Warning kaplan meier negative durations (#40)

* Add warning if use of negatve duartion in kaplan_meier

* Bump version: 0.2.1 → 0.2.2

Co-authored-by: havakv <haavard.kvamme@gmail..com>

pycox/__init__.py

@@ -4,7 +4,7 @@
 
 __author__ = """Haavard Kvamme"""
 __email__ = 'haavard.kvamme@gmail.com'
-__version__ = '0.2.1'
+__version__ = '0.2.2'
 
 import pycox.datasets
 import pycox.evaluation

pycox/utils.py

@@ -1,3 +1,4 @@
+import warnings
 import pandas as pd
 import numpy as np
 import numba
@@ -52,6 +53,9 @@ def kaplan_meier(durations, events, start_duration=0):
     """
     n = len(durations)
     assert n == len(events)
+    if start_duration > durations.min():
+        warnings.warn(f"start_duration {start_duration} is larger than minimum duration {durations.min()}. "
+            "If intentional, consider changing start_duration when calling kaplan_meier.")
     order = np.argsort(durations)
     durations = durations[order]
     events = events[order]
@@ -72,7 +76,7 @@ def kaplan_meier(durations, events, start_duration=0):
         surv[i:] = 0.
     else:
         surv = np.exp(np.log(1 - di / ni).cumsum())
-    if start_duration != surv_idx.min():
+    if start_duration < surv_idx.min():
         tmp = np.ones(len(surv)+ 1, dtype=surv.dtype)
         tmp[1:] = surv
         surv = tmp

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.1
+current_version = 0.2.2
 commit = True
 tag = False
 

setup.py

@@ -32,7 +32,7 @@
 
 setup(
     name='pycox',
-    version='0.2.1',
+    version='0.2.2',
     description="Survival analysis with PyTorch",
     long_description=long_description,
     long_description_content_type='text/markdown',