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

v0.17.3

0.17.3

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

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.

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.

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.

v0.16.3

0.16.3

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

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 #591

v0.16.1

0.16.1

• Fixed py2 division error in concordance method.

v0.16.0

0.16.0

• Drop Python 3.4 support.
• introduction of residual calculations in CoxPHFitter.compute_residuals. Residuals include "schoenfeld", "score", "delta_beta", "deviance", "martingale", and "scaled_schoenfeld".
• 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.

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.