lifelines 0.27.5__tar.gz → 0.28.0__tar.gz

{lifelines-0.27.5/lifelines.egg-info → lifelines-0.28.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lifelines
-Version: 0.27.5
+Version: 0.28.0
 Summary: Survival analysis in Python, including Kaplan Meier, Nelson Aalen and regression
 Home-page: https://github.com/CamDavidsonPilon/lifelines
 Author: Cameron Davidson-Pilon
@@ -9,15 +9,20 @@ License: MIT
 Classifier: Development Status :: 4 - Beta
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3.7
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Topic :: Scientific/Engineering
-Requires-Python: >=3.7
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: numpy<2.0,>=1.14.0
+Requires-Dist: scipy>=1.2.0
+Requires-Dist: pandas>=1.2.0
+Requires-Dist: matplotlib>=3.0
+Requires-Dist: autograd>=1.5
+Requires-Dist: autograd-gamma>=0.3
+Requires-Dist: formulaic>=0.2.2
 
 ![](http://i.imgur.com/EOowdSD.png)
 

{lifelines-0.27.5 → lifelines-0.28.0}/lifelines/__init__.py

@@ -1,7 +1,6 @@
 # -*- coding: utf-8 -*-
 # pylint: skip-file
 
-from typing import List
 from lifelines.fitters.weibull_fitter import WeibullFitter
 from lifelines.fitters.exponential_fitter import ExponentialFitter
 from lifelines.fitters.nelson_aalen_fitter import NelsonAalenFitter
@@ -23,7 +22,7 @@ from lifelines.fitters.generalized_gamma_regression_fitter import GeneralizedGam
 from lifelines.fitters.spline_fitter import SplineFitter
 from lifelines.fitters.mixture_cure_fitter import MixtureCureFitter
 from lifelines.fitters.crc_spline_fitter import CRCSplineFitter
-
+from lifelines import datasets
 
 from lifelines.version import __version__
 

{lifelines-0.27.5 → lifelines-0.28.0}/lifelines/datasets/__init__.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 import pandas as pd
-from pkg_resources import resource_filename
+from importlib import resources
 
 
 def _load_dataset(filename, **kwargs):
@@ -18,7 +18,7 @@ def _load_dataset(filename, **kwargs):
     -------
         output: DataFrame
     """
-    return pd.read_csv(resource_filename("lifelines", "datasets/" + filename), engine="python", **kwargs)
+    return pd.read_csv(resources.files("lifelines") / "datasets" / filename, engine="python", **kwargs)
 
 
 def load_recur(**kwargs):

{lifelines-0.27.5 → lifelines-0.28.0}/lifelines/exceptions.py

@@ -5,6 +5,10 @@ class StatError(Exception):
     pass
 
 
+class ProportionalHazardAssumptionError(Exception):
+    pass
+
+
 class ConvergenceError(ValueError):
     # inherits from ValueError for backwards compatibility reasons
     def __init__(self, msg, original_exception=""):

{lifelines-0.27.5 → lifelines-0.28.0}/lifelines/fitters/__init__.py

@@ -70,6 +70,10 @@ class BaseFitter:
             s = """<lifelines.%s>""" % classname
         return s
 
+    @property
+    def label(self):
+        return self._label
+
     @utils.CensoringType.right_censoring
     def fit(*args, **kwargs):
         raise NotImplementedError()
@@ -135,6 +139,10 @@ class UnivariateFitter(BaseFitter):
             "The `plot` function is deprecated, and will be removed in future versions. Use `plot_%s`" % self._estimate_name,
             DeprecationWarning,
         )
+        # Fix the confidence interval plot bug from Aalen-Johansen
+        # when calculate_variance is False.
+        if getattr(self, "_calc_var", None) is False:
+            kwargs["ci_show"] = False
         return _plot_estimate(self, estimate=self._estimate_name, **kwargs)
 
     def subtract(self, other) -> pd.DataFrame:
@@ -213,10 +221,10 @@ class UnivariateFitter(BaseFitter):
         might be 9 years.
         """
         age = self.survival_function_.index.values[:, None]
-        columns = ["%s - Conditional median duration remaining to event" % self._label]
+        columns = ["%s - Conditional median duration remaining to event" % self.label]
         return (
             pd.DataFrame(
-                utils.qth_survival_times(self.survival_function_[self._label] * 0.5, self.survival_function_)
+                utils.qth_survival_times(self.survival_function_[self.label] * 0.5, self.survival_function_)
                 .sort_index(ascending=False)
                 .values,
                 index=self.survival_function_.index,
@@ -454,7 +462,7 @@ class ParametricUnivariateFitter(UnivariateFitter):
         return -ll / weights.sum()
 
