load and return the AIDS Clinical Trial dataset
+
+    The dataset has 1,151 samples and 11 features.
+    The dataset has 2 endpoints:
+
+    1. AIDS defining event, which occurred for 96 patients (8.3%)
+    2. Death, which occurred for 26 patients (2.3%)
+
+    See [1]_, [2]_ for further description.
+
+    Parameters
+    ----------
+    endpoint : {'aids', 'death'}, default: 'aids'
+        The endpoint.
+
+    Returns
+    -------
+    x : pandas.DataFrame
+        The measurements for each patient.
+
+    y : structured array with 2 fields
+        *censor*: boolean indicating whether the endpoint has been reached
+        or the event time is right-censored.
+
+        *time*: total length of follow-up
+
+        If ``endpoint`` is death, the fields are named *censor_d* and *time_d*.
+
+    References
+    ----------
+    .. [1] https://web.archive.org/web/20170114043458/http://www.umass.edu/statdata/statdata/data/
+
+    .. [2] Hosmer, D., Lemeshow, S., May, S.:
+        "Applied Survival Analysis: Regression Modeling of Time to Event Data."
+        John Wiley & Sons, Inc. (2008)
+    """
+    labels_aids = ["censor", "time"]
+    labels_death = ["censor_d", "time_d"]
+    if endpoint == "aids":
+        attr_labels = labels_aids
+        drop_columns = labels_death
+    elif endpoint == "death":
+        attr_labels = labels_death
+        drop_columns = labels_aids
+    else:
+        raise ValueError("endpoint must be 'aids' or 'death'")
+
+    fn = _get_data_path("actg320.arff")
+    x, y = get_x_y(loadarff(fn), attr_labels=attr_labels, pos_label="1")
+    x.drop(drop_columns, axis=1, inplace=True)
+    return x, y
+
+
+def load_breast_cancer():
+    """Load and return the breast cancer dataset
+
+    The dataset has 198 samples and 80 features.
+    The endpoint is the presence of distance metastases, which occurred for 51 patients (25.8%).
+
+    See [1]_, [2]_ for further description.
+
+    Returns
+    -------
+    x : pandas.DataFrame
+        The measurements for each patient.
+
+    y : structured array with 2 fields
+        *e.tdm*: boolean indicating whether the endpoint has been reached
+        or the event time is right-censored.
+
+        *t.tdm*: time to distant metastasis (days)
+
+    References
+    ----------
+    .. [1] https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7390
+
+    .. [2] Desmedt, C., Piette, F., Loi et al.:
+        "Strong Time Dependence of the 76-Gene Prognostic Signature for Node-Negative Breast Cancer
+        Patients in the TRANSBIG Multicenter Independent Validation Series."
+        Clin. Cancer Res. 13(11), 3207–14 (2007)
+    """
+    fn = _get_data_path("breast_cancer_GSE7390-metastasis.arff")
+    return get_x_y(loadarff(fn), attr_labels=["e.tdm", "t.tdm"], pos_label="1")
+
+
+def load_flchain():
+    """Load and return assay of serum free light chain for 7874 subjects.
+
+    The dataset has 7874 samples and 9 features:
+
+        1. age: age in years
+        2. sex: F=female, M=male
+        3. sample.yr: the calendar year in which a blood sample was obtained
+        4. kappa: serum free light chain, kappa portion
+        5. lambda: serum free light chain, lambda portion
+        6. flc.grp: the serum free light chain group for the subject, as used in the original analysis
+        7. creatinine: serum creatinine
+        8. mgus: whether the subject had been diagnosed with monoclonal gammapothy (MGUS)
+        9. chapter: for those who died, a grouping of their primary cause of death by chapter headings
+           of the International Code of Diseases ICD-9
+
+    The endpoint is death, which occurred for 2169 subjects (27.5%).
+
+    See [1]_, [2]_ for further description.
+
+    Returns
+    -------
+    x : pandas.DataFrame
+        The measurements for each patient.
+
+    y : structured array with 2 fields
+        *death*: boolean indicating whether the subject died
+        or the event time is right-censored.
+
+        *futime*: total length of follow-up or time of death.
