Merge pull request #1095 from CamDavidsonPilon/v0.25.0

V0.25.0

Author: CamDavidsonPilon

CHANGELOG.md

@@ -1,9 +1,39 @@
 ## Changelog
 
+#### 0.25.0 - 2020-07-27
+
+##### New features
+ - Formulas! *lifelines* now supports R-like formulas in regression models. See docs [here]().
+ - `plot_covariate_group` now can plot other y-values like hazards and cumulative hazards (default: survival function).
+ - `CoxPHFitter` now accepts late entries via `entry_col`.
+ - `calibration.survival_probability_calibration` now works with out-of-sample data.
+ - `print_summary` now accepts a `column` argument to filter down the displayed values. This helps with clutter in notebooks, latex, or on the terminal.
+ - `add_at_risk_counts` now follows the cool new KMunicate suggestions
+
+
+##### API Changes
+ - With the introduction of formulas, all models can be using formulas under the hood.
+    - For both custom regression models or non-AFT regression models, this means that you no longer need to add a constant column to your DataFrame (instead add a `1` as a formula string in the `regressors` dict). You may also need to remove the T and E columns from `regressors`. I've updated the models in the `\examples` folder with examples of this new model building.
+ - Unfortunately, if using formulas, your model will not be able to be pickled. This is a problem with an upstream library, and I hope to have it resolved in the near future.
+ - `plot_covariate_groups` has been deprecated in favour of `plot_partial_effects_on_outcome`.
+ - The baseline in `plot_covariate_groups` has changed from the *mean* observation (including dummy-encoded categorical variables) to *median* for ordinal (including continuous) and *mode* for categorical.
+ - Previously, *lifelines* used the label `"_intercept"` to when it added a constant column in regressions. To align with Patsy, we are now using `"Intercept"`.
+ - In AFT models, `ancillary_df` kwarg has been renamed to `ancillary`. This reflects the more general use of the kwarg (not always a DataFrame, but could be a boolean or string now, too).
+ - Some column names in datasets shipped with lifelines have changed.
+ - The never used "lifelines.metrics" is deleted.
+ - With the introduction of formulas, `plot_covariate_groups` (now called `plot_partial_effects_on_outcome`) behaves differently for transformed variables. Users no longer need to add "derivatives" features, and encoding is done implicitly. See docs [here](https://lifelines.readthedocs.io/en/latest/Survival%20Regression.html#plotting-the-effect-of-varying-a-covariate).
+ - all exceptions and warnings have moved to `lifelines.exceptions`
+
+##### Bug fixes
+ - The p-value of the log-likelihood ratio test for the CoxPHFitter with splines was returning the wrong result because the degrees of freedom was incorrect.
+ - better `print_summary` logic in IDEs and Jupyter exports. Previously it should not be displayed.
+ - p-values have been corrected in the `SplineFitter`. Previously, the "null hypothesis" was no coefficient=0, but coefficient=0.01. This is now set to the former.
+ - fixed NaN bug in `survival_table_from_events` with intervals when no events would occur in a interval.
+
 #### 0.24.15 - 2020-07-09
 
 ##### New features
- - improved algorithm choice for large Dataframes for Cox models. Should see a significant performance boost.
+ - improved algorithm choice for large DataFrames for Cox models. Should see a significant performance boost.
 
 ##### Bug fixes
 - fixed `utils.median_survival_time` not accepting Pandas Series.