     def _compute_confidence_bounds_of_cumulative_hazard(self, alpha, ci_labels) -> pd.DataFrame:
-        return self._compute_confidence_bounds_of_transform(self._cumulative_hazard, alpha, ci_labels)
+        return self._compute_confidence_bounds_of_transform(self._cumulative_hazard, alpha, ci_labels, self.timeline)
 
     def _compute_variance_of_transform(self, transform, timeline=None):
         """
@@ -487,7 +495,9 @@ class ParametricUnivariateFitter(UnivariateFitter):
             np.einsum("nj,jk,nk->n", gradient_at_times.T, self.variance_matrix_, gradient_at_times.T), index=timeline
         )
 
-    def _compute_confidence_bounds_of_transform(self, transform, alpha, ci_labels) -> pd.DataFrame:
+    def _compute_confidence_bounds_of_transform(
+        self, transform, alpha: float, ci_labels: tuple[str, str], timeline
+    ) -> pd.DataFrame:
         """
         This computes the confidence intervals of a transform of the parameters. Ex: take
         the fitted parameters, a function/transform and the variance matrix and give me
@@ -503,20 +513,21 @@ class ParametricUnivariateFitter(UnivariateFitter):
         alpha: float
             confidence level
         ci_labels: tuple
+        timeline: iterable
 
         """
         alpha2 = 1 - alpha / 2.0
         z = utils.inv_normal_cdf(alpha2)
-        df = pd.DataFrame(index=self.timeline)
+        df = pd.DataFrame(index=timeline)
 
         std_of_transform = np.sqrt(self._compute_variance_of_transform(transform))
 
         if ci_labels is None:
-            ci_labels = ["%s_lower_%g" % (self._label, 1 - alpha), "%s_upper_%g" % (self._label, 1 - alpha)]
+            ci_labels = ["%s_lower_%g" % (self.label, 1 - alpha), "%s_upper_%g" % (self.label, 1 - alpha)]
         assert len(ci_labels) == 2, "ci_labels should be a length 2 array."
 
-        df[ci_labels[0]] = transform(self._fitted_parameters_, self.timeline) - z * std_of_transform
-        df[ci_labels[1]] = transform(self._fitted_parameters_, self.timeline) + z * std_of_transform
+        df[ci_labels[0]] = transform(self._fitted_parameters_, timeline) - z * std_of_transform
+        df[ci_labels[1]] = transform(self._fitted_parameters_, timeline) + z * std_of_transform
         return df
 
     def _create_initial_point(self, *args) -> np.ndarray:
@@ -539,7 +550,7 @@ class ParametricUnivariateFitter(UnivariateFitter):
             minimizing_results, previous_results, minimizing_ll = None, None, np.inf
             for method, option in zip(
                 ["Nelder-Mead", self._scipy_fit_method],
-                [{"maxiter": 100}, {**{"disp": show_progress}, **self._scipy_fit_options, **fit_options}],
+                [{"maxiter": 400}, {**{"disp": show_progress}, **self._scipy_fit_options, **fit_options}],
             ):
 
                 initial_value = self._initial_values if previous_results is None else utils._to_1d_array(previous_results.x)
@@ -1054,7 +1065,7 @@ class ParametricUnivariateFitter(UnivariateFitter):
           Rename the series returned. Useful for plotting.
 
         """
-        label = utils.coalesce(label, self._label)
+        label = utils.coalesce(label, self.label)
         return pd.Series(self._survival_function(self._fitted_parameters_, times), index=utils._to_1d_array(times), name=label)
 
     def cumulative_density_at_times(self, times, label: t.Optional[str] = None) -> pd.Series:
@@ -1069,7 +1080,7 @@ class ParametricUnivariateFitter(UnivariateFitter):
           Rename the series returned. Useful for plotting.
 
         """
-        label = utils.coalesce(label, self._label)
+        label = utils.coalesce(label, self.label)
         return pd.Series(self._cumulative_density(self._fitted_parameters_, times), index=utils._to_1d_array(times), name=label)
 
     def density_at_times(self, times, label=None) -> pd.Series:
@@ -1084,7 +1095,7 @@ class ParametricUnivariateFitter(UnivariateFitter):
           Rename the series returned. Useful for plotting.
 
