Releases | Open Source Science

0.30.0 - 2024-10-29

update dependencies (numpy >= 1.14.0)
fix for decimal kwarg not working in StatisticalResult

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon about 1 year ago

0.29.0 - 2024-06-25

update dependencies (pandas >= 2.1)
update dependencies (scipy >= 1.7)

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 1 year ago

0.28.0 - 2023-01-03

Fixes bins that are far into the future with using survival_table_from_events, see #1587
Removed sklean_adaptor. It was a terrible hack, and causing more confusion and support debt than I want. This cleans up our API and simplifies the library. ✨ There's no replacement, and I doubt I'll introduce one ✨
Fix pandas>=2.0 compatibility.
Fix overflow issue in NelsonAalenfitter, #1585
officially drop support for < py3.9
update some dependencies (pandas >= 1.2)

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 2 years ago

0.27.8 - 2023-09-13

Estimators now have .label property
Fixed some deprecation warnings
Pinned to numpy < 2.0

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 2 years ago

0.27.7 - 2023-05-01

check_assumptions(show_plots=True) will always show plots, regardless of test outcome. Thanks @nomennominatur!
lifelines.datasets is now importable.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 2 years ago

0.27.5 - 2023-04-27

Support pandas 2.0+

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 2 years ago

0.27.4 - 2022-11-16

New features

Support py3.11

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon about 3 years ago

0.27.3

New features

Fixed and silenced a lot of warnings

Bug fixes

Migrate to newer Pandas Styler for to_latex

API Changes

There were way too many functions on the summary objects, so I've hidden to_* on them.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 3 years ago

0.27.2 - 2022-09-07

Bug fixes

Fixed issue in addatrisk_table when there were very late entries.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 3 years ago

0.27.1 - 2022-03-15

New features

all fit_ methods now accept a fit_options dict that allows one to pass kwargs to the underlying fitting algorithm.

API Changes

step_size is removed from Cox models fit. See fit_options above.

Bug fixes

fixed Cox models when "trival" matrix was passed in (one with no covariates)

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 3 years ago

0.27.0 - 2022-03-15

Dropping Python3.6 support.

Bug fixes

Fix late entry in add_at_risk_counts.

New features

add_at_risk_counts has a new flag to determine to use start or end-of-period at risk counts.
new column in fitter's summary that display the number the parameter is being compared against.

API Changes

plot_lifetimes's duration arg has the interpretation of "relative time the subject died (since birth)", instead of the old "time observed for". These interpretations are different when there is late entry.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 4 years ago

0.26.4 - 2021-11-30

New features

adding weights to log rank functions

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon about 4 years ago

0.26.3 - 2021-09-16

Bug fixes

Fix using formulas with CoxPHFitter.score

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 4 years ago

0.26.2 - 2021-09-15

Error in v0.26.1 deployment

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 4 years ago

0.26.1 - 2021-09-15

API Changes

t_0 in logrank_test now will not remove data, but will instead censor all subjects that experience the event afterwards.
update status column in lifelines.datasets.load_lung to be more standard coding: 0 is censored, 1 is event.

Bug fixes

Fix using formulas with AalenAdditiveFitter.predict_cumulative_hazard
Fix using formulas with CoxPHFitter.score

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 4 years ago

0.26.0 - 2021-05-26

New features

.BIC_ is now present on fitted models.
CoxPHFitter with spline baseline can accept pre-computed knot locations.
Left censoring fitting in KaplanMeierFitter is now "expected". That is, predict always predicts the survival function (as does every other model), confidence_interval_ is always the CI for the survival function (as does every other model), and so on. In summary: the API for estimates doesn't change depending on what your censoring your dataset is.

Bug fixes

Fixed an annoying bug where at_risk-table label's were not aligning properly when data spanned large ranges. See merging PR for details.
Fixed a bug in find_best_parametric_model where the wrong BIC value was being computed.
Fixed regression bug when using an array as a penalizer in Cox models.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 4 years ago

0.25.11 - 2021-04-06

A previous release (on Github) was missing correct metadata and was deleted.

Bug fixes

Fix integer-valued categorical variables in regression model predictions.
numpy > 1.20 is allowed.
Bug fix in the elastic-net penalty for Cox models that wasn't weighting the terms correctly.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 4 years ago

0.25.10 - 2021-03-03

New features

Better appearance when using a single row to show in add_at_risk_table.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 5 years ago

0.25.9 - 2021-02-04

Small bump in dependencies.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 5 years ago

0.25.8 - 2021-01-22

Important: we dropped Patsy as our formula framework, and adopted Formulaic. Will the latter is less mature than Patsy, we feel the core capabilities are satisfactory and it provides new opportunities.

New features

Parametric models with formulas are able to be serialized now.
a _scipy_callback function is available to use in fitting algorithms.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 5 years ago

lifelines - v0.25.7

0.25.7 - 2020-12-09

API Changes

Adding cumulative_hazard_at_times to NelsonAalenFitter

Bug fixes

Fixed error in CoxPHFitter when entry time == event time.
Fixed formulas in AFT interval censoring regression.
Fixed concordance_index_ when no events observed
Fixed label being overwritten in ParametricUnivariate models

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon about 5 years ago

lifelines - v0.25.6

0.25.6 - 2020-10-26 New features Parametric Cox models can now handle left and interval censoring datasets. Bug fixes "improved" the output of addatriskcounts by removing a call to plt.tightlayout() - this works better when you are calling addatriskcounts on multiple axes, but it is recommended you call plt.tightlayout() at the very end of your script. Fix bug in KaplanMeierFitter's interval censoring where max(lower bound) < min(upper bound).

