def test_AssertionErrors(self):
print('Testing Assertion Error checks...')
# Set-up: dataframe + flagger
cols = [
'patient_id', 'encounter_id', 'inpatient', 'admission', 'time',
'creatinine'
]
row = [
1234, 12345, False,
pd.Timestamp('2020-02-27 12:00:01'),
pd.Timestamp('2020-02-27 12:00:02'), 1.3
]
df = pd.DataFrame([row], columns=cols)
flagger = AKIFlagger()
# Now drop the necessary columns and ensure it throws an error
with self.assertRaises(AssertionError):
flagger.returnAKIpatients(
df.drop(['patient_id', 'encounter_id'], axis=1))
with self.assertRaises(AssertionError):
flagger.returnAKIpatients(df.drop('inpatient', axis=1))
with self.assertRaises(AssertionError):
flagger.returnAKIpatients(df.drop('time', axis=1))
with self.assertRaises(AssertionError):
flagger.returnAKIpatients(df.drop('creatinine', axis=1))
print('Success!\n')
def test_HB_notrump(self):
cols = [
'patient_id', 'encounter_id', 'inpatient', 'admission', 'time',
'creatinine'
]
row0 = [
1234, 12345, False,
pd.Timestamp('2020-05-24 12:00:02'),
pd.Timestamp('2020-05-22 12:00:01'), 2.0
]
row1 = [
1234, 12345, True,
pd.Timestamp('2020-05-24 12:00:02'),
pd.Timestamp('2020-05-24 12:00:02'), 1.0
]
row2 = [
1234, 12345, True,
pd.Timestamp('2020-05-24 12:00:02'),
pd.Timestamp('2020-05-24 12:00:03'), 1.3
]
df = pd.DataFrame([row0, row1, row2], columns=cols)
flagger = AKIFlagger(
HB_trumping=True, add_baseline_creat=True
) #HB_trumping is set to True but there is no baseline value... so it should switch to RM then
# Ensure proper output
out = flagger.returnAKIpatients(df)
self.assertTrue(np.all(out.baseline_creat.isnull()))
self.assertEqual(out.aki.iloc[0], 0)
self.assertEqual(out.aki.iloc[1], 0)
self.assertEqual(out.aki.iloc[2], 1)
def test_PatientD_HB(self):
cols = [
'patient_id', 'encounter_id', 'inpatient', 'admission', 'time',
'creatinine'
]
row0 = [
1234, 12345, False,
pd.Timestamp('2020-05-24 12:00:02'),
pd.Timestamp('2020-01-01 12:00:01'), 2.0
] # Patient X has a baseline creatinine of 2
row1 = [
1234, 12345, True,
pd.Timestamp('2020-05-24 12:00:02'),
pd.Timestamp('2020-05-24 12:00:02'), 1
] # Admission creatinine
row2 = [
1234, 12345, True,
pd.Timestamp('2020-05-24 12:00:02'),
pd.Timestamp('2020-05-26 12:00:02'), 1.3
]
row3 = [
1234, 12345, True,
pd.Timestamp('2020-05-24 12:00:02'),
pd.Timestamp('2020-05-28 12:00:02'), 1.6
]
df = pd.DataFrame([row0, row1, row2, row3], columns=cols)
flagger = AKIFlagger(HB_trumping=True)
# Ensure proper output
out = flagger.returnAKIpatients(df)
self.assertFalse(out.aki.iloc[0])
self.assertFalse(out.aki.iloc[1])
self.assertFalse(out.aki.iloc[2])
self.assertTrue(out.aki.iloc[3])
def test_imputeAdmissionandEncounter(self):
cols = ['patient_id', 'inpatient', 'time', 'creatinine']
row0 = [1234, False, pd.Timestamp('2020-01-24 12:00:02'), 1.0]