         """
-        label = utils.coalesce(label, self._label)
+        label = utils.coalesce(label, self.label)
         return pd.Series(self._density(self._fitted_parameters_, times), index=utils._to_1d_array(times), name=label)
 
     def cumulative_hazard_at_times(self, times, label: t.Optional[str] = None) -> pd.Series:
@@ -1098,7 +1109,7 @@ class ParametricUnivariateFitter(UnivariateFitter):
         label: string, optional
           Rename the series returned. Useful for plotting.
         """
-        label = utils.coalesce(label, self._label)
+        label = utils.coalesce(label, self.label)
         return pd.Series(self._cumulative_hazard(self._fitted_parameters_, times), index=utils._to_1d_array(times), name=label)
 
     def hazard_at_times(self, times, label: t.Optional[str] = None) -> pd.Series:
@@ -1113,7 +1124,7 @@ class ParametricUnivariateFitter(UnivariateFitter):
           Rename the series returned. Useful for plotting.
 
         """
-        label = utils.coalesce(label, self._label)
+        label = utils.coalesce(label, self.label)
         return pd.Series(self._hazard(self._fitted_parameters_, times), index=utils._to_1d_array(times), name=label)
 
     @property
@@ -1135,28 +1146,28 @@ class ParametricUnivariateFitter(UnivariateFitter):
         """
         The confidence interval of the hazard.
         """
-        return self._compute_confidence_bounds_of_transform(self._hazard, self.alpha, self._ci_labels)
+        return self._compute_confidence_bounds_of_transform(self._hazard, self.alpha, self._ci_labels, self.timeline)
 
     @property
     def confidence_interval_density_(self) -> pd.DataFrame:
         """
         The confidence interval of the hazard.
         """
-        return self._compute_confidence_bounds_of_transform(self._density, self.alpha, self._ci_labels)
+        return self._compute_confidence_bounds_of_transform(self._density, self.alpha, self._ci_labels, self.timeline)
 
     @property
     def confidence_interval_survival_function_(self) -> pd.DataFrame:
         """
         The lower and upper confidence intervals for the survival function
         """
-        return self._compute_confidence_bounds_of_transform(self._survival_function, self.alpha, self._ci_labels)
+        return self._compute_confidence_bounds_of_transform(self._survival_function, self.alpha, self._ci_labels, self.timeline)
 
     @property
     def confidence_interval_cumulative_density_(self) -> pd.DataFrame:
         """
         The lower and upper confidence intervals for the cumulative density
         """
-        return self._compute_confidence_bounds_of_transform(self._cumulative_density, self.alpha, self._ci_labels)
+        return self._compute_confidence_bounds_of_transform(self._cumulative_density, self.alpha, self._ci_labels, self.timeline)
 
     def plot(self, **kwargs):
         """
@@ -1203,7 +1214,7 @@ class ParametricUnivariateFitter(UnivariateFitter):
 
         """
         age = self.timeline
-        columns = ["%s - Conditional median duration remaining to event" % self._label]
+        columns = ["%s - Conditional median duration remaining to event" % self.label]
 
         return pd.DataFrame(self.percentile(0.5 * self.survival_function_.values) - age[:, None], index=age, columns=columns)
 
@@ -1398,7 +1409,7 @@ class ParametricRegressionFitter(RegressionFitter):
     def _survival_function(self, params, T, Xs):
         return anp.clip(anp.exp(-self._cumulative_hazard(params, T, Xs)), 1e-12, 1 - 1e-12)
 
-    def _log_likelihood_right_censoring(self, params, Ts, E, W, entries, Xs) -> float:
+    def _log_likelihood_right_censoring(self, params, Ts: tuple, E, W, entries, Xs) -> float:
 
         T = Ts[0]
         non_zero_entries = entries > 0
@@ -1965,7 +1976,6 @@ class ParametricRegressionFitter(RegressionFitter):
             raise exceptions.ConvergenceError(
                 dedent(
                     f"""\
-                {minimum_results=}
 
                 Fitting did not converge. Try the following:
 
