scikit-survival 0.25.0__cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl

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Files changed (58) hide show
  1. scikit_survival-0.25.0.dist-info/METADATA +185 -0
  2. scikit_survival-0.25.0.dist-info/RECORD +58 -0
  3. scikit_survival-0.25.0.dist-info/WHEEL +6 -0
  4. scikit_survival-0.25.0.dist-info/licenses/COPYING +674 -0
  5. scikit_survival-0.25.0.dist-info/top_level.txt +1 -0
  6. sksurv/__init__.py +183 -0
  7. sksurv/base.py +115 -0
  8. sksurv/bintrees/__init__.py +15 -0
  9. sksurv/bintrees/_binarytrees.cpython-311-x86_64-linux-gnu.so +0 -0
  10. sksurv/column.py +205 -0
  11. sksurv/compare.py +123 -0
  12. sksurv/datasets/__init__.py +12 -0
  13. sksurv/datasets/base.py +614 -0
  14. sksurv/datasets/data/GBSG2.arff +700 -0
  15. sksurv/datasets/data/actg320.arff +1169 -0
  16. sksurv/datasets/data/bmt.arff +46 -0
  17. sksurv/datasets/data/breast_cancer_GSE7390-metastasis.arff +283 -0
  18. sksurv/datasets/data/cgvhd.arff +118 -0
  19. sksurv/datasets/data/flchain.arff +7887 -0
  20. sksurv/datasets/data/veteran.arff +148 -0
  21. sksurv/datasets/data/whas500.arff +520 -0
  22. sksurv/docstrings.py +99 -0
  23. sksurv/ensemble/__init__.py +2 -0
  24. sksurv/ensemble/_coxph_loss.cpython-311-x86_64-linux-gnu.so +0 -0
  25. sksurv/ensemble/boosting.py +1564 -0
  26. sksurv/ensemble/forest.py +902 -0
  27. sksurv/ensemble/survival_loss.py +151 -0
  28. sksurv/exceptions.py +18 -0
  29. sksurv/functions.py +114 -0
  30. sksurv/io/__init__.py +2 -0
  31. sksurv/io/arffread.py +89 -0
  32. sksurv/io/arffwrite.py +181 -0
  33. sksurv/kernels/__init__.py +1 -0
  34. sksurv/kernels/_clinical_kernel.cpython-311-x86_64-linux-gnu.so +0 -0
  35. sksurv/kernels/clinical.py +348 -0
  36. sksurv/linear_model/__init__.py +3 -0
  37. sksurv/linear_model/_coxnet.cpython-311-x86_64-linux-gnu.so +0 -0
  38. sksurv/linear_model/aft.py +208 -0
  39. sksurv/linear_model/coxnet.py +592 -0
  40. sksurv/linear_model/coxph.py +637 -0
  41. sksurv/meta/__init__.py +4 -0
  42. sksurv/meta/base.py +35 -0
  43. sksurv/meta/ensemble_selection.py +724 -0
  44. sksurv/meta/stacking.py +370 -0
  45. sksurv/metrics.py +1028 -0
  46. sksurv/nonparametric.py +911 -0
  47. sksurv/preprocessing.py +183 -0
  48. sksurv/svm/__init__.py +11 -0
  49. sksurv/svm/_minlip.cpython-311-x86_64-linux-gnu.so +0 -0
  50. sksurv/svm/_prsvm.cpython-311-x86_64-linux-gnu.so +0 -0
  51. sksurv/svm/minlip.py +690 -0
  52. sksurv/svm/naive_survival_svm.py +249 -0
  53. sksurv/svm/survival_svm.py +1236 -0
  54. sksurv/testing.py +108 -0
  55. sksurv/tree/__init__.py +1 -0
  56. sksurv/tree/_criterion.cpython-311-x86_64-linux-gnu.so +0 -0
  57. sksurv/tree/tree.py +790 -0
  58. sksurv/util.py +415 -0
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+ Metadata-Version: 2.4
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+ Name: scikit-survival
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+ Version: 0.25.0
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+ Summary: Survival analysis built on top of scikit-learn
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+ Author-email: Sebastian Pölsterl <sebp@k-d-w.org>
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+ License-Expression: GPL-3.0-or-later
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+ Project-URL: Homepage, https://github.com/sebp/scikit-survival
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+ Project-URL: Documentation, https://scikit-survival.readthedocs.io
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+ Project-URL: Source Code, https://github.com/sebp/scikit-survival
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+ Project-URL: Bug Tracker, https://github.com/sebp/scikit-survival/issues
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+ Project-URL: Release Notes, https://scikit-survival.readthedocs.io/en/latest/release_notes.html
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+ Classifier: Development Status :: 4 - Beta
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+ Classifier: Intended Audience :: Science/Research
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+ Classifier: Intended Audience :: Developers
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+ Classifier: Operating System :: MacOS
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+ Classifier: Operating System :: Microsoft :: Windows
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+ Classifier: Operating System :: POSIX
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+ Classifier: Programming Language :: C++
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+ Classifier: Programming Language :: Cython
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+ Classifier: Programming Language :: Python
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+ Classifier: Programming Language :: Python :: 3
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+ Classifier: Programming Language :: Python :: 3.10
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+ Classifier: Programming Language :: Python :: 3.11
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+ Classifier: Programming Language :: Python :: 3.12
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+ Classifier: Programming Language :: Python :: 3.13
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+ Classifier: Topic :: Software Development
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+ Classifier: Topic :: Scientific/Engineering
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+ Requires-Python: >=3.10
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+ Description-Content-Type: text/x-rst
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+ License-File: COPYING
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+ Requires-Dist: ecos
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+ Requires-Dist: joblib
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+ Requires-Dist: numexpr
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+ Requires-Dist: numpy
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+ Requires-Dist: osqp<1.0.0,>=0.6.3