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon about 5 years ago

lifelines - v0.25.5

0.25.5 - 2020-09-23

API Changes

check_assumptions now returns a list of list of axes that can be manipulated

Bug fixes

fixed error when using plot_partial_effects with categorical data in AFT models
improved warning when Hessian matrix contains NaNs.
fixed performance regression in interval censoring fitting in parametric models
weights wasn't being applied properly in NPMLE

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 5 years ago

lifelines - v0.25.4

0.25.4 - 2020-08-26

New features

New baseline estimator for Cox models: piecewise
Performance improvements for parametric models' log_likelihood_ratio_test() and print_summary()
Better step-size defaults for Cox model -> more robust convergence.

Bug fixes

fix check_assumptions when using formulas.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 5 years ago

lifelines - v0.25.3

0.25.3 - 2020-08-24

New features

survival_difference_at_fixed_point_in_time_test now accepts fitters instead of raw data, meaning that you can use this function on left, right or interval censored data.

API Changes

See note on survival_difference_at_fixed_point_in_time_test above.

Bug fixes

fix StatisticalResult printing in notebooks
fix Python error when calling plot_covariate_groups
fix dtype mismatches in plot_partial_effects_on_outcome.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 5 years ago

lifelines - v0.25.2

0.25.2 - 2020-08-08

New features

Spline CoxPHFitter can now use strata.

API Changes

a small parameterization change of the spline CoxPHFitter. The linear term in the spline part was moved to a new Intercept term in the beta_.
n_baseline_knots in the spline CoxPHFitter now refers to all knots, and not just interior knots (this was confusing to me, the author.). So add 2 to n_baseline_knots to recover the identical model as previously.

Bug fixes

fix splines CoxPHFitter with when predict_hazard was called.
fix some exception imports I missed.
fix log-likelihood p-value in splines CoxPHFitter

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 5 years ago

lifelines - v0.25.1

0.25.1 - 2020-08-01

Bug fixes

ok actually ship the out-of-sample calibration code
fix labels=False in add_at_risk_counts
all for specific rows to be shown in add_at_risk_counts
put patsy as a proper dependency.
suppress some Pandas 1.1 warnings.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 5 years ago

lifelines - v0.25.0

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.
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.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 5 years ago

lifelines - v0.24.16

0.24.16 - 2020-07-09

New features

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.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 5 years ago

lifelines - v0.24.15

0.24.15 - 2020-07-07

Bug fixes

fixed an edge case in KaplanMeierFitter where a really late entry would occur after all other population had died.
fixed plot in BreslowFlemingtonHarrisFitter
fixed bug where using conditional_after and times in CoxPHFitter("spline") prediction methods would be ignored.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 5 years ago

lifelines - v0.24.14

0.24.14 - 2020-07-02

Bug fixes

fixed a bug where using conditional_after and times in prediction methods would result in a shape error
fixed a bug where score was not able to be used in splined CoxPHFitter
fixed a bug where some columns would not be displayed in print_summary

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 5 years ago

lifelines - v0.24.13

0.24.13 - 2020-06-22

Bug fixes

fixed a bug where CoxPHFitter would ignore inputed alpha levels for confidence intervals
fixed a bug where CoxPHFitter would fail with working with sklearn_adapter

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 5 years ago

lifelines - v0.24.12

0.24.12 - 2020-06-20

New features

improved convergence of GeneralizedGamma(Regression)Fitter.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 5 years ago

lifelines - v0.24.11

0.24.11 - 2020-06-17

New features

new spline regression model CRCSplineFitter based on the paper "A flexible parametric accelerated failure time model" by Michael J. Crowther, Patrick Royston, Mark Clements.
new survival probability calibration tool lifelines.calibration.survival_probability_calibration to help validate regression models. Based on “Graphical calibration curves and the integrated calibration index (ICI) for survival models” by P. Austin, F. Harrell, and D. van Klaveren.

API Changes

(and bug fix) scalar parameters in regression models were not being penalized by penalizer - we now penalizing everything except intercept terms in linear relationships.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 5 years ago

lifelines - v0.24.10

0.24.10

New features

New improvements when using splines model in CoxPHFitter - it should offer much better prediction and baseline-hazard estimation, including extrapolation and interpolation.

API Changes

Related to above: the fitted spline parameters are now available in the .summary and .print_summary methods.

Bug fixes

fixed a bug in initialization of some interval-censoring models -> better convergence.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 5 years ago

lifelines - v0.24.9

0.24.9 - 2020-06-05

New features

Faster NPMLE for interval censored data
New weightings available in the logrank_test: wilcoxon, tarone-ware, peto, fleming-harrington. Thanks @sean-reed
new interval censored dataset: lifelines.datasets.load_mice

Bug fixes

Cleared up some mislabeling in plot_loglogs. Thanks @sean-reed!
tuples are now able to be used as input in univariate models.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 5 years ago

lifelines - v0.24.8

0.24.8

New features

Non parametric interval censoring is now available, experimentally. Not all edge cases are fully checked, and some features are missing. Try it under KaplanMeierFitter.fit_interval_censoring

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 5 years ago

lifelines - v0.24.7

0.24.7

New features

find_best_parametric_model can handle left and interval censoring. Also allows for more fitting options.
AIC_ is a property on parametric models, and AIC_partial_ is a property on Cox models.
penalizer in all regression models can now be an array instead of a float. This enables new functionality and better control over penalization. This is similar (but not identical) to penalty.factors in glmnet in R.
some convergence tweaks which should help recent performance regressions.