@@ -1976,6 +1986,8 @@ class ParametricRegressionFitter(RegressionFitter):
                 4. Try using an alternate minimizer: ``fitter._scipy_fit_method = "SLSQP"``.
                 5. Trying adding a small penalizer (or changing it, if already present). Example: `{self._class_name}(penalizer=0.01).fit(...)`.
                 6. Are there any extreme outliers? Try modeling them or dropping them to see if it helps convergence.
+
+                minimum_results={minimum_results}
             """
                 )
             )
@@ -3353,6 +3365,8 @@ class ParametericAFTRegressionFitter(ParametricRegressionFitter):
             also display the baseline survival, defined as the survival at the mean of the original dataset.
         times: iterable
             pass in a times to plot
+        y: str
+            one of "survival_function", "hazard", "cumulative_hazard". Default "survival_function"
         kwargs:
             pass in additional plotting commands
 

{lifelines-0.27.5 → lifelines-0.28.0}/lifelines/fitters/aalen_johansen_fitter.py

@@ -7,6 +7,7 @@ import warnings
 from lifelines.fitters import NonParametricUnivariateFitter
 from lifelines.utils import _preprocess_inputs, inv_normal_cdf, CensoringType, coalesce
 from lifelines import KaplanMeierFitter
+from lifelines.plotting import _plot_estimate
 
 
 class AalenJohansenFitter(NonParametricUnivariateFitter):
@@ -261,3 +262,46 @@ class AalenJohansenFitter(NonParametricUnivariateFitter):
 
         # Detect duplicated times with different event types
         return (dup_times & (~dup_events)).any()
+
+    def plot_cumulative_density(self, **kwargs):
+        """Plots a pretty figure of the model
+
+        Matplotlib plot arguments can be passed in inside the kwargs.
+
+        Parameters
+        -----------
+        show_censors: bool
+            place markers at censorship events. Default: False
+        censor_styles: dict
+            If show_censors, this dictionary will be passed into the plot call.
+        ci_alpha: float
+            the transparency level of the confidence interval. Default: 0.3
+        ci_force_lines: bool
+            force the confidence intervals to be line plots (versus default shaded areas). Default: False
+        ci_show: bool
+            show confidence intervals. Default: True
+        ci_legend: bool
+            if ci_force_lines is True, this is a boolean flag to add the lines' labels to the legend. Default: False
+        at_risk_counts: bool
+            show group sizes at time points. See function ``add_at_risk_counts`` for details. Default: False
+        loc: slice
+            specify a time-based subsection of the curves to plot, ex:
+
+            >>> model.plot(loc=slice(0.,10.))
+
+            will plot the time values between t=0. and t=10.
+        iloc: slice
+            specify a location-based subsection of the curves to plot, ex:
+
+            >>> model.plot(iloc=slice(0,10))
+
+            will plot the first 10 time points.
+
+        Returns
+        -------
+        ax:
+            a pyplot axis object
+        """
+        if not self._calc_var:
+            kwargs["ci_show"] = False
+        _plot_estimate(self, estimate=self._estimate_name, **kwargs)

{lifelines-0.27.5 → lifelines-0.28.0}/lifelines/fitters/breslow_fleming_harrington_fitter.py

@@ -72,7 +72,14 @@ class BreslowFlemingHarringtonFitter(NonParametricUnivariateFitter):
         alpha = coalesce(alpha, self.alpha)
 
         naf = NelsonAalenFitter(alpha=alpha)
-        naf.fit(durations, event_observed=event_observed, timeline=timeline, label=self._label, entry=entry, ci_labels=ci_labels)
+        naf.fit(
+            durations,
+            event_observed=event_observed,
+            timeline=timeline,
+            label=self._label,
+            entry=entry,
+            ci_labels=ci_labels,
+        )
         self.durations, self.event_observed, self.timeline, self.entry, self.event_table, self.weights = (
             naf.durations,
             naf.event_observed,
@@ -87,6 +94,7 @@ class BreslowFlemingHarringtonFitter(NonParametricUnivariateFitter):
         self.confidence_interval_ = np.exp(-naf.confidence_interval_)
         self.confidence_interval_survival_function_ = self.confidence_interval_
         self.confidence_interval_cumulative_density = 1 - self.confidence_interval_
+        self.confidence_interval_cumulative_density[:] = np.fliplr(self.confidence_interval_cumulative_density.values)
 
         # estimation methods
         self._estimation_method = "survival_function_"

{lifelines-0.27.5 → lifelines-0.28.0}/lifelines/fitters/cox_time_varying_fitter.py

