scikit-survival 0.24.0__cp311-cp311-macosx_11_0_arm64.whl → 0.25.0__cp311-cp311-macosx_11_0_arm64.whl

scikit_survival-0.25.0.dist-info/METADATA

@@ -0,0 +1,185 @@
+Metadata-Version: 2.4
+Name: scikit-survival
+Version: 0.25.0
+Summary: Survival analysis built on top of scikit-learn
+Author-email: Sebastian Pölsterl <sebp@k-d-w.org>
+License-Expression: GPL-3.0-or-later
+Project-URL: Homepage, https://github.com/sebp/scikit-survival
+Project-URL: Documentation, https://scikit-survival.readthedocs.io
+Project-URL: Source Code, https://github.com/sebp/scikit-survival
+Project-URL: Bug Tracker, https://github.com/sebp/scikit-survival/issues
+Project-URL: Release Notes, https://scikit-survival.readthedocs.io/en/latest/release_notes.html
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: POSIX
+Classifier: Programming Language :: C++
+Classifier: Programming Language :: Cython
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Software Development
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.10
+Description-Content-Type: text/x-rst
+License-File: COPYING
+Requires-Dist: ecos
+Requires-Dist: joblib
+Requires-Dist: numexpr
+Requires-Dist: numpy
+Requires-Dist: osqp<1.0.0,>=0.6.3
+Requires-Dist: pandas>=1.4.0
+Requires-Dist: scipy>=1.3.2
+Requires-Dist: scikit-learn<1.8,>=1.6.1
+Dynamic: license-file
+
+|License| |Docs| |DOI|
+
+|build-tests| |build-windows| |Codecov| |Codacy|
+
+***************
+scikit-survival
+***************
+
+scikit-survival is a Python module for `survival analysis`_
+built on top of `scikit-learn <https://scikit-learn.org/>`_. It allows doing survival analysis
+while utilizing the power of scikit-learn, e.g., for pre-processing or doing cross-validation.
+
+=======================
+About Survival Analysis
+=======================
+
+The objective in `survival analysis`_ (also referred to as time-to-event or reliability analysis)
+is to establish a connection between covariates and the time of an event.
+What makes survival analysis differ from traditional machine learning is the fact that
+parts of the training data can only be partially observed – they are *censored*.
+
+For instance, in a clinical study, patients are often monitored for a particular time period,
+and events occurring in this particular period are recorded.
+If a patient experiences an event, the exact time of the event can
+be recorded – the patient’s record is uncensored. In contrast, right censored records
+refer to patients that remained event-free during the study period and
+it is unknown whether an event has or has not occurred after the study ended.
+Consequently, survival analysis demands for models that take
+this unique characteristic of such a dataset into account.
+
+============
+Requirements
+============
+
+- Python 3.10 or later
+- ecos
+- joblib
+- numexpr
+- numpy
+- osqp
+- pandas 1.4.0 or later
+- scikit-learn 1.6 or 1.7
+- scipy
+- C/C++ compiler
+
+============
+Installation
+============
+
+The easiest way to install scikit-survival is to use
+`conda-forge <https://conda-forge.org/docs/user/introduction/>`_ by running::
+
+  conda install -c conda-forge scikit-survival
+
+Alternatively, you can install scikit-survival `from PyPI <https://scikit-survival.readthedocs.io/en/stable/install.html#pip>`_
+or `from source <https://scikit-survival.readthedocs.io/en/stable/install.html#from-source>`_.
+
+========
+Examples
+========
+
+The `user guide <https://scikit-survival.readthedocs.io/en/stable/user_guide/index.html>`_ provides