+
+    References
+    ----------
+    .. [1] https://doi.org/10.1016/j.mayocp.2012.03.009
+
+    .. [2] Dispenzieri, A., Katzmann, J., Kyle, R., Larson, D., Therneau, T., Colby, C., Clark, R.,
+           Mead, G., Kumar, S., Melton III, LJ. and Rajkumar, SV.
+           Use of nonclonal serum immunoglobulin free light chains to predict overall survival in
+           the general population, Mayo Clinic Proceedings 87:512-523. (2012)
+    """
+    fn = _get_data_path("flchain.arff")
+    return get_x_y(loadarff(fn), attr_labels=["death", "futime"], pos_label="dead")
+
+
+def load_bmt():
+    """Load and return response to hematopoietic stem cell transplantation (HSCT) for acute leukemia patients.
+
+    The dataset has 35 samples and 1 feature "dis" indicating the type of leukemia::
+
+        0=ALL (Acute Lymphoblastic Leukemia)
+        1=AML (Acute Myeloid Leukemia)
+
+    The endpoint (status) is defined as
+
+    +-------+------------------------------------+---------------------+
+    | Value | Description                        | Count (%)           |
+    +=======+====================================+=====================+
+    | 0     | Survival (Right-censored data)     | 11 patients (31.4%) |
+    +-------+------------------------------------+---------------------+
+    | 1     | Transplant related mortality (TRM) | 9 events (25.7%)    |
+    +-------+------------------------------------+---------------------+
+    | 2     | Relapse                            | 15 events (42.8%)   |
+    +-------+------------------------------------+---------------------+
+
+    See [1]_ for further description and [2]_ for the dataset.
+
+    Returns
+    -------
+    x : pandas.DataFrame
+        The measurements for each patient.
+
+    y : structured array with 2 fields
+        *status*: Integer indicating the endpoint: 0-(survival i.e. right-censored data), 1-(TRM), 2-(relapse)
+
+        *ftime*: total length of follow-up or time of event.
+
+    References
+    ----------
+    .. [1] https://doi.org/10.1038/sj.bmt.1705727
+           Scrucca, L., Santucci, A. & Aversa, F.:
+           "Competing risk analysis using R: an easy guide for clinicians. Bone Marrow Transplant 40, 381–387 (2007)"
+
+    .. [2] https://luca-scr.github.io/R/bmt.csv
+    """
+    full_path = _get_data_path("bmt.arff")
+    data = loadarff(full_path)
+    data = data.astype({"ftime": int})
+    return get_x_y(data, attr_labels=["status", "ftime"], competing_risks=True)
+
+
+def load_cgvhd():
+    r"""Load and return data from multicentre randomized clinical trial
+    initiated for patients with a myeloid malignancy who were to
+    undergo an allogeneic bone marrow transplant.
+
+    The dataset is a 100 patient subsample of the full data set. See [2]_ for further details.
+
+    +-------+------------+----------------------------------------------+-------------------------------------------+
+    | Index | Name       | Description                                  | Encoding                                  |
+    +=======+============+==============================================+===========================================+
+    | 1     | dx         | Diagnosis                                    | | AML=acute myeloid leukaemia             |
+    |       |            |                                              | | CML=chronic myeloid leukaemia           |
+    +-------+------------+----------------------------------------------+-------------------------------------------+
+    | 2     | tx         | Randomized treatment                         | | BM=cell harvested from the bone marrow  |
+    |       |            |                                              | | PB=cell harvested from peripheral blood |
+    +-------+------------+----------------------------------------------+-------------------------------------------+
+    | 3     | extent     | Extent of disease                            | L=limited, E=extensive                    |
+    +-------+------------+----------------------------------------------+-------------------------------------------+
+    | 4     | agvhdgd    | Grade of acute GVHD                          |                                           |
+    +-------+------------+----------------------------------------------+-------------------------------------------+
+    | 5     | age        | Age                                          | Years                                     |
+    +-------+------------+----------------------------------------------+-------------------------------------------+
+    | 6     | survtime   | Time from date of transplant to death        | Years                                     |
+    |       |            | or last follow-up                            |                                           |
+    +-------+------------+----------------------------------------------+-------------------------------------------+