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+ Requires-Dist: pandas>=1.4.0
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+ Requires-Dist: scipy>=1.3.2
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+ Requires-Dist: scikit-learn<1.8,>=1.6.1
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+ Dynamic: license-file
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+
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+ |License| |Docs| |DOI|
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+
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+ |build-tests| |build-windows| |Codecov| |Codacy|
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+
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+ ***************
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+ scikit-survival
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+ ***************
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+
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+ scikit-survival is a Python module for `survival analysis`_
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+ built on top of `scikit-learn <https://scikit-learn.org/>`_. It allows doing survival analysis
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+ while utilizing the power of scikit-learn, e.g., for pre-processing or doing cross-validation.
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+
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+ =======================
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+ About Survival Analysis
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+ =======================
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+
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+ The objective in `survival analysis`_ (also referred to as time-to-event or reliability analysis)
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+ is to establish a connection between covariates and the time of an event.
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+ What makes survival analysis differ from traditional machine learning is the fact that
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+ parts of the training data can only be partially observed – they are *censored*.
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+
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+ For instance, in a clinical study, patients are often monitored for a particular time period,
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+ and events occurring in this particular period are recorded.
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+ If a patient experiences an event, the exact time of the event can
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+ be recorded – the patient’s record is uncensored. In contrast, right censored records
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+ refer to patients that remained event-free during the study period and
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+ it is unknown whether an event has or has not occurred after the study ended.
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+ Consequently, survival analysis demands for models that take
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+ this unique characteristic of such a dataset into account.
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+
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+ ============
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+ Requirements
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+ ============
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+
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+ - Python 3.10 or later
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+ - ecos
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+ - joblib
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+ - numexpr
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+ - numpy
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+ - osqp
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+ - pandas 1.4.0 or later
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+ - scikit-learn 1.6 or 1.7
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+ - scipy
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+ - C/C++ compiler
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+
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+ ============
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+ Installation
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+ ============
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+
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+ The easiest way to install scikit-survival is to use
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+ `conda-forge <https://conda-forge.org/docs/user/introduction/>`_ by running::
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+
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+ conda install -c conda-forge scikit-survival
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+
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+ Alternatively, you can install scikit-survival `from PyPI <https://scikit-survival.readthedocs.io/en/stable/install.html#pip>`_
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+ or `from source <https://scikit-survival.readthedocs.io/en/stable/install.html#from-source>`_.
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+
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+ ========
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+ Examples
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+ ========
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+
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+ The `user guide <https://scikit-survival.readthedocs.io/en/stable/user_guide/index.html>`_ provides
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+ in-depth information on the key concepts of scikit-survival, an overview of available survival models,
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+ and hands-on examples in the form of `Jupyter notebooks <https://jupyter.org/>`_.
