From 5aa17b8d1e7e41f588468d4c6f51fc2e1c101173 Mon Sep 17 00:00:00 2001 From: CamDavidsonPilon Date: Thu, 5 Mar 2020 19:03:12 -0500 Subject: [PATCH] bump version --- CHANGELOG.md | 2 +- docs/Changelog.rst | 326 +++++++++++++++-------------- lifelines/tests/test_estimation.py | 4 + lifelines/version.py | 2 +- 4 files changed, 179 insertions(+), 155 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e764d9f21..cd6694bbf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,6 @@ ## Changelog -#### 0.24.1 - unreleased +#### 0.24.1 - 2020-03-05 ##### New features - Stability improvements for GeneralizedGammaRegressionFitter and CoxPHFitter with spline estimation. diff --git a/docs/Changelog.rst b/docs/Changelog.rst index 3d95748d7..c43e15918 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -1,6 +1,22 @@ Changelog --------- +0.24.1 - 2020-03-05 +^^^^^^^^^^^^^^^^^^^ + +New features +'''''''''''' + +- Stability improvements for GeneralizedGammaRegressionFitter and + CoxPHFitter with spline estimation. + +Bug fixes +''''''''' + +- Fixed bug with plotting hazards in NelsonAalenFitter. + +.. _section-1: + 0.24.0 - 2020-02-20 ^^^^^^^^^^^^^^^^^^^ @@ -8,6 +24,8 @@ This version and future versions of lifelines no longer support py35. Pandas 1.0 is fully supported, along with previous version. Minimum Scipy has been bumped to 1.2.0 +.. _new-features-1: + New features '''''''''''' @@ -56,6 +74,8 @@ API Changes to ``scoring_method``. - removed ``_score_`` and ``path`` from Cox model. +.. _bug-fixes-1: + Bug fixes ''''''''' @@ -67,12 +87,12 @@ Bug fixes - Cox models now incorporate any penalizers in their ``log_likelihood_`` -.. _section-1: +.. _section-2: 0.23.9 - 2020-01-28 ^^^^^^^^^^^^^^^^^^^ -.. _bug-fixes-1: +.. _bug-fixes-2: Bug fixes ''''''''' @@ -83,12 +103,12 @@ Bug fixes of ``GeneralizedGammaRegressionFitter`` and any custom regression models should update their code as soon as possible. -.. _section-2: +.. _section-3: 0.23.8 - 2020-01-21 ^^^^^^^^^^^^^^^^^^^ -.. _bug-fixes-2: +.. _bug-fixes-3: Bug fixes ''''''''' @@ -99,19 +119,19 @@ Bug fixes ``GeneralizedGammaRegressionFitter`` and any custom regression models should update their code as soon as possible. -.. _section-3: +.. _section-4: 0.23.7 - 2020-01-14 ^^^^^^^^^^^^^^^^^^^ Bug fixes for py3.5. -.. _section-4: +.. _section-5: 0.23.6 - 2020-01-07 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-1: +.. _new-features-2: New features '''''''''''' @@ -125,12 +145,12 @@ New features - custom parametric regression models can now do left and interval censoring. -.. _section-5: +.. _section-6: 0.23.5 - 2020-01-05 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-2: +.. _new-features-3: New features '''''''''''' @@ -139,7 +159,7 @@ New features - New lymph node cancer dataset, originally from *H.F. for the German Breast Cancer Study Group (GBSG) (1994)* -.. _bug-fixes-3: +.. _bug-fixes-4: Bug fixes ''''''''' @@ -149,26 +169,26 @@ Bug fixes - fixed bug where large exponential numbers in ``print_summary`` were not being suppressed correctly. -.. _section-6: +.. _section-7: 0.23.4 - 2019-12-15 ^^^^^^^^^^^^^^^^^^^ - Bug fix for PyPI -.. _section-7: +.. _section-8: 0.23.3 - 2019-12-11 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-3: +.. _new-features-4: New features '''''''''''' - ``StatisticalResult.print_summary`` supports html output. -.. _bug-fixes-4: +.. _bug-fixes-5: Bug fixes ''''''''' @@ -176,12 +196,12 @@ Bug fixes - fix import in ``printer.py`` - fix html printing with Univariate models. -.. _section-8: +.. _section-9: 0.23.2 - 2019-12-07 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-4: +.. _new-features-5: New features '''''''''''' @@ -193,7 +213,7 @@ New features - performance improvements on regression models’ preprocessing. Should make datasets with high number of columns more performant. -.. _bug-fixes-5: +.. _bug-fixes-6: Bug fixes ''''''''' @@ -202,12 +222,12 @@ Bug fixes - fixed repr for ``sklearn_adapter`` classes. - fixed ``conditional_after`` in Cox model with strata was used. -.. _section-9: +.. _section-10: 0.23.1 - 2019-11-27 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-5: +.. _new-features-6: New features '''''''''''' @@ -217,7 +237,7 @@ New features - performance improvements for ``CoxPHFitter`` - up to 30% performance improvements for some datasets. -.. _bug-fixes-6: +.. _bug-fixes-7: Bug fixes ''''''''' @@ -229,12 +249,12 @@ Bug fixes - fixed bug when using ``print_summary`` with left censored models. - lots of minor bug fixes. -.. _section-10: +.. _section-11: 0.23.0 - 2019-11-17 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-6: +.. _new-features-7: New features '''''''''''' @@ -243,7 +263,7 @@ New features Jupyter notebooks! - silenced some warnings. -.. _bug-fixes-7: +.. _bug-fixes-8: Bug fixes ''''''''' @@ -265,7 +285,7 @@ API Changes - ``left_censorship`` in ``fit`` has been removed in favour of ``fit_left_censoring``. -.. _section-11: +.. _section-12: 0.22.10 - 2019-11-08 ^^^^^^^^^^^^^^^^^^^^ @@ -273,7 +293,7 @@ API Changes The tests were re-factored to be shipped with the package. Let me know if this causes problems. -.. _bug-fixes-8: +.. _bug-fixes-9: Bug fixes ''''''''' @@ -283,12 +303,12 @@ Bug fixes - fixed bug in plot_covariate_groups for AFT models when >1d arrays were used for values arg. -.. _section-12: +.. _section-13: 0.22.9 - 2019-10-30 ^^^^^^^^^^^^^^^^^^^ -.. _bug-fixes-9: +.. _bug-fixes-10: Bug fixes ''''''''' @@ -300,12 +320,12 @@ Bug fixes - ``CoxPHFitter`` now displays correct columns values when changing alpha param. -.. _section-13: +.. _section-14: 0.22.8 - 2019-10-06 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-7: +.. _new-features-8: New features '''''''''''' @@ -315,19 +335,19 @@ New features - ``conditional_after`` now available in ``CoxPHFitter.predict_median`` - Suppressed some unimportant warnings. -.. _bug-fixes-10: +.. _bug-fixes-11: Bug fixes ''''''''' - fixed initial_point being ignored in AFT models. -.. _section-14: +.. _section-15: 0.22.7 - 2019-09-29 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-8: +.. _new-features-9: New features '''''''''''' @@ -335,7 +355,7 @@ New features - new ``ApproximationWarning`` to tell you if the package is making an potentially mislead approximation. -.. _bug-fixes-11: +.. _bug-fixes-12: Bug fixes ''''''''' @@ -354,19 +374,19 @@ API Changes - Some previous ``StatisticalWarnings`` have been replaced by ``ApproximationWarning`` -.. _section-15: +.. _section-16: 0.22.6 - 2019-09-25 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-9: +.. _new-features-10: New features '''''''''''' - ``conditional_after`` works for ``CoxPHFitter`` prediction models 😅 -.. _bug-fixes-12: +.. _bug-fixes-13: Bug fixes ''''''''' @@ -382,12 +402,12 @@ API Changes - ``utils.dataframe_interpolate_at_times`` renamed