+    | 7     | reltime    | Time from date of transplant to relapse      | Years                                     |
+    |       |            | or last follow-up                            |                                           |
+    +-------+------------+----------------------------------------------+-------------------------------------------+
+    | 8     | agvhtime   | Time from date of transplant to acute GVHD   | Years                                     |
+    |       |            | or last follow-up                            |                                           |
+    +-------+------------+----------------------------------------------+-------------------------------------------+
+    | 9     | cgvhtime   | Time from date of transplant to chronic GVHD | Years                                     |
+    |       |            | or last follow-up                            |                                           |
+    +-------+------------+----------------------------------------------+-------------------------------------------+
+    | 10    | stat       | Status                                       | 1=Dead, 0=Alive                           |
+    +-------+------------+----------------------------------------------+-------------------------------------------+
+    | 11    | rcens      | Relapse                                      | 1=Yes, 0=No                               |
+    +-------+------------+----------------------------------------------+-------------------------------------------+
+    | 12    | agvh       | Acute GVHD                                   | 1=Yes, 0=No                               |
+    +-------+------------+----------------------------------------------+-------------------------------------------+
+    | 13    | cgvh       | Chronic GVHD                                 | 1=Yes, 0=No                               |
+    +-------+------------+----------------------------------------------+-------------------------------------------+
+    | 14    | stnum      | patient ID                                   |                                           |
+    +-------+------------+----------------------------------------------+-------------------------------------------+
+
+    Columns 6,7 and 9 contain the time to death, relapse and CGVHD
+    calculated in years (survtime, reltime, cgvhtime) and the
+    respective indicator variables are in columns 10,11 and 13 (stat,
+    rcens, cgvh). The earliest time that any of these events happened
+    is calculated by taking the minimum of the observed times. The
+    censoring variable cens is coded as 0 when no events were
+    observed, 1 if CGVHD was observed as first event, 2 if a relapse
+    was observed as the first event and 3 if death occurred before
+    either of the events: The endpoint (status) is therefore defined as
+
+    +-------+-------------------------------------------+-----------------+
+    | Value | Description                               | Count (%)       |
+    +=======+===========================================+=================+
+    | 0     | Survival (Right-censored data)            | 4 patients (4%) |
+    +-------+-------------------------------------------+-----------------+
+    | 1     | Chronic graft versus host disease (CGVHD) | 86 events (86%) |
+    +-------+-------------------------------------------+-----------------+
+    | 2     | Relapse (TRM)                             | 5 events (5%)   |
+    +-------+-------------------------------------------+-----------------+
+    | 3     | Death                                     | 5 events (5%)   |
+    +-------+-------------------------------------------+-----------------+
+
+    The dataset has been obtained from [1]_.
+
+    Returns
+    -------
+    x : pandas.DataFrame
+        The measurements for each patient.
+
+    y : structured array with 2 fields
+        *status*: Integer indicating the endpoint: 0: right-censored data; 1: CGVHD; 2: relapse; 3: death.
+
+        *ftime*: total length of follow-up or time of event.
+
+    References
+    ----------
+    .. [1] https://sites.google.com/view/melaniapintiliemscstatistics/home/statistics
+
+    .. [2] Melania Pintilie: "Competing Risks: A Practical Perspective". John Wiley & Sons, 2006
+    """
+    full_path = _get_data_path("cgvhd.arff")
+    data = loadarff(full_path)
+    data.loc[:, "ftime"] = data[["survtime", "reltime", "cgvhtime"]].min(axis=1)
+    data.loc[:, "status"] = (
+        ((data["ftime"] == data["cgvhtime"]) & (data["cgvh"] == "1")).astype(int)
+        + 2 * ((data["ftime"] == data["reltime"]) & (data["rcens"] == "1")).astype(int)
+        + 3 * ((data["ftime"] == data["survtime"]) & (data["stat"] == "1")).astype(int)
+    )
+    data = data[["ftime", "status", "dx", "tx", "extent", "age"]]
+
+    return get_x_y(data, attr_labels=["status", "ftime"], competing_risks=True)