@@ -153,6 +153,7 @@ class CoxTimeVaryingFitter(SemiParametricRegressionFitter, ProportionalHazardMix
             Override the default values in NR algorithm:
                 step_size: 0.95,
                 precision: 1e-07,
+                r_precision=1e-9,
                 max_steps: 500,
 
         Returns
@@ -328,12 +329,13 @@ class CoxTimeVaryingFitter(SemiParametricRegressionFitter, ProportionalHazardMix
         weights,
         show_progress=False,
         step_size=0.95,
-        precision=10e-6,
+        precision=1e-8,
+        r_precision=1e-9,
         max_steps=50,
         initial_point=None,
     ):  # pylint: disable=too-many-arguments,too-many-locals,too-many-branches,too-many-statements
         """
-        Newton Rhaphson algorithm for fitting CPH model.
+        Newton Raphson algorithm for fitting CPH model.
 
         Parameters
         ----------
@@ -345,8 +347,11 @@ class CoxTimeVaryingFitter(SemiParametricRegressionFitter, ProportionalHazardMix
         step_size: float
             > 0 to determine a starting step size in NR algorithm.
         precision: float
-            the convergence halts if the norm of delta between
-                     successive positions is less than epsilon.
+            the algorithm stops if the norm of delta between
+            successive positions is less than ``precision``.
+        r_precision: float, optional
+            the algorithms stops if the relative decrease in log-likelihood
+            between successive iterations goes below ``r_precision``.
 
         Returns
         --------
@@ -443,17 +448,17 @@ https://lifelines.readthedocs.io/en/latest/Examples.html#problems-with-convergen
 
             if show_progress:
                 print(
-                    "\rIteration %d: norm_delta = %.5f, step_size = %.5f, ll = %.5f, newton_decrement = %.5f, seconds_since_start = %.1f"
+                    "\rIteration %d: norm_delta = %.2e, step_size = %.4f, log_lik = %.5f, newton_decrement = %.2e, seconds_since_start = %.1f"
                     % (i, norm_delta, step_size, ll, newton_decrement, time.time() - start_time)
                 )
 
             # convergence criteria
             if norm_delta < precision:
                 converging, completed = False, True
-            elif previous_ll > 0 and abs(ll - previous_ll) / (-previous_ll) < 1e-09:
-                # this is what R uses by default
+            elif previous_ll > 0 and abs(ll - previous_ll) / (-previous_ll) < r_precision:
+                # this is what R uses by default with r_precision=1e-9
                 converging, completed = False, True
-            elif newton_decrement < 10e-8:
+            elif newton_decrement < precision:
                 converging, completed = False, True
             elif i >= max_steps:
                 # 50 iterations steps with N-R is a lot.
@@ -481,12 +486,12 @@ See https://stats.stackexchange.com/questions/11109/how-to-deal-with-perfect-sep
         # report to the user problems that we detect.
         if completed and norm_delta > 0.1:
             warnings.warn(
-                "Newton-Rhapson convergence completed but norm(delta) is still high, %.3f. This may imply non-unique solutions to the maximum likelihood. Perhaps there is colinearity or complete separation in the dataset?"
+                "Newton-Raphson convergence completed but norm(delta) is still high, %.3f. This may imply non-unique solutions to the maximum likelihood. Perhaps there is colinearity or complete separation in the dataset?"
                 % norm_delta,
                 ConvergenceWarning,
             )
         elif not completed:
-            warnings.warn("Newton-Rhapson failed to converge sufficiently in %d steps." % max_steps, ConvergenceWarning)
+            warnings.warn("Newton-Raphson failed to converge sufficiently in %d steps." % max_steps, ConvergenceWarning)
 
         return beta, ll, hessian
 

{lifelines-0.27.5 → lifelines-0.28.0}/lifelines/fitters/coxph_fitter.py

@@ -80,7 +80,7 @@ class CoxPHFitter(RegressionFitter, ProportionalHazardMixin):
         When ``baseline_estimation_method="spline"``, this allows customizing the points in the time axis for the baseline hazard curve.
         To use evenly-spaced points in time, the ``n_baseline_knots`` parameter can be employed instead.
 
-      breakpoints: int
+      breakpoints: list, optional
         Used when ``baseline_estimation_method="piecewise"``. Set the positions of the baseline hazard breakpoints.
 