Bug fixes

fixed bug where cdf_plot and qq_plot were not factoring in the weights correctly.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 5 years ago

lifelines - 0.24.6

0.24.6 - 2020-05-05

New features

At the cost of some performance, convergence is improved in many models.
New lifelines.plotting.plot_interval_censored_lifetimes for plotting interval censored data - thanks @sean-reed!

Bug fixes

fixed bug where cdf_plot and qq_plot were not factoring in the weights correctly.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 5 years ago

lifelines - v0.24.5

New features

plot_lifetimes accepts pandas Series.

Bug fixes

Fixed important bug in interval censoring models. Users using interval censoring are strongly advised to upgrade.
Improved at_risk_counts for subplots.
More data validation checks for CoxTimeVaryingFitter

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 5 years ago

lifelines - v0.24.4

0.24.4 - 2020-04-13

Bug fixes

Improved stability of interval censoring in parametric models.
setting a dataframe in ancillary_df works for interval censoring
.score works for interval censored models

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 5 years ago

lifelines - v0.24.3

0.24.3 - 2020-03-25

New features

new logx kwarg in plotting curves
PH models have compute_followup_hazard_ratios for simulating what the hazard ratio would be at previous times. This is useful because the final hazard ratio is some weighted average of these.

Bug fixes

Fixed error in HTML printer that was hiding concordance index information.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 6 years ago

lifelines - v0.24.2

0.24.2 - 2020-03-15

Bug fixes

Fixed bug when no covariates were passed into CoxPHFitter. See #975
Fixed error in StatisticalResult where the test name was not displayed correctly.
Fixed a keyword bug in plot_covariate_groups for parametric models.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 6 years ago

lifelines - v0.24.1

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.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 6 years ago

lifelines - v0.24.0

0.24.0 - 2020-02-20

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

CoxPHFitter and CoxTimeVaryingFitter has support for an elastic net penalty, which includes L1 and L2 regression.
CoxPHFitter has new baseline survival estimation methods. Specifically, spline now estimates the coefficients and baseline survival using splines. The traditional method, breslow, is still the default however.
Regression models have a new score method that will score your model against a dataset (ex: a testing or validation dataset). The default is to evaluate the log-likelihood, but also the concordance index can be chose.
New MixtureCureFitter for quickly creating univariate mixture models.
Univariate parametric models have a plot_density, density_at_times, and property density_ that computes the probability density function estimates.
new dataset for interval regression involving C. Botulinum.
new lifelines.fitters.mixins.ProportionalHazardMixin that implements proportional hazard checks.

API Changes

Models' prediction method that return a single array now return a Series (use to return a DataFrame). This includes predict_median, predict_percentile, predict_expectation, predict_log_partial_hazard, and possibly others.
The penalty in Cox models is now scaled by the number of observations. This makes it invariant to changing sample sizes. This change also make the penalty magnitude behave the same as any parametric regression model.
score_ on models has been renamed concordance_index_
models' .variance_matrix_ is now a DataFrame.
CoxTimeVaryingFitter no longer requires an id_col. It's optional, and some checks may be done for integrity if provided.
Significant changes to utils.k_fold_cross_validation.
removed automatically adding inf from PiecewiseExponentialRegressionFitter.breakpoints and PiecewiseExponentialFitter.breakpoints
tie_method was dropped from Cox models (it was always Efron anyways...)
Mixins are moved to lifelines.fitters.mixins
find_best_parametric_model evaluation kwarg has been changed to scoring_method.
removed _score_ and path from Cox model.

Bug fixes

Fixed show_censors with KaplanMeierFitter.plot_cumulative_density see issue #940.
Fixed error in "BIC" code path in find_best_parametric_model
Fixed a bug where left censoring in AFT models was not converging well
Cox models now incorporate any penalizers in their log_likelihood_

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 6 years ago

lifelines - v0.23.9

0.23.9 - 2020-01-28

Bug fixes

fixed important error when a parametric regression model would not assign the correct labels to fitted parameters' variances. See more here: https://github.com/CamDavidsonPilon/lifelines/issues/931. Users of GeneralizedGammaRegressionFitter and any custom regression models should update their code as soon as possible.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 6 years ago

lifelines - v0.23.8

Bug fixes

fixed important error when a parametric regression model would not assign the correct labels to fitted parameters. See more here: https://github.com/CamDavidsonPilon/lifelines/issues/931. Users of GeneralizedGammaRegressionFitter and any custom regression models should update their code as soon as possible.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 6 years ago

lifelines - v0.23.7

Bug fixes for py3.5. This will be the last version of lifelines that supports Python 3.5.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 6 years ago

lifelines - v0.23.6

0.23.6 - 2020-01-07

New features

New univariate model, SplineFitter, that uses cubic splines to model the cumulative hazard.
To aid users with selecting the best parametric model, there is a new lifelines.utils.find_best_parametric_model function that will iterate through the models and return the model with the lowest AIC (by default).
custom parametric regression models can now do left and interval censoring.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 6 years ago

lifelines - v0.23.5

0.23.5 - 2020-01-05

New features

New predict_hazard for parametric regression models.
New lymph node cancer dataset, originally from H.F. for the German Breast Cancer Study Group (GBSG) (1994)

Bug fixes

fixes error thrown when converge of regression models fails.
kwargs is now used in plot_covariate_groups
fixed bug where large exponential numbers in print_summary were not being suppressed correctly.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 6 years ago

lifelines - v0.23.4

Bugfix for PyPI

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon about 6 years ago

lifelines - v0.23.3

0.23.2

New features

StatisticalResult.print_summary supports html output.