to ``utils.interpolate_at_times_and_return_pandas``. -.. _section-16: +.. _section-17: 0.22.5 - 2019-09-20 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-10: +.. _new-features-11: New features '''''''''''' @@ -396,7 +416,7 @@ New features weights. - Better support for predicting on Pandas Series -.. _bug-fixes-13: +.. _bug-fixes-14: Bug fixes ''''''''' @@ -413,12 +433,12 @@ API Changes - ``_get_initial_value`` in parametric univariate models is renamed ``_create_initial_point`` -.. _section-17: +.. _section-18: 0.22.4 - 2019-09-04 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-11: +.. _new-features-12: New features '''''''''''' @@ -437,7 +457,7 @@ API changes - ``KaplanMeierFitter.survival_function_``\ ‘s’ index is no longer given the name “timeline”. -.. _bug-fixes-14: +.. _bug-fixes-15: Bug fixes ''''''''' @@ -445,12 +465,12 @@ Bug fixes - Fixed issue where ``concordance_index`` would never exit if NaNs in dataset. -.. _section-18: +.. _section-19: 0.22.3 - 2019-08-08 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-12: +.. _new-features-13: New features '''''''''''' @@ -474,7 +494,7 @@ API changes gains only in Cox models, and only a small fraction of the API was being used. -.. _bug-fixes-15: +.. _bug-fixes-16: Bug fixes ''''''''' @@ -486,19 +506,19 @@ Bug fixes - Fixed an error in the ``predict_percentile`` of ``LogLogisticAFTFitter``. New tests have been added around this. -.. _section-19: +.. _section-20: 0.22.2 - 2019-07-25 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-13: +.. _new-features-14: New features '''''''''''' - lifelines is now compatible with scipy>=1.3.0 -.. _bug-fixes-16: +.. _bug-fixes-17: Bug fixes ''''''''' @@ -509,12 +529,12 @@ Bug fixes errors when using the library. The correctly numpy has been pinned (to 1.14.0+) -.. _section-20: +.. _section-21: 0.22.1 - 2019-07-14 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-14: +.. _new-features-15: New features '''''''''''' @@ -542,7 +562,7 @@ API changes ``.print_summary`` includes confidence intervals for the exponential of the value. -.. _bug-fixes-17: +.. _bug-fixes-18: Bug fixes ''''''''' @@ -552,12 +572,12 @@ Bug fixes - fixed an overflow bug in ``KaplanMeierFitter`` confidence intervals - improvements in data validation for ``CoxTimeVaryingFitter`` -.. _section-21: +.. _section-22: 0.22.0 - 2019-07-03 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-15: +.. _new-features-16: New features '''''''''''' @@ -591,7 +611,7 @@ API changes could set ``fit_intercept`` to False and not have to set ``ancillary_df`` - now one must specify a DataFrame. -.. _bug-fixes-18: +.. _bug-fixes-19: Bug fixes ''''''''' @@ -600,21 +620,21 @@ Bug fixes is now exact instead of an approximation. - fixed a name error bug in ``CoxTimeVaryingFitter.plot`` -.. _section-22: +.. _section-23: 0.21.5 - 2019-06-22 ^^^^^^^^^^^^^^^^^^^ I’m skipping 0.21.4 version because of deployment issues. -.. _new-features-16: +.. _new-features-17: New features '''''''''''' - ``scoring_method`` now a kwarg on ``sklearn_adapter`` -.. _bug-fixes-19: +.. _bug-fixes-20: Bug fixes ''''''''' @@ -624,12 +644,12 @@ Bug fixes - fixed visual bug that misaligned x-axis ticks and at-risk counts. Thanks @christopherahern! -.. _section-23: +.. _section-24: 0.21.3 - 2019-06-04 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-17: +.. _new-features-18: New features '''''''''''' @@ -643,19 +663,19 @@ New features - ``CoxPHFitter.check_assumptions`` now accepts a ``columns`` parameter to specify only checking a subset of columns. -.. _bug-fixes-20: +.. _bug-fixes-21: Bug fixes ''''''''' - ``covariates_from_event_matrix`` handle nulls better -.. _section-24: +.. _section-25: 0.21.2 - 2019-05-16 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-18: +.. _new-features-19: New features '''''''''''' @@ -679,17 +699,17 @@ API changes - removing ``_compute_likelihood_ratio_test`` on regression models. Use ``log_likelihood_ratio_test`` now. -.. _bug-fixes-21: +.. _bug-fixes-22: Bug fixes ''''''''' -.. _section-25: +.. _section-26: 0.21.1 - 2019-04-26 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-19: +.. _new-features-20: New features '''''''''''' @@ -706,19 +726,19 @@ API changes - output of ``survival_table_from_events`` when collapsing rows to intervals now removes the “aggregate” column multi-index. -.. _bug-fixes-22: +.. _bug-fixes-23: Bug fixes ''''''''' - fixed bug in CoxTimeVaryingFitter when ax is provided, thanks @j-i-l! -.. _section-26: +.. _section-27: 0.21.0 - 2019-04-12 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-20: +.. _new-features-21: New features '''''''''''' @@ -743,7 +763,7 @@ API changes - ``entries`` property in multivariate parametric models has a new Series name: ``entry`` -.. _bug-fixes-23: +.. _bug-fixes-24: Bug fixes ''''''''' @@ -753,12 +773,12 @@ Bug fixes - Fixed an error that didn’t let users use Numpy arrays in prediction for AFT models -.. _section-27: +.. _section-28: 0.20.5 - 2019-04-08 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-21: +.. _new-features-22: New features '''''''''''' @@ -775,7 +795,7 @@ API changes - in ``AalenJohansenFitter``, the ``variance`` parameter is renamed to ``variance_`` to align with the usual lifelines convention. -.. _bug-fixes-24: +.. _bug-fixes-25: Bug fixes ''''''''' @@ -784,12 +804,12 @@ Bug fixes test when using strata. - Fixed some plotting bugs with ``AalenJohansenFitter`` -.. _section-28: +.. _section-29: 0.20.4 - 2019-03-27 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-22: +.. _new-features-23: New features '''''''''''' @@ -808,7 +828,7 @@ API changes - Pandas is now correctly pinned to >= 0.23.0. This was always the case, but not specified in setup.py correctly. -.. _bug-fixes-25: +.. _bug-fixes-26: Bug fixes ''''''''' @@ -817,12 +837,12 @@ Bug fixes - ``PiecewiseExponentialFitter`` is available with ``from lifelines import *``. -.. _section-29: +.. _section-30: 0.20.3 - 2019-03-23 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-23: +.. _new-features-24: New features '''''''''''' @@ -835,12 +855,12 @@ New features ``plot_survival_function`` and ``confidence_interval_survival_function_``. -.. _section-30: +.. _section-31: 0.20.2 - 2019-03-21 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-24: +.. _new-features-25: New features '''''''''''' @@ -864,7 +884,7 @@ API changes @vpolimenov! - The ``C`` column in ``load_lcd`` dataset is renamed to ``E``. -.. _bug-fixes-26: +.. _bug-fixes-27: Bug fixes ''''''''' @@ -880,7 +900,7 @@ Bug fixes the q parameter was below the truncation limit. This should have been ``-np.inf`` -.. _section-31: +.. _section-32: 0.20.1 - 2019-03-16 ^^^^^^^^^^^^^^^^^^^ @@ -904,7 +924,7 @@ API changes This is no longer the case. A 0 will still be added if there is