+in-depth information on the key concepts of scikit-survival, an overview of available survival models,
+and hands-on examples in the form of `Jupyter notebooks <https://jupyter.org/>`_.
+
+================
+Help and Support
+================
+
+**Documentation**
+
+- HTML documentation for the latest release: https://scikit-survival.readthedocs.io/en/stable/
+- HTML documentation for the development version (master branch): https://scikit-survival.readthedocs.io/en/latest/
+- For a list of notable changes, see the `release notes <https://scikit-survival.readthedocs.io/en/stable/release_notes.html>`_.
+
+**Bug reports**
+
+- If you encountered a problem, please submit a
+  `bug report <https://github.com/sebp/scikit-survival/issues/new?template=bug_report.md>`_.
+
+**Questions**
+
+- If you have a question on how to use scikit-survival, please use `GitHub Discussions <https://github.com/sebp/scikit-survival/discussions>`_.
+- For general theoretical or methodological questions on survival analysis, please use
+  `Cross Validated <https://stats.stackexchange.com/questions/tagged/survival>`_.
+
+============
+Contributing
+============
+
+New contributors are always welcome. Please have a look at the
+`contributing guidelines <https://scikit-survival.readthedocs.io/en/latest/contributing.html>`_
+on how to get started and to make sure your code complies with our guidelines.
+
+==========
+References
+==========
+
+Please cite the following paper if you are using **scikit-survival**.
+
+  S. Pölsterl, "scikit-survival: A Library for Time-to-Event Analysis Built on Top of scikit-learn,"
+  Journal of Machine Learning Research, vol. 21, no. 212, pp. 1–6, 2020.
+
+.. code::
+
+  @article{sksurv,
+    author  = {Sebastian P{\"o}lsterl},
+    title   = {scikit-survival: A Library for Time-to-Event Analysis Built on Top of scikit-learn},
+    journal = {Journal of Machine Learning Research},
+    year    = {2020},
+    volume  = {21},
+    number  = {212},
+    pages   = {1-6},
+    url     = {http://jmlr.org/papers/v21/20-729.html}
+  }
+
+.. |License| image:: https://img.shields.io/badge/license-GPLv3-blue.svg
+  :target: COPYING
+  :alt: License
+
+.. |Codecov| image:: https://codecov.io/gh/sebp/scikit-survival/branch/master/graph/badge.svg
+  :target: https://codecov.io/gh/sebp/scikit-survival
+  :alt: codecov
+
+.. |Codacy| image:: https://api.codacy.com/project/badge/Grade/17242004cdf6422c9a1052bf1ec63104
+   :target: https://app.codacy.com/gh/sebp/scikit-survival/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade
+   :alt: Codacy Badge
+
+.. |Docs| image:: https://readthedocs.org/projects/scikit-survival/badge/?version=latest
+  :target: https://scikit-survival.readthedocs.io/en/latest/
+  :alt: readthedocs.org
+
+.. |DOI| image:: https://zenodo.org/badge/77409504.svg
+   :target: https://zenodo.org/badge/latestdoi/77409504
+   :alt: Digital Object Identifier (DOI)
+
+.. |build-tests| image:: https://github.com/sebp/scikit-survival/actions/workflows/tests-workflow.yaml/badge.svg?branch=master
+  :target: https://github.com/sebp/scikit-survival/actions?query=workflow%3Atests+branch%3Amaster
+  :alt: GitHub Actions Tests Status
+
+.. |build-windows| image:: https://ci.appveyor.com/api/projects/status/github/sebp/scikit-survival?branch=master&svg=true
+   :target: https://ci.appveyor.com/project/sebp/scikit-survival
+   :alt: Windows Build Status on AppVeyor
+
+.. _survival analysis: https://en.wikipedia.org/wiki/Survival_analysis