Bug fixes

fix import in printer.py
fix html printing with Univariate models.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon about 6 years ago

lifelines - v0.23.2

0.23.2

New features

new lifelines.plotting.rmst_plot for pretty figures of survival curves and RMSTs.
new variance calculations for lifelines.utils.resticted_mean_survival_time
performance improvements on regression models' preprocessing. Should make datasets with high number of columns more performant.

Bug fixes

fixed print_summary for AAF class.
fixed repr for sklearn_adapter classes.
fixed conditional_after in Cox model with strata was used.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon about 6 years ago

lifelines - v0.23.1

0.23.1

New features

new print_summary option style to print HTML, LaTeX or ASCII output
performance improvements for CoxPHFitter - up to 30% performance improvements for some datasets.

Bug fixes

fixed bug where computed statistics were not being shown in print_summary for HTML output.
fixed bug where "None" was displayed in models' __repr__
fixed bug in StatisticalResult.print_summary
fixed bug when using print_summary with left censored models.
lots of minor bug fixes.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon about 6 years ago

lifelines - v0.23.0

0.23.0

New features

new print_summary abstraction that allows HTML printing in Jupyter notebooks!
silenced some warnings.

Bug fixes

The "comparison" value of some parametric univariate models wasn't standard, so the null hypothesis p-value may have been wrong. This is now fixed.
fixed a NaN error in confidence intervals for KaplanMeierFitter

API Changes

To align values across models, the column names for the confidence intervals in parametric univariate models summary have changed.
Fixed typo in ParametricUnivariateFitter name.
median_ has been removed in favour of median_survival_time_.
left_censorship in fit has been removed in favour of fit_left_censoring.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon about 6 years ago

lifelines - v0.22.10

0.22.10

The tests were re-factored to be shipped with the package. Let me know if this causes problems.

Bug fixes

fixed error in plotting models with "lower" or "upper" was in the label name.
fixed bug in plotcovariategroups for AFT models when >1d arrays were used for values arg.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon about 6 years ago

lifelines - v0.22.9

0.22.9 - 2019-10-30

Bug fixes

fixed predict_ methods in AFT models when timeline was not specified.
fixed error in qq_plot
fixed error when submitting a model in qth_survival_time
CoxPHFitter now displays correct columns values when changing alpha param.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon about 6 years ago

lifelines - v0.22.8

0.22.8

New features

Serializing lifelines is better supported. Packages like joblib and pickle are now supported. Thanks @AbdealiJK!
conditional_after now available in CoxPHFitter.predict_median
Suppressed some unimportant warnings.

Bug fixes

fixed initial_point being ignored in AFT models.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon about 6 years ago

lifelines - v0.22.7

Changelog

0.22.7

New features

new ApproximationWarning to tell you if the package is making an potentially bad approximation.

Bug fixes

fixed a bug in parametric prediction for interval censored data.
realigned values in print_summary.
fixed bug in survival_difference_at_fixed_point_in_time_test

API Changes

utils.qth_survival_time no longer takes a cdf argument - users should take the compliment (1-cdf).
Some previous StatisticalWarnings have been replaced by ApproximationWarning

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon about 6 years ago

lifelines - v0.22.6

0.22.6

New features

conditional_after works for CoxPHFitter prediction models 😅

Bug fixes

API Changes

CoxPHFitter.baseline_cumulative_hazard_'s column is renamed "baseline cumulative hazard" - previously it was "baseline hazard". (Only applies if the model has no strata.)
utils.dataframe_interpolate_at_times renamed to utils.interpolate_at_times_and_return_pandas.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 6 years ago

lifelines - v0.22.5

0.22.5 - 2019-09-20

New features

Improvements to the repr of models that takes into accounts weights.
Better support for predicting on Pandas Series

Bug fixes

Fixed issue where fit_interval_censoring wouldn't accept lists.
Fixed an issue with AalenJohansenFitter failing to plot confidence intervals.

API Changes

_get_initial_value in parametric univariate models is renamed _create_initial_point

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 6 years ago

lifelines - v0.22.4

0.22.4 - 2019-09-04

New features

Some performance improvements to regression models.
lifelines will avoid penalizing the intercept (aka bias) variables in regression models.
new utils.restricted_mean_survival_time that approximates the RMST using numerical integration against survival functions.

API changes

KaplanMeierFitter.survival_function_'s' index is no longer given the name "timeline".

Bug fixes

Fixed issue where concordance_index would never exit if NaNs in dataset.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 6 years ago

lifelines - v0.22.3

0.22.3

New features

model's now expose a log_likelihood_ property.
new conditional_after argument on predict_* methods that make prediction on censored subjects easier.
new lifelines.utils.safe_exp to make exp overflows easier to handle.
smarter initial conditions for parametric regression models.
New regression model: GeneralizedGammaRegressionFitter

API changes

removed lifelines.utils.gamma - use autograd_gamma library instead.
removed bottleneck as a dependency. It offered slight performance gains only in Cox models, and only a small fraction of the API was being used.