row1 = [1234, False, pd.Timestamp('2020-02-24 12:00:02'), 1.0]
row2 = [1234, False, pd.Timestamp('2020-03-24 12:00:02'), 1.0]
row3 = [1234, True, pd.Timestamp('2020-05-24 12:00:02'), 1.5]
df = pd.DataFrame([row0, row1, row2, row3], columns=cols)
flagger = AKIFlagger(HB_trumping=True)
out = flagger.returnAKIpatients(df)
def test_patientA_HB(self):
cols = [
'patient_id', 'encounter_id', 'inpatient', 'admission', 'time',
'creatinine'
]
row0 = [
1234, 12345, False,
pd.Timestamp('2020-05-24 12:00:02'),
pd.Timestamp('2020-01-01 12:00:01'), 1.0
] # Baseline creatinine
row1 = [
1234, 12345, True,
pd.Timestamp('2020-05-24 12:00:02'),
pd.Timestamp('2020-05-24 12:00:02'), 1.0
] # Admission creatinine
row2 = [
1234, 12345, True,
pd.Timestamp('2020-05-24 12:00:02'),
pd.Timestamp('2020-05-25 12:00:01'), 1.29
]
row3 = [
1234, 12345, True,
pd.Timestamp('2020-05-24 12:00:02'),
pd.Timestamp('2020-05-25 12:00:02'), 1.3
]
row4 = [
1234, 12345, True,
pd.Timestamp('2020-05-24 12:00:02'),
pd.Timestamp('2020-05-28 12:00:02'), 2
]
row5 = [
1234, 12345, True,
pd.Timestamp('2020-05-24 12:00:02'),
pd.Timestamp('2020-05-30 12:00:02'), 3
]
df = pd.DataFrame([row0, row1, row2, row3, row4, row5], columns=cols)
flagger = AKIFlagger(HB_trumping=True)
# Ensure proper output
out = flagger.returnAKIpatients(df)
self.assertFalse(out.aki.iloc[0]) # 1.0
self.assertFalse(out.aki.iloc[1]) # 1.0
self.assertFalse(out.aki.iloc[2]) # 1.29
self.assertEqual(
out.aki.iloc[3], 1
) # 1.3 --> UPDATED Version 0.3.5+: 0.3 condition is counted in HB_trumping now.
self.assertEqual(out.aki.iloc[4], 2) # 2
self.assertEqual(out.aki.iloc[5], 3) # 3
print('Sucess!\n')
def test_differentNames(self):
print('Testing different names for identifiers...')
# Set-up
cols = ['fish', 'dog', 'rabbit', 'snail', 'james', 'buffboys']
row0 = [
1234, 12345, False,
pd.Timestamp('2020-02-27 12:00:01'),
pd.Timestamp('2020-02-26 12:00:02'), 1.2
]
row1 = [
1234, 12345, True,
pd.Timestamp('2020-02-27 12:00:01'),
pd.Timestamp('2020-02-28 12:00:01'), 1.5
]
row2 = [
1234, 12345, True,
pd.Timestamp('2020-02-27 12:00:01'),
pd.Timestamp('2020-02-29 12:00:01'), 1.6
]
row3 = [
1234, 12345, True,
pd.Timestamp('2020-02-27 12:00:01'),
pd.Timestamp('2020-03-01 12:00:01'), 1.8
]
row4 = [
1234, 12345, True,
pd.Timestamp('2020-02-27 12:00:01'),
pd.Timestamp('2020-03-03 12:00:01'), 1.8
]
df = pd.DataFrame([row0, row1, row2, row3, row4], columns=cols)
flagger = AKIFlagger(patient_id='fish',
inpatient='rabbit',
time='james',
creatinine='buffboys')
# Ensure proper output
out = flagger.returnAKIpatients(df)
self.assertFalse(out.aki.iloc[0])
self.assertTrue(out.aki.iloc[1])
self.assertFalse(out.aki.iloc[2])
self.assertTrue(out.aki.iloc[3])
self.assertTrue(out.aki.iloc[4])
print('Success!\n')
def test_patientC_HB(