scikit_survival-0.25.0.dist-info/RECORD

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{scikit_survival-0.24.0.dist-info → scikit_survival-0.25.0.dist-info}/WHEEL

@@ -1,5 +1,6 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: false
 Tag: cp311-cp311-macosx_11_0_arm64
+Generator: delocate 0.13.0
 

sksurv/__init__.py

@@ -17,6 +17,7 @@ def _get_version(name):
 
 
 def show_versions():
+    """Print debugging information."""
     sys_info = {
         "Platform": platform.platform(),
         "Python version": f"{platform.python_implementation()} {platform.python_version()}",
@@ -60,14 +61,14 @@ def show_versions():
 
 @available_if(_final_estimator_has("predict_cumulative_hazard_function"))
 def predict_cumulative_hazard_function(self, X, **kwargs):
-    """Predict cumulative hazard function.
+    r"""Predict cumulative hazard function for a pipeline.
 
     The cumulative hazard function for an individual
     with feature vector :math:`x` is defined as
 
     .. math::
 
-        H(t \\mid x) = \\exp(x^\\top \\beta) H_0(t) ,
+        H(t \mid x) = \exp(x^\top \beta) H_0(t) ,
 
     where :math:`H_0(t)` is the baseline hazard function,
     estimated by Breslow's estimator.
@@ -80,7 +81,29 @@ def predict_cumulative_hazard_function(self, X, **kwargs):
     Returns
     -------
     cum_hazard : ndarray, shape = (n_samples,)
-        Predicted cumulative hazard functions.
+        Predicted cumulative hazard functions. Each element is an instance
+        of :class:`sksurv.functions.StepFunction`.
+
+    See Also
+    --------
+    predict_survival_function : Predict survival function for a pipeline.
+
+    Examples
+    --------
+    >>> from sksurv.datasets import load_whas500
+    >>> from sksurv.linear_model import CoxPHSurvivalAnalysis
+    >>> from sksurv.preprocessing import OneHotEncoder
+    >>> from sklearn.pipeline import Pipeline
+    >>>
+    >>> X, y = load_whas500()
+    >>> pipe = Pipeline([('encode', OneHotEncoder()),
+    ...                  ('cox', CoxPHSurvivalAnalysis())])
+    >>> pipe.fit(X, y)
+    Pipeline(...)
+    >>> chf = pipe.predict_cumulative_hazard_function(X.iloc[:5])
+    >>> for fn in chf:
+    ...     print(fn.x, fn.y)
+    [...]
     """
     Xt = X
     for _, _, transform in self._iter(with_final=False):
@@ -90,14 +113,14 @@ def predict_cumulative_hazard_function(self, X, **kwargs):
 
 @available_if(_final_estimator_has("predict_survival_function"))
 def predict_survival_function(self, X, **kwargs):
-    """Predict survival function.
+    r"""Predict survival function for a pipeline.
 
     The survival function for an individual
     with feature vector :math:`x` is defined as
 
     .. math::
 
-        S(t \\mid x) = S_0(t)^{\\exp(x^\\top \\beta)} ,
+        S(t \mid x) = S_0(t)^{\exp(x^\top \beta)} ,
 
     where :math:`S_0(t)` is the baseline survival function,
     estimated by Breslow's estimator.
@@ -110,7 +133,29 @@ def predict_survival_function(self, X, **kwargs):
     Returns
     -------
     survival : ndarray, shape = (n_samples,)
-        Predicted survival functions.
+        Predicted survival functions. Each element is an instance
+        of :class:`sksurv.functions.StepFunction`.
+
+    See Also
+    --------
+    predict_cumulative_hazard_function : Predict cumulative hazard function for a pipeline.
+
+    Examples
+    --------
+    >>> from sksurv.datasets import load_whas500
+    >>> from sksurv.linear_model import CoxPHSurvivalAnalysis
+    >>> from sksurv.preprocessing import OneHotEncoder
+    >>> from sklearn.pipeline import Pipeline
+    >>>
+    >>> X, y = load_whas500()
+    >>> pipe = Pipeline([('encode', OneHotEncoder()),
+    ...                  ('cox', CoxPHSurvivalAnalysis())])
+    >>> pipe.fit(X, y)
+    Pipeline(...)
+    >>> surv_fn = pipe.predict_survival_function(X.iloc[:5])
+    >>> for fn in surv_fn:
+    ...     print(fn.x, fn.y)
+    [...]
     """
     Xt = X
     for _, _, transform in self._iter(with_final=False):

sksurv/base.py

@@ -44,7 +44,10 @@ class SurvivalAnalysisMixin:
 