Bug fixes

AFT log-likelihood ratio test was not using weights correctly.
corrected (by bumping) scipy and autograd dependencies
convergence is improved for most models, and many exp overflow warnings have been eliminated.
Fixed an error in the predict_percentile of LogLogisticAFTFitter. New tests have been added around this.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 6 years ago

lifelines - v0.22.2

0.22.2

New features

lifelines is now compatible with scipy>=1.3.0

Bug fixes

fixed printing error when using robust=True in regression models
GeneralizedGammaFitter is more stable, maybe.
lifelines was allowing old version of numpy (1.6), but this caused errors when using the library. The correctly numpy has been pinned (to 1.14.0+)

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 6 years ago

lifelines - v0.22.1

0.22.1

New features

New univariate model, GeneralizedGammaFitter. This model contains many sub-models, so it is a good model to check fits.
added a warning when a time-varying dataset had instantaneous deaths.
added a initial_point option in univariate parametric fitters.
initial_point kwarg is present in parametric univariate fitters .fit
event_table is now an attribute on all univariate fitters (if right censoring)
improvements to lifelines.utils.gamma

API changes

In AFT models, the column names in confidence_intervals_ has changed to include the alpha value.
In AFT models, some column names in .summary and .print_summary has changed to include the alpha value.
In AFT models, some column names in .summary and .print_summary includes confidence intervals for the exponential of the value.

Bug fixes

when using censors_show in plotting functions, the censor ticks are now reactive to the estimate being shown.
fixed an overflow bug in KaplanMeierFitter confidence intervals
improvements in data validation for CoxTimeVaryingFitter

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 6 years ago

lifelines - v0.22.0

New features

Ability to create custom parametric regression models by specifying the cumulative hazard. This enables new and extensions of AFT models.
percentile(p) method added to univariate models that solves the equation p = S(t) for t
for parametric univariate models, the conditional_time_to_event_ is now exact instead of an approximation.

API changes

In Cox models, the attribute hazards_ has been renamed to params_. This aligns better with the other regression models, and is more clear (what is a hazard anyways?)
In Cox models, a new hazard_ratios_ attribute is available which is the exponentiation of params_.
In regression models, the column names in confidence_intervals_ has changed to include the alpha value.
In regression models, some column names in .summary and .print_summary has changed to include the alpha value.
In regression models, some column names in .summary and .print_summary includes confidence intervals for the exponential of the value.
Significant changes to internal AFT code.
A change to how fit_intercept works in AFT models. Previously one could set fit_intercept to False and not have to set ancillary_df - now one must specify a DataFrame.

Bug fixes

for parametric univariate models, the conditional_time_to_event_ is now exact instead of an approximation.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 6 years ago

lifelines - v0.21.3

0.21.3 - 2019-06-04

New features

include in lifelines is a scikit-learn adapter so lifeline's models can be used with scikit-learn's API. See documentation here.
CoxPHFitter.plot now accepts a hazard_ratios (boolean) parameter that will plot the hazard ratios (and CIs) instead of the log-hazard ratios.
CoxPHFitter.check_assumptions now accepts a columns parameter to specify only checking a subset of columns.

Bug fixes

covariates_from_event_matrix handle nulls better

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 6 years ago

lifelines - v0.21.2

0.21.2 - 2019-05-16

New features

New regression model: PiecewiseExponentialRegressionFitter is available. See blog post here: https://dataorigami.net/blogs/napkin-folding/churn
Regression models have a new method log_likelihood_ratio_test that computes, you guessed it, the log-likelihood ratio test. Previously this was an internal API that is being exposed.

API changes

The default behavior of the predict method on non-parametric estimators (KaplanMeierFitter, etc.) has changed from (previous) linear interpolation to (new) return last value. Linear interpolation is still possible with the interpolate flag.
removing _compute_likelihood_ratio_test on regression models. Use log_likelihood_ratio_test now.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 6 years ago

lifelines - v0.21.1

0.21.1 - 2019-04-26

New features

users can provided their own start and stop column names in add_covariate_to_timeline
PiecewiseExponentialFitter now allows numpy arrays as breakpoints

API changes

output of survival_table_from_events when collapsing rows to intervals now removes the "aggregate" column multi-index.

Bug fixes

fixed bug in CoxTimeVaryingFitter when ax is provided, thanks @j-i-l!

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 6 years ago

lifelines - v0.21.0

0.21.0

New features

weights is now a optional kwarg for parametric univariate models.
all univariate and multivariate parametric models now have ability to handle left, right and interval censored data (the former two being special cases of the latter). Users can use the fit_right_censoring (which is an alias for fit), fit_left_censoring and fit_interval_censoring.
a new interval censored dataset is available under lifelines.datasets.load_diabetes

API changes

left_censorship on all univariate fitters has been deprecated. Please use the new api model.fit_left_censoring(...).
invert_y_axis in model.plot(... has been removed.
entries property in multivariate parametric models has a new Series name: entry

Bug fixes

lifelines was silently converting any NaNs in the event vector to True. An error is now thrown instead.
Fixed an error that didn't let users use Numpy arrays in prediction for AFT models

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 6 years ago

lifelines - v0.20.5

0.20.5 - 2019-04-08

New features

performance improvements for print_summary.