     Examples
@@ -242,7 +242,7 @@ class CoxPHFitter(RegressionFitter, ProportionalHazardMixin):
             algorithm. Default is the zero vector.
 
         fit_options: dict, optional
-            pass kwargs for the fitting algorithm. For semi-parametric models, this is the Newton-Rhapson method (see method _newton_raphson_for_efron_model for kwargs)
+            pass kwargs for the fitting algorithm. For semi-parametric models, this is the Newton-Raphson method (see method _newton_raphson_for_efron_model for kwargs)
 
         Returns
         -------
@@ -1430,10 +1430,11 @@ estimate the variances. See paper "Variance estimation when using inverse probab
         show_progress: bool = True,
         step_size: float = 0.95,
         precision: float = 1e-07,
+        r_precision: float = 1e-9,
         max_steps: int = 500,
     ):  # pylint: disable=too-many-statements,too-many-branches
         """
-        Newton Rhaphson algorithm for fitting CPH model.
+        Newton Raphson algorithm for fitting CPH model.
 
         Note
         ----
@@ -1450,13 +1451,15 @@ estimate the variances. See paper "Variance estimation when using inverse probab
         step_size: float, optional
             > 0.001 to determine a starting step size in NR algorithm.
         precision: float, optional
-            the convergence halts if the norm of delta between
-            successive positions is less than epsilon.
+            the algorithm stops if the norm of delta between
+            successive positions is less than ``precision``.
+        r_precision: float, optional
+            the algorithms stops if the relative decrease in log-likelihood
+            between successive iterations goes below ``r_precision``.
         show_progress: bool, optional
-            since the fitter is iterative, show convergence
-                 diagnostics.
+            since the fitter is iterative, show convergence diagnostics.
         max_steps: int, optional
-            the maximum number of iterations of the Newton-Rhaphson algorithm.
+            the maximum number of iterations of the Newton-Raphson algorithm.
 
         Returns
         -------
@@ -1564,15 +1567,15 @@ estimate the variances. See paper "Variance estimation when using inverse probab
 
             if show_progress:
                 print(
-                    "\rIteration %d: norm_delta = %.5f, step_size = %.4f, log_lik = %.5f, newton_decrement = %.5f, seconds_since_start = %.1f"
+                    "\rIteration %d: norm_delta = %.2e, step_size = %.4f, log_lik = %.5f, newton_decrement = %.2e, seconds_since_start = %.1f"
                     % (i, norm_delta, step_size, ll_, newton_decrement, time.time() - start)
                 )
 
             # convergence criteria
             if norm_delta < precision:
                 converging, success = False, True
-            elif previous_ll_ != 0 and abs(ll_ - previous_ll_) / (-previous_ll_) < 1e-09:
-                # this is what R uses by default
+            elif previous_ll_ != 0 and abs(ll_ - previous_ll_) / (-previous_ll_) < r_precision:
+                # this is what R uses by default, with r_precision = 1e-9
                 converging, success = False, True
             elif newton_decrement < precision:
                 converging, success = False, True
@@ -1602,14 +1605,14 @@ See https://stats.stackexchange.com/q/11109/11867 for more.\n",
         if success and norm_delta > 0.1:
             self._check_values_post_fitting(X, T, E, weights)
             warnings.warn(
-                "Newton-Rhaphson convergence completed successfully but norm(delta) is still high, %.3f. This may imply non-unique solutions to the maximum likelihood. Perhaps there is collinearity or complete separation in the dataset?\n"
+                "Newton-Raphson convergence completed successfully but norm(delta) is still high, %.3f. This may imply non-unique solutions to the maximum likelihood. Perhaps there is collinearity or complete separation in the dataset?\n"
                 % norm_delta,
                 exceptions.ConvergenceWarning,
             )
         elif not success:
             self._check_values_post_fitting(X, T, E, weights)
             warnings.warn(
-                "Newton-Rhaphson failed to converge sufficiently. {0}".format(CONVERGENCE_DOCS), exceptions.ConvergenceWarning
+                "Newton-Raphson failed to converge sufficiently. {0}".format(CONVERGENCE_DOCS), exceptions.ConvergenceWarning
             )
 
         return beta, ll_, hessian
@@ -2855,6 +2858,7 @@ class ParametricCoxModelFitter(ParametricRegressionFitter, ProportionalHazardMix
             df = df.to_frame().T.infer_objects()
 
         df = df.copy()
+        df.index.name = None
 
         if self.strata is not None:
             df = df.reset_index().set_index(self.strata)