         Returns
         -------
-        survival : ndarray
+        survival : ndarray of StepFunction
+            If `return_array` is True, an array of shape (n_samples, n_unique_times)
+            containing the survival function values. Otherwise, a list of
+            :class:`sksurv.functions.StepFunction` instances.
         """
         return self._predict_function("get_survival_function", baseline_model, prediction, return_array)
 
@@ -66,7 +69,10 @@ class SurvivalAnalysisMixin:
 
         Returns
         -------
-        cum_hazard : ndarray
+        cum_hazard : ndarray of StepFunction
+            If `return_array` is True, an array of shape (n_samples, n_unique_times)
+            containing the cumulative hazard function values. Otherwise, a list of
+            :class:`sksurv.functions.StepFunction` instances.
         """
         return self._predict_function("get_cumulative_hazard_function", baseline_model, prediction, return_array)
 
@@ -87,6 +93,10 @@ class SurvivalAnalysisMixin:
         -------
         cindex : float
             Estimated concordance index.
+
+        See also
+        --------
+        sksurv.metrics.concordance_index_censored : Computes the concordance index.
         """
         from .metrics import concordance_index_censored
 

sksurv/column.py

@@ -42,27 +42,28 @@ def standardize_column(series_or_array, with_std=True):
 
 
 def standardize(table, with_std=True):
-    """
-    Perform Z-Normalization on each numeric column of the given table.
+    """Standardize numeric features by removing the mean and scaling to unit variance.
+
+    This function performs Z-Normalization on each numeric column of the given
+    table.
 
-    If `table` is a pandas.DataFrame, only numeric columns are modified,
-    all other columns remain unchanged. If `table` is a numpy.ndarray,
-    it is only modified if it has numeric dtype, in which case the returned
-    array will have floating point dtype.
+    If `table` is a :class:`pandas.DataFrame`, only numeric columns are modified;
+    all other columns remain unchanged. If `table` is a :class:`numpy.ndarray`,
+    it is only modified if it has a numeric dtype, in which case the returned
+    array will have a floating-point dtype.
 
     Parameters
     ----------
     table : pandas.DataFrame or numpy.ndarray
         Data to standardize.
-
     with_std : bool, optional, default: True
-        If ``False`` data is only centered and not converted to unit variance.
+        If ``False``, data is only centered (mean removed) and not scaled to
+        unit variance.
 
     Returns
     -------
-    normalized : pandas.DataFrame
-        Table with numeric columns normalized.
-        Categorical columns in the input table remain unchanged.
+    normalized : pandas.DataFrame or numpy.ndarray
+        The standardized data. The output type will be the same as the input type.
     """
     new_frame = _apply_along_column(table, standardize_column, with_std=with_std)
 
@@ -90,28 +91,30 @@ def _encode_categorical_series(series, allow_drop=True):
 
 
 def encode_categorical(table, columns=None, **kwargs):
-    """
-    Encode categorical columns with `M` categories into `M-1` columns according
-    to the one-hot scheme.
+    """One-hot encode categorical features.
+
+    This function creates a binary column for each category and, by default,
+    drops one of the categories per feature: a column with `M` categories
+    is encoded as `M-1` integer columns according to the one-hot
+    scheme.
 