a duration (observed or not) at 0 occurs however. -.. _section-32: +.. _section-33: 0.20.0 - 2019-03-05 ^^^^^^^^^^^^^^^^^^^ @@ -913,7 +933,7 @@ API changes recent installs where Py3. - Updated minimum dependencies, specifically Matplotlib and Pandas. -.. _new-features-25: +.. _new-features-26: New features '''''''''''' @@ -933,19 +953,19 @@ API changes transposed now (previous parameters where columns, now parameters are rows). -.. _bug-fixes-27: +.. _bug-fixes-28: Bug fixes ''''''''' - Fixed a bug with plotting and ``check_assumptions``. -.. _section-33: +.. _section-34: 0.19.5 - 2019-02-26 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-26: +.. _new-features-27: New features '''''''''''' @@ -955,24 +975,24 @@ New features features or categorical variables. - Convergence improvements for AFT models. -.. _section-34: +.. _section-35: 0.19.4 - 2019-02-25 ^^^^^^^^^^^^^^^^^^^ -.. _bug-fixes-28: +.. _bug-fixes-29: Bug fixes ''''''''' - remove some bad print statements in ``CoxPHFitter``. -.. _section-35: +.. _section-36: 0.19.3 - 2019-02-25 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-27: +.. _new-features-28: New features '''''''''''' @@ -984,12 +1004,12 @@ New features - Performance increase to ``print_summary`` in the ``CoxPHFitter`` and ``CoxTimeVaryingFitter`` model. -.. _section-36: +.. _section-37: 0.19.2 - 2019-02-22 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-28: +.. _new-features-29: New features '''''''''''' @@ -997,7 +1017,7 @@ New features - ``ParametricUnivariateFitters``, like ``WeibullFitter``, have smoothed plots when plotting (vs stepped plots) -.. _bug-fixes-29: +.. _bug-fixes-30: Bug fixes ''''''''' @@ -1007,12 +1027,12 @@ Bug fixes - Univariate fitters are more flexiable and can allow 2-d and DataFrames as inputs. -.. _section-37: +.. _section-38: 0.19.1 - 2019-02-21 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-29: +.. _new-features-30: New features '''''''''''' @@ -1029,12 +1049,12 @@ API changes ``PiecewiseExponential`` to the same as ``ExponentialFitter`` (from ``\lambda * t`` to ``t / \lambda``). -.. _section-38: +.. _section-39: 0.19.0 - 2019-02-20 ^^^^^^^^^^^^^^^^^^^ -.. _new-features-30: +.. _new-features-31: New features '''''''''''' @@ -1073,7 +1093,7 @@ API changes means that the *default* for alpha is set to 0.05 in the latest lifelines, instead of 0.95 in previous versions. -.. _bug-fixes-30: +.. _bug-fixes-31: Bug Fixes ''''''''' @@ -1090,7 +1110,7 @@ Bug Fixes models. Thanks @airanmehr! - Fixed some Pandas <0.24 bugs. -.. _section-39: +.. _section-40: 0.18.6 - 2019-02-13 ^^^^^^^^^^^^^^^^^^^ @@ -1100,7 +1120,7 @@ Bug Fixes ``rank`` and ``km`` p-values now. - some performance improvements to ``qth_survival_time``. -.. _section-40: +.. _section-41: 0.18.5 - 2019-02-11 ^^^^^^^^^^^^^^^^^^^ @@ -1121,7 +1141,7 @@ Bug Fixes that can be used to turn off variance calculations since this can take a long time for large datasets. Thanks @pzivich! -.. _section-41: +.. _section-42: 0.18.4 - 2019-02-10 ^^^^^^^^^^^^^^^^^^^ @@ -1131,7 +1151,7 @@ Bug Fixes - adding left-truncation support to parametric univarite models with the ``entry`` kwarg in ``.fit`` -.. _section-42: +.. _section-43: 0.18.3 - 2019-02-07 ^^^^^^^^^^^^^^^^^^^ @@ -1141,7 +1161,7 @@ Bug Fixes warnings are more noticeable. - Improved some warning and error messages. -.. _section-43: +.. _section-44: 0.18.2 - 2019-02-05 ^^^^^^^^^^^^^^^^^^^ @@ -1157,7 +1177,7 @@ Bug Fixes Moved them all (most) to use ``autograd``. - ``LogNormalFitter`` no longer models ``log_sigma``. -.. _section-44: +.. _section-45: 0.18.1 - 2019-02-02 ^^^^^^^^^^^^^^^^^^^ @@ -1168,7 +1188,7 @@ Bug Fixes - use the ``autograd`` lib to help with gradients. - New ``LogLogisticFitter`` univariate fitter available. -.. _section-45: +.. _section-46: 0.18.0 - 2019-01-31 ^^^^^^^^^^^^^^^^^^^ @@ -1205,7 +1225,7 @@ Bug Fixes ``LinAlgError: Matrix is singular.