{lifelines-0.27.5 → lifelines-0.28.0}/lifelines/fitters/generalized_gamma_fitter.py

@@ -105,6 +105,7 @@ class GeneralizedGammaFitter(KnownModelParametricUnivariateFitter):
     """
 
     _scipy_fit_method = "SLSQP"
+    _scipy_fit_options = {"maxiter": 10_000, "maxfev": 10_000}
     _fitted_parameter_names = ["mu_", "ln_sigma_", "lambda_"]
     _bounds = [(None, None), (None, None), (None, None)]
     _compare_to_values = np.array([0.0, 0.0, 1.0])
@@ -117,14 +118,14 @@ class GeneralizedGammaFitter(KnownModelParametricUnivariateFitter):
         elif CensoringType.is_interval_censoring(self):
             # this fails if Ts[1] == Ts[0], so we add a some fudge factors.
             log_data = log(Ts[1] - Ts[0] + 0.1)
-        return np.array([log_data.mean(), log(log_data.std() + 0.01), 0.1])
+        return np.array([log_data.mean() * 1.5, log(log_data.std() + 0.1), 1.0])
 
     def _cumulative_hazard(self, params, times):
         mu_, ln_sigma_, lambda_ = params
 
         sigma_ = safe_exp(ln_sigma_)
         Z = (log(times) - mu_) / sigma_
-        ilambda_2 = 1 / lambda_ ** 2
+        ilambda_2 = 1 / lambda_**2
         clipped_exp = np.clip(safe_exp(lambda_ * Z) * ilambda_2, 1e-300, 1e20)
 
         if lambda_ > 0:
@@ -137,7 +138,7 @@ class GeneralizedGammaFitter(KnownModelParametricUnivariateFitter):
 
     def _log_hazard(self, params, times):
         mu_, ln_sigma_, lambda_ = params
-        ilambda_2 = 1 / lambda_ ** 2
+        ilambda_2 = 1 / lambda_**2
         Z = (log(times) - mu_) / safe_exp(ln_sigma_)
         clipped_exp = np.clip(safe_exp(lambda_ * Z) * ilambda_2, 1e-300, 1e20)
         if lambda_ > 0:
@@ -171,5 +172,5 @@ class GeneralizedGammaFitter(KnownModelParametricUnivariateFitter):
         sigma_ = exp(self.ln_sigma_)
 
         if lambda_ > 0:
-            return exp(sigma_ * log(gammainccinv(1 / lambda_ ** 2, p) * lambda_ ** 2) / lambda_) * exp(self.mu_)
-        return exp(sigma_ * log(gammaincinv(1 / lambda_ ** 2, p) * lambda_ ** 2) / lambda_) * exp(self.mu_)
+            return exp(sigma_ * log(gammainccinv(1 / lambda_**2, p) * lambda_**2) / lambda_) * exp(self.mu_)
+        return exp(sigma_ * log(gammaincinv(1 / lambda_**2, p) * lambda_**2) / lambda_) * exp(self.mu_)

{lifelines-0.27.5 → lifelines-0.28.0}/lifelines/fitters/kaplan_meier_fitter.py

@@ -351,9 +351,14 @@ class KaplanMeierFitter(NonParametricUnivariateFitter):
         primary_estimate_name = "survival_function_"
         secondary_estimate_name = "cumulative_density_"
 
-        (self.durations, self.event_observed, self.timeline, self.entry, self.event_table, self.weights) = _preprocess_inputs(
-            durations, event_observed, timeline, entry, weights
-        )
+        (
+            self.durations,
+            self.event_observed,
+            self.timeline,
+            self.entry,
+            self.event_table,
+            self.weights,
+        ) = _preprocess_inputs(durations, event_observed, timeline, entry, weights)
 
         alpha = alpha if alpha else self.alpha
         log_estimate, cumulative_sq_ = _additive_estimate(
@@ -386,6 +391,7 @@ class KaplanMeierFitter(NonParametricUnivariateFitter):
 
         self.confidence_interval_survival_function_ = self.confidence_interval_
         self.confidence_interval_cumulative_density_ = 1 - self.confidence_interval_
+        self.confidence_interval_cumulative_density_[:] = np.fliplr(self.confidence_interval_cumulative_density_.values)
         self._median = median_survival_times(self.survival_function_)
         self._cumulative_sq_ = cumulative_sq_