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+
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+ ================
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+ Help and Support
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+ ================
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+
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+ **Documentation**
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+
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+ - HTML documentation for the latest release: https://scikit-survival.readthedocs.io/en/stable/
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+ - HTML documentation for the development version (master branch): https://scikit-survival.readthedocs.io/en/latest/
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+ - For a list of notable changes, see the `release notes <https://scikit-survival.readthedocs.io/en/stable/release_notes.html>`_.
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+
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+ **Bug reports**
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+
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+ - If you encountered a problem, please submit a
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+ `bug report <https://github.com/sebp/scikit-survival/issues/new?template=bug_report.md>`_.
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+
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+ **Questions**
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+
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+ - If you have a question on how to use scikit-survival, please use `GitHub Discussions <https://github.com/sebp/scikit-survival/discussions>`_.
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+ - For general theoretical or methodological questions on survival analysis, please use
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+ `Cross Validated <https://stats.stackexchange.com/questions/tagged/survival>`_.
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+
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+ ============
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+ Contributing
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+ ============
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+
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+ New contributors are always welcome. Please have a look at the
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+ `contributing guidelines <https://scikit-survival.readthedocs.io/en/latest/contributing.html>`_
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+ on how to get started and to make sure your code complies with our guidelines.
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+
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+ ==========
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+ References
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+ ==========
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+
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+ Please cite the following paper if you are using **scikit-survival**.
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+
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+ S. Pölsterl, "scikit-survival: A Library for Time-to-Event Analysis Built on Top of scikit-learn,"
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+ Journal of Machine Learning Research, vol. 21, no. 212, pp. 1–6, 2020.
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+
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+ .. code::
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+
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+ @article{sksurv,
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+ author = {Sebastian P{\"o}lsterl},
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+ title = {scikit-survival: A Library for Time-to-Event Analysis Built on Top of scikit-learn},
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+ journal = {Journal of Machine Learning Research},
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+ year = {2020},
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+ volume = {21},
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+ number = {212},
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+ pages = {1-6},
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+ url = {http://jmlr.org/papers/v21/20-729.html}
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+ }
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+
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+ .. |License| image:: https://img.shields.io/badge/license-GPLv3-blue.svg
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+ :target: COPYING
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+ :alt: License
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+
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+ .. |Codecov| image:: https://codecov.io/gh/sebp/scikit-survival/branch/master/graph/badge.svg
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+ :target: https://codecov.io/gh/sebp/scikit-survival
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+ :alt: codecov
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+
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+ .. |Codacy| image:: https://api.codacy.com/project/badge/Grade/17242004cdf6422c9a1052bf1ec63104
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+ :target: https://app.codacy.com/gh/sebp/scikit-survival/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade
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+ :alt: Codacy Badge
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+
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+ .. |Docs| image:: https://readthedocs.org/projects/scikit-survival/badge/?version=latest
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+ :target: https://scikit-survival.readthedocs.io/en/latest/
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+ :alt: readthedocs.org
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+
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+ .. |DOI| image:: https://zenodo.org/badge/77409504.svg
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+ :target: https://zenodo.org/badge/latestdoi/77409504
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+ :alt: Digital Object Identifier (DOI)
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+
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+ .. |build-tests| image:: https://github.com/sebp/scikit-survival/actions/workflows/tests-workflow.yaml/badge.svg?branch=master
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+ :target: https://github.com/sebp/scikit-survival/actions?query=workflow%3Atests+branch%3Amaster
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+ :alt: GitHub Actions Tests Status
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+
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+ .. |build-windows| image:: https://ci.appveyor.com/api/projects/status/github/sebp/scikit-survival?branch=master&svg=true
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+ :target: https://ci.appveyor.com/project/sebp/scikit-survival
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+ :alt: Windows Build Status on AppVeyor
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+
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+ .. _survival analysis: https://en.wikipedia.org/wiki/Survival_analysis
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+ Wheel-Version: 1.0
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+ Generator: setuptools (80.9.0)
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+ Root-Is-Purelib: false
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+ Tag: cp311-cp311-manylinux_2_17_x86_64
5
+ Tag: cp311-cp311-manylinux2014_x86_64
6
+