     Parameters
     ----------
-    table : pandas.DataFrame
-        Table with categorical columns to encode.
-
+    table : pandas.DataFrame or pandas.Series
+        Data with categorical columns to encode.
     columns : list-like, optional, default: None
         Column names in the DataFrame to be encoded.
-        If `columns` is None then all the columns with
-        `object` or `category` dtype will be converted.
-
-    allow_drop : boolean, optional, default: True
+        If `columns` is `None`, all columns with `object` or `category`
+        dtype will be converted. This parameter is ignored if `table` is a
+        pandas.Series.
+    allow_drop : bool, optional, default: True
         Whether to allow dropping categorical columns that only consist
         of a single category.
 
     Returns
     -------
     encoded : pandas.DataFrame
-        Table with categorical columns encoded as numeric.
+        The transformed data with categorical columns encoded as numeric.
         Numeric columns in the input table remain unchanged.
     """
     if isinstance(table, pd.Series):
@@ -165,19 +168,20 @@ def _get_dummies_1d(data, allow_drop=True):
 
 
 def categorical_to_numeric(table):
-    """Encode categorical columns to numeric by converting each category to
-    an integer value.
+    """Encode categorical features as integers.
+
+    This function converts each category to a unique integer value.
 
     Parameters
     ----------
-    table : pandas.DataFrame
-        Table with categorical columns to encode.
+    table : pandas.DataFrame or pandas.Series
+        Data with categorical columns to encode.
 
     Returns
     -------
-    encoded : pandas.DataFrame
-        Table with categorical columns encoded as numeric.
-        Numeric columns in the input table remain unchanged.
+    encoded : pandas.DataFrame or pandas.Series
+        The transformed data with categorical columns encoded as integers.
+        The output type will be the same as the input type.
     """
 
     def transform(column):

sksurv/compare.py

@@ -11,43 +11,43 @@ __all__ = ["compare_survival"]
 
 
 def compare_survival(y, group_indicator, return_stats=False):
-    """K-sample log-rank hypothesis test of identical survival functions.
+    """Compare survival functions of two or more groups using the log-rank test.
 
-    Compares the pooled hazard rate with each group-specific
-    hazard rate. The alternative hypothesis is that the hazard
-    rate of at least one group differs from the others at some time.
+    The log-rank test is a non-parametric hypothesis test for comparing the
+    survival functions of two or more independent groups. The null hypothesis is
+    that the survival functions of the groups are identical. The alternative
+    hypothesis is that at least one survival function differs from the others.
+
+    The test statistic is approximately chi-squared distributed with :math:`K-1`
+    degrees of freedom, where :math:`K` is the number of groups.
 
     See [1]_ for more details.
 
     Parameters
     ----------
     y : structured array, shape = (n_samples,)
-        A structured array containing the binary event indicator
-        as first field, and time of event or time of censoring as
-        second field.
-
+        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.
     group_indicator : array-like, shape = (n_samples,)
         Group membership of each sample.
-
     return_stats : bool, optional, default: False
-        Whether to return a data frame with statistics for each group
-        and the covariance matrix of the test statistic.
+        Whether to return a data frame with statistics for each group and the
+        covariance matrix of the test statistic.
 
     Returns
     -------
     chisq : float
-        Test statistic.
+        The test statistic.
     pvalue : float
-        Two-sided p-value with respect to the null hypothesis
-        that the hazard rates across all groups are equal.
-    stats : pandas.DataFrame
-        Summary statistics for each group:  number of samples,
-        observed number of events, expected number of events,
-        and test statistic.
-        Only provided if `return_stats` is True.
-    covariance : array, shape=(n_groups, n_groups)
-        Covariance matrix of the test statistic.
-        Only provided if `return_stats` is True.
+        The two-sided p-value for the test.
+    stats : pandas.DataFrame, optional
+        A DataFrame with summary statistics for each group. This includes the
+        number of samples, observed number of events, expected number of events,
+        and the test statistic. Only returned if ``return_stats`` is ``True``.
+    covariance : ndarray, shape=(n_groups, n_groups), optional
+        The covariance matrix of the test statistic. Only returned if
+        ``return_stats`` is ``True``.
 
     References
     ----------