Mercurial > repos > fubar > lifelines_km_cph_tool

comparison lifelines_tool/test-data/readme_sample @ 2:dd5e65893cb8 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
add survival and collapsed life table outputs suggested by Wolfgang
author fubar
date Thu, 10 Aug 2023 22:52:45 +0000
parents 232b874046a7
children
comparison
equal deleted inserted replaced
1:232b874046a7 2:dd5e65893cb8
1 ## Lifelines tool starting. 1 ## Lifelines tool
2 Using data header = Index(['Unnamed: 0', 'week', 'arrest', 'fin', 'age', 'race', 'wexp', 'mar', 2 Input data header = Index(['Unnamed: 0', 'week', 'arrest', 'fin', 'age', 'race', 'wexp', 'mar',
3 'paro', 'prio'], 3 'paro', 'prio'],
4 dtype='object') time column = week status column = arrest 4 dtype='object') time column = week status column = arrest
5 Logrank test for race - 0 vs 1 5 Logrank test for race - 0 vs 1
6 6
7 <lifelines.StatisticalResult: logrank_test> 7 <lifelines.StatisticalResult: logrank_test>
12 test_name = logrank_test 12 test_name = logrank_test
13 13
14 --- 14 ---
15 test_statistic p -log2(p) 15 test_statistic p -log2(p)
16 0.58 0.45 1.16 16 0.58 0.45 1.16
17 #### Survival table using time week and event arrest
18 removed observed censored entrance at_risk
19 event_at
20 0.0 0 0 0 432 432
21 1.0 1 1 0 0 432
22 2.0 1 1 0 0 431
23 3.0 1 1 0 0 430
24 4.0 1 1 0 0 429
25 5.0 1 1 0 0 428
26 6.0 1 1 0 0 427
27 7.0 1 1 0 0 426
28 8.0 5 5 0 0 425
29 9.0 2 2 0 0 420
30 10.0 1 1 0 0 418
31 11.0 2 2 0 0 417
32 12.0 2 2 0 0 415
33 13.0 1 1 0 0 413
34 14.0 3 3 0 0 412
35 15.0 2 2 0 0 409
36 16.0 2 2 0 0 407
37 17.0 3 3 0 0 405
38 18.0 3 3 0 0 402
39 19.0 2 2 0 0 399
40 20.0 5 5 0 0 397
41 21.0 2 2 0 0 392
42 22.0 1 1 0 0 390
43 23.0 1 1 0 0 389
44 24.0 4 4 0 0 388
45 25.0 3 3 0 0 384
46 26.0 3 3 0 0 381
47 27.0 2 2 0 0 378
48 28.0 2 2 0 0 376
49 30.0 2 2 0 0 374
50 31.0 1 1 0 0 372
51 32.0 2 2 0 0 371
52 33.0 2 2 0 0 369
53 34.0 2 2 0 0 367
54 35.0 4 4 0 0 365
55 36.0 3 3 0 0 361
56 37.0 4 4 0 0 358
57 38.0 1 1 0 0 354
58 39.0 2 2 0 0 353
59 40.0 4 4 0 0 351
60 42.0 2 2 0 0 347
61 43.0 4 4 0 0 345
62 44.0 2 2 0 0 341
63 45.0 2 2 0 0 339
64 46.0 4 4 0 0 337
65 47.0 1 1 0 0 333
66 48.0 2 2 0 0 332
67 49.0 5 5 0 0 330
68 50.0 3 3 0 0 325
69 52.0 322 4 318 0 322
70 #### Life table using time week and event arrest
71 removed observed censored at_risk
72 event_at
73 (-0.001, 13.844] 20 20 0 432
74 (13.844, 27.687] 36 36 0 412
75 (27.687, 41.531] 29 29 0 376
76 (41.531, 55.374] 347 29 318 347
17 ### Lifelines test of Proportional Hazards results with prio, age, race, paro, mar, fin as covariates on KM and CPH in lifelines test 77 ### Lifelines test of Proportional Hazards results with prio, age, race, paro, mar, fin as covariates on KM and CPH in lifelines test
18 <lifelines.CoxPHFitter: fitted with 432 total observations, 318 right-censored observations> 78 <lifelines.CoxPHFitter: fitted with 432 total observations, 318 right-censored observations>
19 duration col = 'week' 79 duration col = 'week'
20 event col = 'arrest' 80 event col = 'arrest'
21 baseline estimation = breslow 81 baseline estimation = breslow
22 number of observations = 432 82 number of observations = 432
23 number of events observed = 114 83 number of events observed = 114
24 partial log-likelihood = -659.00 84 partial log-likelihood = -659.00
25 time fit was run = 2023-08-10 05:49:04 UTC 85 time fit was run = 2023-08-10 12:00:14 UTC
26 86
27 --- 87 ---
28 coef exp(coef) se(coef) coef lower 95% coef upper 95% exp(coef) lower 95% exp(coef) upper 95% 88 coef exp(coef) se(coef) coef lower 95% coef upper 95% exp(coef) lower 95% exp(coef) upper 95%
29 covariate 89 covariate
30 prio 0.10 1.10 0.03 0.04 0.15 1.04 1.16 90 prio 0.10 1.10 0.03 0.04 0.15 1.04 1.16