`` and report back to the user advice. -.. _section-46: +.. _section-47: 0.17.5 - 2019-01-25 ^^^^^^^^^^^^^^^^^^^ @@ -1213,7 +1233,7 @@ Bug Fixes - more bugs in ``plot_covariate_groups`` fixed when using non-numeric strata. -.. _section-47: +.. _section-48: 0.17.4 -2019-01-25 ^^^^^^^^^^^^^^^^^^ @@ -1225,7 +1245,7 @@ Bug Fixes - ``groups`` is now called ``values`` in ``CoxPHFitter.plot_covariate_groups`` -.. _section-48: +.. _section-49: 0.17.3 - 2019-01-24 ^^^^^^^^^^^^^^^^^^^ @@ -1233,7 +1253,7 @@ Bug Fixes - Fix in ``compute_residuals`` when using ``schoenfeld`` and the minumum duration has only censored subjects. -.. _section-49: +.. _section-50: 0.17.2 2019-01-22 ^^^^^^^^^^^^^^^^^ @@ -1244,7 +1264,7 @@ Bug Fixes ``for`` loop. The downside is the code is more esoteric now. I’ve added comments as necessary though 🤞 -.. _section-50: +.. _section-51: 0.17.1 - 2019-01-20 ^^^^^^^^^^^^^^^^^^^ @@ -1261,7 +1281,7 @@ Bug Fixes - Fixes a Pandas performance warning in ``CoxTimeVaryingFitter``. - Performances improvements to ``CoxTimeVaryingFitter``. -.. _section-51: +.. _section-52: 0.17.0 - 2019-01-11 ^^^^^^^^^^^^^^^^^^^ @@ -1282,7 +1302,7 @@ Bug Fixes - some plotting improvemnts to ``plotting.plot_lifetimes`` -.. _section-52: +.. _section-53: 0.16.3 - 2019-01-03 ^^^^^^^^^^^^^^^^^^^ @@ -1290,7 +1310,7 @@ Bug Fixes - More ``CoxPHFitter`` performance improvements. Up to a 40% reduction vs 0.16.2 for some datasets. -.. _section-53: +.. _section-54: 0.16.2 - 2019-01-02 ^^^^^^^^^^^^^^^^^^^ @@ -1301,14 +1321,14 @@ Bug Fixes has lots of duplicate times. See https://github.com/CamDavidsonPilon/lifelines/issues/591 -.. _section-54: +.. _section-55: 0.16.1 - 2019-01-01 ^^^^^^^^^^^^^^^^^^^ - Fixed py2 division error in ``concordance`` method. -.. _section-55: +.. _section-56: 0.16.0 - 2019-01-01 ^^^^^^^^^^^^^^^^^^^ @@ -1344,7 +1364,7 @@ Bug Fixes ``lifelines.utils.to_episodic_format``. - ``CoxTimeVaryingFitter`` now accepts ``strata``. -.. _section-56: +.. _section-57: 0.15.4 ^^^^^^ @@ -1352,14 +1372,14 @@ Bug Fixes - bug fix for the Cox model likelihood ratio test when using non-trivial weights. -.. _section-57: +.. _section-58: 0.15.3 - 2018-12-18 ^^^^^^^^^^^^^^^^^^^ - Only allow matplotlib less than 3.0. -.. _section-58: +.. _section-59: 0.15.2 - 2018-11-23 ^^^^^^^^^^^^^^^^^^^ @@ -1370,7 +1390,7 @@ Bug Fixes - removed ``entry`` from ``ExponentialFitter`` and ``WeibullFitter`` as it was doing nothing. -.. _section-59: +.. _section-60: 0.15.1 - 2018-11-23 ^^^^^^^^^^^^^^^^^^^ @@ -1379,7 +1399,7 @@ Bug Fixes - Raise NotImplementedError if the ``robust`` flag is used in ``CoxTimeVaryingFitter`` - that’s not ready yet. -.. _section-60: +.. _section-61: 0.15.0 - 2018-11-22 ^^^^^^^^^^^^^^^^^^^ @@ -1450,7 +1470,7 @@ Bug Fixes When Estimating Risks in Pharmacoepidemiology” for a nice overview of the model. -.. _section-61: +.. _section-62: 0.14.6 - 2018-07-02 ^^^^^^^^^^^^^^^^^^^ @@ -1458,7 +1478,7 @@ Bug Fixes - fix for n > 2 groups in ``multivariate_logrank_test`` (again). - fix bug for when ``event_observed`` column was not boolean. -.. _section-62: +.. _section-63: 0.14.5 - 2018-06-29 ^^^^^^^^^^^^^^^^^^^ @@ -1466,7 +1486,7 @@ Bug Fixes - fix for n > 2 groups in ``multivariate_logrank_test`` - fix weights in KaplanMeierFitter when using a pandas Series. -.. _section-63: +.. _section-64: 0.14.4 - 2018-06-14 ^^^^^^^^^^^^^^^^^^^ @@ -1483,7 +1503,7 @@ Bug Fixes - New ``delay`` parameter in ``add_covariate_to_timeline`` - removed ``two_sided_z_test`` from ``statistics`` -.. _section-64: +.. _section-65: 0.14.3 - 2018-05-24 ^^^^^^^^^^^^^^^^^^^ @@ -1495,7 +1515,7 @@ Bug Fixes - adds a ``column`` argument to ``CoxTimeVaryingFitter`` and ``CoxPHFitter`` ``plot`` method to plot only a subset of columns. -.. _section-65: +.. _section-66: 0.14.2 - 2018-05-18 ^^^^^^^^^^^^^^^^^^^ @@ -1503,7 +1523,7 @@ Bug Fixes - some quality of life improvements for working with ``CoxTimeVaryingFitter`` including new ``predict_`` methods. -.. _section-66: +.. _section-67: 0.14.1 - 2018-04-01 ^^^^^^^^^^^^^^^^^^^ @@ -1521,7 +1541,7 @@ Bug Fixes faster completion of ``fit`` for large dataframes, and up to 10% faster for small dataframes. -.. _section-67: +.. _section-68: 0.14.0 - 2018-03-03 ^^^^^^^^^^^^^^^^^^^ @@ -1543,7 +1563,7 @@ Bug Fixes of a ``RuntimeWarning`` - New checks for complete separation in the dataset for regressions. -.. _section-68: +.. _section-69: 0.13.0 - 2017-12-22 ^^^^^^^^^^^^^^^^^^^ @@ -1572,7 +1592,7 @@ Bug Fixes group the same subjects together and give that observation a weight equal to the count. Altogether, this means a much faster regression. -.. _section-69: +.. _section-70: 0.12.0 ^^^^^^ @@ -1589,7 +1609,7 @@ Bug Fixes - Additional functionality to ``utils.survival_table_from_events`` to bin the index to make the resulting table more readable. -.. _section-70: +.. _section-71: 0.11.3 ^^^^^^ @@ -1601,7 +1621,7 @@ Bug Fixes observation or censorship. - More accurate prediction methods parametrics univariate models. -.. _section-71: +.. _section-72: 0.11.2 ^^^^^^ @@ -1609,14 +1629,14 @@ Bug Fixes - Changing liscense to valilla MIT. - Speed up ``NelsonAalenFitter.fit`` considerably. -.. _section-72: +.. _section-73: 0.11.1 - 2017-06-22 ^^^^^^^^^^^^^^^^^^^ - Python3 fix for ``CoxPHFitter.plot``. -.. _section-73: +.. _section-74: 0.11.0 - 2017-06-21 ^^^^^^^^^^^^^^^^^^^ @@ -1630,14 +1650,14 @@ Bug Fixes of a new ``loc`` kwarg. This is to align with Pandas deprecating ``ix`` -.. _section-74: +.. _section-75: 0.10.1 - 2017-06-05 ^^^^^^^^^^^^^^^^^^^ - fix in internal normalization for ``CoxPHFitter`` predict methods. -.. _section-75: +.. _section-76: 0.10.0 ^^^^^^ @@ -1652,7 +1672,7 @@ Bug Fixes mimic R’s ``basehaz`` API. - new ``predict_log_partial_hazards`` to ``CoxPHFitter`` -.. _section-76: +.. _section-77: 0.9.4 ^^^^^ @@ -1675,7 +1695,7 @@ Bug Fixes - performance improvements in ``CoxPHFitter`` - should see at least a 10% speed improvement in ``fit``. -.. _section-77: +.. _section-78: 0.9.2 ^^^^^ @@ -1684,7 +1704,7 @@ Bug Fixes - throw an error if no admissable pairs in the c-index calculation. Previously a NaN was returned. -.. _section-78: +.. _section-79: 0.9.1 ^^^^^ @@ -1692,7 +1712,7 @@ Bug Fixes - add two summary functions to Weibull and Exponential fitter, solves #224 -.. _section-79: +.. _section-80: 