The aim of this package is to facilitate the use of survival data by switching from temporal data in the form of acollection of survival functions to temporal matrices calculating other functions derived from survival analysis,such as residual life, hazard function, etc. analysis, such as residual life expectancy, hazard function, etc.
pip install survival-data-handler
importpandasaspdfromlifelinesimportCoxPHFitterfromlifelines.datasetsimportload_rossirossi=load_rossi()cph=CoxPHFitter()cph.fit(rossi,duration_col='week',event_col='arrest')curves=cph.predict_survival_function(rossi).Tcurves.columns=pd.to_timedelta(curves.columns.to_numpy()*7,unit="D")print(curves.head())
| 7 days 00:00:00 | 14 days 00:00:00 | 21 days 00:00:00 | 28 days 00:00:00 | 35 days 00:00:00 | 42 days 00:00:00 | 49 days 00:00:00 | 56 days 00:00:00 | 63 days 00:00:00 | 70 days 00:00:00 |
|---|
| 0 | 0.997616 | 0.99523 | 0.992848 | 0.990468 | 0.988085 | 0.985699 | 0.983305 | 0.971402 | 0.966614 | 0.964223 |
| 1 | 0.993695 | 0.987411 | 0.981162 | 0.974941 | 0.968739 | 0.962552 | 0.95637 | 0.926001 | 0.913958 | 0.907978 |
| 2 | 0.994083 | 0.988183 | 0.982314 | 0.976468 | 0.970639 | 0.96482 | 0.959004 | 0.930402 | 0.919043 | 0.913399 |
| 3 | 0.999045 | 0.998089 | 0.997133 | 0.996176 | 0.995216 | 0.994254 | 0.993287 | 0.98846 | 0.986508 | 0.985531 |
| 4 | 0.997626 | 0.99525 | 0.992878 | 0.990507 | 0.988135 | 0.985758 | 0.983374 | 0.97152 | 0.966752 | 0.96437 |
fromsurvival_data_handlerimportLifespanage=pd.to_timedelta(rossi["age"]*365.25,unit="D")birth=pd.to_datetime('2000')rossi["index"]=rossi.indexbirth=pd.to_datetime('2000')lifespan=Lifespan(curves,index=rossi["index"],birth=birth,age=age,window=(pd.to_datetime("2000"),pd.to_datetime("2001")))We now add the supervision data (in the form of duration)
lifespan.add_supervision(event=rossi["arrest"],# True if the data is observed False, when censoreddurations=rossi["duration"]+birth# The duration)
Let's calculate the associated performance
lifespan.assess_metric("survival_function")| Date | Performance (1 - AUC) |
|---|
| 2000-01-31 | 0.468458 |
| 2000-03-01 | 0.384425 |
| 2000-03-31 | 0.432012 |
| 2000-04-30 | 0.357338 |
| 2000-05-30 | 0.365263 |
| 2000-06-29 | 0.365190 |
| 2000-07-29 | 0.371438 |
| 2000-08-28 | 0.343447 |
| 2000-09-27 | 0.340607 |
| 2000-10-27 | 0.344628 |
| 2000-11-26 | 0.334398 |
| 2000-12-26 | 0.334444 |