API changes

utils.survival_events_from_table returns an integer weight vector as well as durations and censoring vector.
in AalenJohansenFitter, the variance parameter is renamed to variance_ to align with the usual lifelines convention.

Bug fixes

Fixed an error in the CoxTimeVaryingFitter's likelihood ratio test when using strata.
Fixed some plotting bugs with AalenJohansenFitter

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon over 6 years ago

lifelines - v0.20.4

0.20.4

New features

left-truncation support in AFT models, using the entry_col kwarg in fit()
generate_datasets.piecewise_exponential_survival_data for generating piecewise exp. data
Faster print_summary for AFT models.

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

Better handling for extremely large numbers in print_summary
PiecewiseExponentialFitter is available with from lifelines import *.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.20.3

0.20.3

New features

Now cumulative_density_ & survival_function_ are always present on a fitted KaplanMeierFitter.
New attributes/methods on KaplanMeierFitter: plot_cumulative_density(), confidence_interval_cumulative_density_, plot_survival_function and confidence_interval_survival_function_.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.20.2

0.20.2

New features

Left censoring is now supported in univariate parametric models: .fit(..., left_censorship=True). Examples are in the docs.
new dataset: lifelines.datasets.load_nh4()
Univariate parametric models now include, by default, support for the cumulative density function: .cumulative_density_, .confidence_interval_cumulative_density_, plot_cumulative_density(), cumulative_density_at_times(t).
add a lifelines.plotting.qq_plot for univariate parametric models that handles censored data.

API changes

plot_lifetimes no longer reverses the order when plotting. Thanks @vpolimenov!
The C column in load_lcd dataset is renamed to E.

Bug fixes

fixed a naming error in KaplanMeierFitter when left_censorship was set to True, plot_cumulative_density_() is now plot_cumulative_density().
added some error handling when passing in timedeltas. Ideally, users don't pass in timedeltas, as the scale is ambiguous. However, the error message before was not obvious, so we do some conversion, warn the user, and pass it through.
qth_survival_times for a truncated CDF would return np.inf if the q parameter was below the truncation limit. This should have been -np.inf

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.20.1

0.20.1

Some performance improvements to CoxPHFitter (about 30%). I know it may seem silly, but we are now about the same or slighty faster than the Cox model in R's survival package (for some testing datasets and some configurations). This is a big deal, because 1) lifelines does more error checking prior, 2) R's cox model is written in C, and we are still pure Python/NumPy, 3) R's cox model has decades of development.
suppressed unimportant warnings

API changes

Previously, lifelines always added a 0 row to cph.baseline_hazard_, even if there were no event at this time. This is no longer the case. A 0 will still be added if there is a duration (observed or not) at 0 occurs however.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.20.0

Changelog

0.20.0

Starting with 0.20.0, only Python3 will be supported. Over 75% of recent installs where Py3.
Updated minimum dependencies, specifically Matplotlib and Pandas.

New features

smarter initialization for AFT models which should improve convergence.

API changes

inital_beta in Cox model's .fit is now initial_point.
initial_point is now available in AFT models and CoxTimeVaryingFitter
the DataFrame confidence_intervals_ for univariate models is transposed now (previous parameters where columns, now parameters are rows).

Bug fixes

Fixed a bug with plotting and check_assumptions.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.19.5

0.19.5

New features

plot_covariate_group can accept multiple covariates to plot. This is useful for columns that have implicit correlation like polynomial features or categorical variables.
Convergence improvements for AFT models.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.19.4

0.19.4

Bug fixes

remove some bad print statements in CoxPHFitter.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.19.3

0.19.3

New features

new AFT models: LogNormalAFTFitter and LogLogisticAFTFitter.
AFT models now accept a weights_col argument to fit.
Robust errors (sandwich errors) are now avilable in AFT models using the robust=True kwarg in fit.
Performance increase to print_summary in the CoxPHFitter and CoxTimeVaryingFitter model.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.19.2

0.19.2

New features

ParametricUnivariateFitters, like WeibullFitter, have smoothed plots when plotting (vs stepped plots)

Bug fixes

The ExponentialFitter log likelihood value was incorrect - inference was correct however.
Univariate fitters are more flexiable and can allow 2-d and DataFrames as inputs.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.19.1

0.19.1

New features

improved stability of LogNormalFitter
Matplotlib for Python3 users are not longer forced to use 2.x.

API changes

Important: we changed the parameterization of the PiecewiseExponential to the same as ExponentialFitter (from \lambda * t to t / \lambda).

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.19.0

0.19.0

New features

New regression model WeibullAFTFitter for fitting accelerated failure time models. Docs have been added to our documentation about how to use WeibullAFTFitter (spoiler: it's API is similar to the other regression models) and how to interpret the output.
CoxPHFitter performance improvements (about 10%)
CoxTimeVaryingFitter performance improvements (about 10%)

API changes

Important: we changed the .hazards_ and .standard_errors_ on Cox models to be pandas Series (instead of Dataframes). This felt like a more natural representation of them. You may need to update your code to reflect this. See notes here: https://github.com/CamDavidsonPilon/lifelines/issues/636
Important: we changed the .confidence_intervals_ on Cox models to be transposed. This felt like a more natural representation of them. You may need to update your code to reflect this. See notes here: https://github.com/CamDavidsonPilon/lifelines/issues/636
Important: we changed the parameterization of the WeibullFitter and ExponentialFitter from \lambda * t to t / \lambda. This was for a few reasons: 1) it is a more common parameterization in literature, 2) it helps in convergence.
Important: in models where we add an intercept (currently only AalenAdditiveModel), the name of the added column has been changed from baseline to _intercept
Important: the meaning of alpha in all fitters has changed to be the standard interpretation of alpha in confidence intervals. That means that the default for alpha is set to 0.05 in the latest lifelines, instead of 0.95 in previous versions.