0.9.0 ^^^^^ @@ -1708,7 +1728,7 @@ Bug Fixes - Default predict method in ``k_fold_cross_validation`` is now ``predict_expectation`` -.. _section-80: +.. _section-81: 0.8.1 - 2015-08-01 ^^^^^^^^^^^^^^^^^^ @@ -1725,7 +1745,7 @@ Bug Fixes - scaling of smooth hazards in NelsonAalenFitter was off by a factor of 0.5. -.. _section-81: +.. _section-82: 0.8.0 ^^^^^ @@ -1744,7 +1764,7 @@ Bug Fixes ``lifelines.statistics. power_under_cph``. - fixed a bug when using KaplanMeierFitter for left-censored data. -.. _section-82: +.. _section-83: 0.7.1 ^^^^^ @@ -1763,7 +1783,7 @@ Bug Fixes - refactor each fitter into it’s own submodule. For now, the tests are still in the same file. This will also *not* break the API. -.. _section-83: +.. _section-84: 0.7.0 - 2015-03-01 ^^^^^^^^^^^^^^^^^^ @@ -1782,7 +1802,7 @@ Bug Fixes duration remaining until the death event, given survival up until time t. -.. _section-84: +.. _section-85: 0.6.1 ^^^^^ @@ -1794,7 +1814,7 @@ Bug Fixes your work is to sum up the survival function (for expected values or something similar), it’s more difficult to make a mistake. -.. _section-85: +.. _section-86: 0.6.0 - 2015-02-04 ^^^^^^^^^^^^^^^^^^ @@ -1817,7 +1837,7 @@ Bug Fixes - In ``KaplanMeierFitter``, ``epsilon`` has been renamed to ``precision``. -.. _section-86: +.. _section-87: 0.5.1 - 2014-12-24 ^^^^^^^^^^^^^^^^^^ @@ -1838,7 +1858,7 @@ Bug Fixes ``lifelines.plotting.add_at_risk_counts``. - Fix bug Epanechnikov kernel. -.. _section-87: +.. _section-88: 0.5.0 - 2014-12-07 ^^^^^^^^^^^^^^^^^^ @@ -1851,7 +1871,7 @@ Bug Fixes - add test for summary() - Alternate metrics can be used for ``k_fold_cross_validation``. -.. _section-88: +.. _section-89: 0.4.4 - 2014-11-27 ^^^^^^^^^^^^^^^^^^ @@ -1863,7 +1883,7 @@ Bug Fixes - Fixes bug in 1-d input not returning in CoxPHFitter - Lots of new tests. -.. _section-89: +.. _section-90: 0.4.3 - 2014-07-23 ^^^^^^^^^^^^^^^^^^ @@ -1884,7 +1904,7 @@ Bug Fixes - Adds option ``include_likelihood`` to CoxPHFitter fit method to save the final log-likelihood value. -.. _section-90: +.. _section-91: 0.4.2 - 2014-06-19 ^^^^^^^^^^^^^^^^^^ @@ -1904,7 +1924,7 @@ Bug Fixes from failing so often (this a stop-gap) - pep8 everything -.. _section-91: +.. _section-92: 0.4.1.1 ^^^^^^^ @@ -1917,7 +1937,7 @@ Bug Fixes - Adding more robust cross validation scheme based on issue #67. - fixing ``regression_dataset`` in ``datasets``. -.. _section-92: +.. _section-93: 0.4.1 - 2014-06-11 ^^^^^^^^^^^^^^^^^^ @@ -1936,7 +1956,7 @@ Bug Fixes - Adding a Changelog. - more sanitizing for the statistical tests =) -.. _section-93: +.. _section-94: 0.4.0 - 2014-06-08 ^^^^^^^^^^^^^^^^^^ diff --git a/lifelines/tests/test_estimation.py b/lifelines/tests/test_estimation.py index a2a73080e..f95a02a6c 100644 --- a/lifelines/tests/test_estimation.py +++ b/lifelines/tests/test_estimation.py @@ -203,6 +203,10 @@ def test_repr_without_fitter(self): class TestParametricUnivariateFitters: + def test_spline_fitter_has_specific_fit_method(self): + sp = SplineFitter([1, 2, 3]) + assert sp._scipy_fit_method == "SLSQP" + @flaky def test_confidence_interval_is_expected(self): diff --git a/lifelines/version.py b/lifelines/version.py index b3f711909..51fe4c844 100644 --- a/lifelines/version.py +++ b/lifelines/version.py @@ -1,4 +1,4 @@ # -*- coding: utf-8 -*- from __future__ import unicode_literals -__version__ = "0.24.0" +__version__ = "0.24.1"