scikit-survival 0.24.1__tar.gz → 0.25.0__tar.gz

scikit_survival-0.25.0/PKG-INFO

@@ -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-0.24.1 → scikit_survival-0.25.0}/README.rst

@@ -39,7 +39,7 @@ Requirements
 - numpy
 - osqp
 - pandas 1.4.0 or later
-- scikit-learn 1.6
+- scikit-learn 1.6 or 1.7
 - scipy
 - C/C++ compiler
 
@@ -48,12 +48,12 @@ Installation
 ============
 
 The easiest way to install scikit-survival is to use
-`Anaconda <https://www.anaconda.com/distribution/>`_ by running::
+`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 source
-following `this guide <https://scikit-survival.readthedocs.io/en/stable/install.html#from-source>`_.
+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

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scikit_survival-0.25.0/doc/_static/images/metrics-diagram.mmd

@@ -0,0 +1,17 @@
+graph TD
+    A[Survival Model Estimator]-->|<tt>predict&#40X&#41</tt>|B(Time-independent Risk Scores)
+    A-->|<tt>predict_cumulative_hazard_function&#40X&#41</tt>|B2(Time-dependent Risk Scores)
+    A-->|<tt>predict_survival_function&#40X&#41</tt>|C(Survival Probabilities)
+
+    B --> D([<tt>concordance_index_censored</tt>])
+    B --> E([<tt>concordance_index_ipcw</tt>])
+    B --> F([<tt>cumulative_dynamic_auc</tt>])
+    B2 --> F2([<tt>cumulative_dynamic_auc</tt>])
+
+    C --> G([<tt>brier_score</tt>])
+    C --> H([<tt>integrated_brier_score</tt>])
+
+    D & F --> I[Assess model discrimation &#40<i>time-independent</i>&#41]
+    E --> I
+    F2 --> J2[Assess model discrimation &#40<i>time-dependent</i>&#41]
+    G & H --> K[Assess model discrimation and calibration &#40<i>time-dependent</i>&#41]