Bug Fixes

Fixed a bug in the _log_likelihood_ property of ParametericUnivariateFitter models. It was showing the "average" log-likelihood (i.e. scaled by 1/n) instead of the total. It now displays the total.
In model print_summarys, correct a label erroring. Instead of "Likelihood test", it should have read "Log-likelihood test".
Fixed a bug that was too frequently rejecting the dtype of event columns.
Fixed a calculation bug in the concordance index for stratified Cox models. Thanks @airanmehr!
Fixed some Pandas <0.24 bugs.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.18.6

0.18.6

some improvements to the output of check_assumptions. show_plots is turned to False by default now. It only shows rank and km p-values now.
some performance improvements to qth_survival_time.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.18.5

0.18.5

added new plotting methods to parametric univariate models: plot_survival_function, plot_hazard and plot_cumulative_hazard. The last one is an alias for plot.
added new properties to parametric univarite models: confidence_interval_survival_function_, confidence_interval_hazard_, confidence_interval_cumulative_hazard_. The last one is an alias for confidence_interval_.
Fixed some overflow issues with AalenJohansenFitter's variance calculations when using large datasets.
Fixed an edgecase in AalenJohansenFitter that causing some datasets with to be jittered too often.
Add a new kwarg to AalenJohansenFitter, calculate_variance that can be used to turn off variance calculations since this can take a long time for large datasets. Thanks @pzivich!

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.18.4

0.18.4

fixed confidence intervals in cumulative hazards for parametric univarite models. They were previously serverly depressed.
adding left-truncation support to parametric univarite models with the entry kwarg in .fit

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.18.3

0.18.3

Some performance improvements to parametric univariate models.
Suppressing some irrelevant NumPy and autograd warnings, so lifeline warnings are more noticeable.
Improved some warning and error messages.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.18.2

0.18.2

New univariate fitter PiecewiseExponentialFitter for creating a stepwise hazard model. See docs online.
Ability to create novel parametric univariate models using the new ParametericUnivariateFitter super class. See docs online for how to do this.
Unfortunately, parametric univariate fitters are not serializable with pickle. The library dill is still useable.
Complete overhaul of all internals for parametric univariate fitters. Moved them all (most) to use autograd.
LogNormalFitter no longer models log_sigma.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.18.1

0.18.1

bug fixes in LogNormalFitter variance estimates
improve convergence of LogNormalFitter. We now model the log of sigma internally, but still expose sigma externally.
use the autograd lib to help with gradients.
New LogLogisticFitter univariate fitter available.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.18.0

0.18.0

LogNormalFitter is a new univariate fitter you can use.
WeibullFitter now correctly returns the confidence intervals (previously returned only NaNs)
WeibullFitter.print_summary() displays p-values associated with its parameters not equal to 1.0 - previously this was (implicitly) comparing against 0, which is trivially always true (the parameters must be greater than 0)
ExponentialFitter.print_summary() displays p-values associated with its parameters not equal to 1.0 - previously this was (implicitly) comparing against 0, which is trivially always true (the parameters must be greater than 0)
ExponentialFitter.plot now displays the cumulative hazard, instead of the survival function. This is to make it easier to compare to WeibullFitter and LogNormalFitter
Univariate fitters' cumulative_hazard_at_times, hazard_at_times, survival_function_at_times return pandas Series now (use to be numpy arrays)
remove alpha keyword from all statistical functions. This was never being used.
Gone are astericks and dots in print_summary functions that represent signficance thresholds.
In models' summary (including print_summary), the log(p) term has changed to -log2(p). This is known as the s-value. See https://lesslikely.com/statistics/s-values/
introduce new statistical tests between univariate datasets: survival_difference_at_fixed_point_in_time_test,...
new warning message when Cox models detects possible non-unique solutions to maximum likelihood.
Generally: clean up lifelines exception handling. Ex: catch LinAlgError: Matrix is singular. and report back to the user advice.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.17.5

0.17.5

more bugs in plot_covariate_groups fixed when using non-numeric strata.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.17.4

0.17.4

Fix bug in plot_covariate_groups that wasn't allowing for strata to be used.
change name of multicenter_aids_cohort_study to load_multicenter_aids_cohort_study

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.17.3

0.17.3

Fix in compute_residuals when using schoenfeld and the minumum duration has only censored subjects.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.17.2

v0.17.2

Another round of serious performance improvements for the Cox models. Up to 2x faster for CoxPHFitter and CoxTimeVaryingFitter. This was mostly the result of using NumPy's einsum to simplify a previous for loop. The downside is the code is more esoteric now.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.17.1