self): # Patient C doesn't meet the rolling minimum criterion
cols = [
'patient_id', 'encounter_id', 'inpatient', 'admission', 'time',
'creatinine'
]
row0 = [
1234, 12345, False,
pd.Timestamp('2020-05-24 12:00:02'),
pd.Timestamp('2020-01-01 12:00:01'), 1.0
] # Baseline creatinine
row1 = [
1234, 12345, True,
pd.Timestamp('2020-05-24 12:00:02'),
pd.Timestamp('2020-05-24 12:00:02'), 1.1
] # Admission creatinine
row2 = [
1234, 12345, True,
pd.Timestamp('2020-05-24 12:00:02'),
pd.Timestamp('2020-05-25 12:00:01'), 1.1
]
row3 = [
1234, 12345, True,
pd.Timestamp('2020-05-24 12:00:02'),
pd.Timestamp('2020-05-26 12:00:04'), 1.3
]
row4 = [
1234, 12345, True,
pd.Timestamp('2020-05-24 12:00:02'),
pd.Timestamp('2020-05-28 12:00:02'), 1.5
]
df = pd.DataFrame([row0, row1, row2, row3, row4], columns=cols)
flagger = AKIFlagger(HB_trumping=True)
# Ensure proper output
out = flagger.returnAKIpatients(df)
self.assertFalse(out.aki.iloc[0])
self.assertFalse(out.aki.iloc[1])
self.assertFalse(out.aki.iloc[2])
self.assertTrue(out.aki.iloc[3])
self.assertTrue(
out.aki.iloc[4]) # But on the last one, RM should trigger
def test_patientB_RM(
self
): # Identical to patientA, except their baseline is now 1.1 instead of 1.0
cols = [
'patient_id', 'encounter_id', 'inpatient', 'admission', 'time',
'creatinine'
]
row0 = [
1234, 12345, False,
pd.Timestamp('2020-05-24 12:00:02'),
pd.Timestamp('2020-01-01 12:00:01'), 1.1
] # Baseline creatinine
row1 = [
1234, 12345, True,
pd.Timestamp('2020-05-24 12:00:02'),
pd.Timestamp('2020-05-24 12:00:02'), 1.0
] # Admission creatinine
row2 = [
1234, 12345, True,
pd.Timestamp('2020-05-24 12:00:02'),
pd.Timestamp('2020-05-25 12:00:01'), 1.29
]
row3 = [
1234, 12345, True,
pd.Timestamp('2020-05-24 12:00:02'),
pd.Timestamp('2020-05-25 12:00:02'), 1.3
]
row4 = [
1234, 12345, True,
pd.Timestamp('2020-05-24 12:00:02'),
pd.Timestamp('2020-05-28 12:00:02'), 2
]
row5 = [
1234, 12345, True,
pd.Timestamp('2020-05-24 12:00:02'),
pd.Timestamp('2020-05-29 12:00:02'), 2.2
]
row6 = [
1234, 12345, True,
pd.Timestamp('2020-05-24 12:00:02'),
pd.Timestamp('2020-05-30 12:00:02'), 3
]
row7 = [
1234, 12345, True,
pd.Timestamp('2020-05-24 12:00:02'),
pd.Timestamp('2020-05-30 12:00:03'), 3.3
]
df = pd.DataFrame([row0, row1, row2, row3, row4, row5, row6, row7],
columns=cols)
flagger = AKIFlagger(HB_trumping=False)
#Ensure proper output
out = flagger.returnAKIpatients(df)
self.assertFalse(out.aki.iloc[0]) # 1.1
self.assertFalse(out.aki.iloc[1]) # 1.0
self.assertFalse(out.aki.iloc[2]) # 1.29
self.assertTrue(
out.aki.iloc[3]
) # 1.3 ---> This is the criterion that meets RM but not HB
self.assertEqual(out.aki.iloc[4], 2) # 2
self.assertEqual(out.aki.iloc[5], 2) # 2.2
self.assertEqual(out.aki.iloc[6], 3) # 3
self.assertEqual(out.aki.iloc[7], 3) # 3.3