CamDavidsonPilon/lifelines: v0.19.0

Published February 20, 2019 | Version v0.19.0

Software Open

1. @neo4j
2. Wave
3. Fred Hutchinson Cancer Research Center
4. @nubank
5. @Esri
6. Autodesk
7. ID Analytics
8. ENS de Cachan - Paris Saclay University
9. Berlin Institute for Medical Systems Biology
10. Bell
11. Ampion, Inc.
12. @TheJacksonLaboratory
13. Origin Rose
14. @Microsoft
15. Shopify
16. @VirginiaTech - @bi-sdal - GBCB
17. IKNL
18. CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

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.

Files

Name	Size	Download all
CamDavidsonPilon/lifelines-v0.19.0.zip md5:7dae59cb21c3fe7bb855505994329526	4.2 MB	Preview Download

Is supplement to: https://github.com/CamDavidsonPilon/lifelines/tree/v0.19.0 (URL)