0.17.1

adding bottleneck as a dependency. This library is highly-recommended by Pandas, and in lifelines we see some nice performance improvements with it too. (~15% for CoxPHFitter)
There was a small bug in CoxPHFitter when using batch_mode that was causing coefficients to deviate from their MLE value. This bug eluded tests, which means that it's discrepancy was less than 0.0001 difference. It's fixed now, and even more accurate tests are added.
Faster CoxPHFitter._compute_likelihood_ratio_test()
Fixes a Pandas performance warning in CoxTimeVaryingFitter.
Performances improvements to CoxTimeVaryingFitter.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.17.0

0.17.0

corrected behaviour in CoxPHFitter where score_ was not being refreshed on every new fit.
Reimplentation of AalenAdditiveFitter. There were significant changes to it:
- implementation is at least 10x faster, and possibly up to 100x faster for some datasets.
- memory consumption is way down
- removed the time-varying component from AalenAdditiveFitter. This will return in a future release.
- new print_summary
- weights_col is added
- nn_cumulative_hazard is removed (may add back)
new dataset add: multicenter_aids_cohort_study from Cole SR, Hudgens MG. Survival analysis in infectious disease research: describing events in time. AIDS. 2010;24(16):2423-31.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.16.3

0.16.3

More CoxPHFitter performance improvements. Up to a 40% reduction vs 0.16.2 for some datasets.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.16.2

0.16.2

Fixed CoxTimeVaryingFitter to allow more than one variable to be stratafied
Significant performance improvements for CoxPHFitter with dataset has lots of duplicate times. See https://github.com/CamDavidsonPilon/lifelines/issues/591

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.16.1

0.16.1

Fixed py2 division error in concordance method.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - v0.16.0

0.16.0

Drop Python 3.4 support.
introduction of residual calculations in CoxPHFitter.compute_residuals. Residuals include "schoenfeld", "score", "deltabeta", "deviance", "martingale", and "scaledschoenfeld".
removes estimation namespace for fitters. Should be using from lifelines import xFitter now. Thanks @usmanatron
removes predict_log_hazard_relative_to_mean from Cox model. Thanks @usmanatron
StatisticalResult has be generalized to allow for multiple results (ex: from pairwise comparisons). This means a slightly changed API that is mostly backwards compatible. See doc string for how to use it.
statistics.pairwise_logrank_test now returns a StatisticalResult object instead of a nasty NxN DataFrame 💗
Display log(p-values) as well as p-values in print_summary. Also, p-values below thesholds will be truncated. The orignal p-values are still recoverable using .summary.
Floats print_summary is now displayed to 2 decimal points. This can be changed using the decimal kwarg.
removed standardized from Cox model plotting. It was confusing.
visual improvements to Cox models .plot
print_summary methods accepts kwargs to also be displayed.
CoxPHFitter has a new human-readable method, check_assumptions, to check the assumptions of your Cox proportional hazard model.
A new helper util to "expand" static datasets into long-form: lifelines.utils.to_episodic_format.
CoxTimeVaryingFitter now accepts strata.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon almost 7 years ago

lifelines - 0.15.3

0.15.3

Only allow matplotlib less than 3.0.

0.15.2

API changes to plotting.plot_lifetimes
cluster_col and strata can be used together in CoxPHFitter
removed entry from ExponentialFitter and WeibullFitter as it was doing nothing.

Scientific Software - Peer-reviewed - Python
Published by CamDavidsonPilon about 7 years ago

Recent Releases of lifelines

lifelines - v0.30.0

0.30.0 - 2024-10-29

lifelines - v0.29.0

0.29.0 - 2024-06-25

lifelines - v0.28.0

0.28.0 - 2023-01-03

lifelines - v0.27.8

0.27.8 - 2023-09-13

lifelines - v0.27.7

0.27.7 - 2023-05-01

lifelines - v0.27.5

0.27.5 - 2023-04-27

lifelines - v0.27.4

0.27.4 - 2022-11-16

New features

lifelines - v0.27.3

0.27.3

New features

Bug fixes

API Changes

lifelines - v0.27.2

0.27.2 - 2022-09-07

Bug fixes

lifelines - v0.27.1

0.27.1 - 2022-03-15

New features

API Changes

Bug fixes

lifelines - v0.27.0

0.27.0 - 2022-03-15

Bug fixes

New features

API Changes

lifelines - v0.26.4

0.26.4 - 2021-11-30

New features

lifelines - v0.26.3

0.26.3 - 2021-09-16

Bug fixes

lifelines - v0.26.2

0.26.2 - 2021-09-15

lifelines - v0.26.1

0.26.1 - 2021-09-15

API Changes

Bug fixes

lifelines - 0.26.0

0.26.0 - 2021-05-26

New features

Bug fixes

lifelines - v0.25.11

0.25.11 - 2021-04-06

Bug fixes

lifelines - v0.25.10

0.25.10 - 2021-03-03

New features

lifelines - v0.25.9

0.25.9 - 2021-02-04

lifelines - v0.25.8

0.25.8 - 2021-01-22

New features

lifelines - v0.25.7

0.25.7 - 2020-12-09

API Changes

Bug fixes

lifelines - v0.25.6

lifelines - v0.25.5

0.25.5 - 2020-09-23

API Changes

Bug fixes

lifelines - v0.25.4

0.25.4 - 2020-08-26

New features

Bug fixes

lifelines - v0.25.3

0.25.3 - 2020-08-24

New features

API Changes

Bug fixes

lifelines - v0.25.2