class TestResetPersonAndRollBackEvents(unittest.TestCase):
def setUp(self):
self.baseAge = 55
self.baseSBP = 120
self._white_male = Person(
age=self.baseAge,
gender=NHANESGender.MALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_WHITE,
sbp=self.baseSBP,
dbp=80,
a1c=6,
hdl=50,
totChol=213,
ldl=90,
trig=150,
bmi=22,
waist=34,
anyPhysicalActivity=0,
education=Education.COLLEGEGRADUATE,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.NONE,
antiHypertensiveCount=0,
statin=0,
otherLipidLoweringMedicationCount=0,
initializeAfib=initializeAfib)
self._white_male_copy_paste = Person(
age=self.baseAge,
gender=NHANESGender.MALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_WHITE,
sbp=self.baseSBP,
dbp=80,
a1c=6,
hdl=50,
totChol=213,
ldl=90,
trig=150,
bmi=22,
waist=34,
anyPhysicalActivity=0,
education=Education.COLLEGEGRADUATE,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.NONE,
antiHypertensiveCount=0,
statin=0,
otherLipidLoweringMedicationCount=0,
initializeAfib=initializeAfib)
self._white_male_plus_one_year = Person(
age=self.baseAge + 1,
gender=NHANESGender.MALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_WHITE,
sbp=self.baseSBP,
dbp=80,
a1c=6,
hdl=50,
totChol=213,
ldl=90,
trig=150,
bmi=22,
waist=34,
anyPhysicalActivity=0,
education=Education.COLLEGEGRADUATE,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.NONE,
antiHypertensiveCount=0,
statin=0,
otherLipidLoweringMedicationCount=0,
initializeAfib=initializeAfib)
self._white_female = Person(
age=self.baseAge,
gender=NHANESGender.FEMALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_WHITE,
sbp=self.baseSBP,
dbp=80,
a1c=6,
hdl=50,
totChol=213,
ldl=90,
trig=150,
bmi=22,
waist=34,
anyPhysicalActivity=0,
education=Education.COLLEGEGRADUATE,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.NONE,
antiHypertensiveCount=0,
statin=0,
otherLipidLoweringMedicationCount=0,
initializeAfib=initializeAfib)
self._black_female = Person(
age=self.baseAge,
gender=NHANESGender.FEMALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_BLACK,
sbp=self.baseSBP,
dbp=80,
a1c=6,
hdl=50,
totChol=213,
ldl=90,
trig=150,
bmi=22,
waist=34,
anyPhysicalActivity=0,
education=Education.COLLEGEGRADUATE,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.NONE,
antiHypertensiveCount=0,
statin=0,
otherLipidLoweringMedicationCount=0,
initializeAfib=initializeAfib)
self._white_male_plus_sbp = Person(
age=self.baseAge + 1,
gender=NHANESGender.MALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_WHITE,
sbp=self.baseSBP + 10,
dbp=80,
a1c=6,
hdl=50,
totChol=213,
ldl=90,
trig=150,
bmi=22,
waist=34,
anyPhysicalActivity=0,
education=Education.COLLEGEGRADUATE,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.NONE,
antiHypertensiveCount=0,
statin=0,
otherLipidLoweringMedicationCount=0,
initializeAfib=initializeAfib)
self._white_male_plus_dbp = Person(
age=self.baseAge + 1,
gender=NHANESGender.MALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_WHITE,
sbp=self.baseSBP,
dbp=90,
a1c=6,
hdl=50,
totChol=213,
ldl=90,
trig=150,
bmi=22,
waist=34,
anyPhysicalActivity=0,
education=Education.COLLEGEGRADUATE,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.NONE,
antiHypertensiveCount=0,
statin=0,
otherLipidLoweringMedicationCount=0,
initializeAfib=initializeAfib)
self._white_male_plus_a1c = Person(
age=self.baseAge + 1,
gender=NHANESGender.MALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_WHITE,
sbp=self.baseSBP,
dbp=80,
a1c=7,
hdl=50,
totChol=213,
ldl=90,
trig=150,
bmi=22,
waist=34,
anyPhysicalActivity=0,
education=Education.COLLEGEGRADUATE,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.NONE,
antiHypertensiveCount=0,
statin=0,
otherLipidLoweringMedicationCount=0,
initializeAfib=initializeAfib)
self._white_male_plus_hdl = Person(
age=self.baseAge + 1,
gender=NHANESGender.MALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_WHITE,
sbp=self.baseSBP,
dbp=80,
a1c=6,
hdl=60,
totChol=213,
ldl=90,
trig=150,
bmi=22,
waist=34,
anyPhysicalActivity=0,
education=Education.COLLEGEGRADUATE,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.NONE,
antiHypertensiveCount=0,
statin=0,
otherLipidLoweringMedicationCount=0,
initializeAfib=initializeAfib)
self._white_male_plus_totChol = Person(
age=self.baseAge + 1,
gender=NHANESGender.MALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_WHITE,
sbp=self.baseSBP,
dbp=80,
a1c=6,
hdl=50,
totChol=223,
ldl=90,
trig=150,
bmi=22,
waist=34,
anyPhysicalActivity=0,
education=Education.COLLEGEGRADUATE,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.NONE,
antiHypertensiveCount=0,
statin=0,
otherLipidLoweringMedicationCount=0,
initializeAfib=initializeAfib)
self._white_male_plus_ldl = Person(
age=self.baseAge + 1,
gender=NHANESGender.MALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_WHITE,
sbp=self.baseSBP,
dbp=80,
a1c=6,
hdl=50,
totChol=213,
ldl=100,
trig=150,
bmi=22,
waist=34,
anyPhysicalActivity=0,
education=Education.COLLEGEGRADUATE,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.NONE,
antiHypertensiveCount=0,
statin=0,
otherLipidLoweringMedicationCount=0,
initializeAfib=initializeAfib)
self._white_male_plus_trig = Person(
age=self.baseAge + 1,
gender=NHANESGender.MALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_WHITE,
sbp=self.baseSBP,
dbp=80,
a1c=6,
hdl=50,
totChol=213,
ldl=90,
trig=160,
bmi=22,
waist=34,
anyPhysicalActivity=0,
education=Education.COLLEGEGRADUATE,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.NONE,
antiHypertensiveCount=0,
statin=0,
otherLipidLoweringMedicationCount=0,
initializeAfib=initializeAfib)
self._white_male_plus_bmi = Person(
age=self.baseAge + 1,
gender=NHANESGender.MALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_WHITE,
sbp=self.baseSBP,
dbp=80,
a1c=6,
hdl=50,
totChol=213,
ldl=90,
trig=150,
bmi=25,
waist=34,
anyPhysicalActivity=0,
education=Education.COLLEGEGRADUATE,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.NONE,
antiHypertensiveCount=0,
statin=0,
otherLipidLoweringMedicationCount=0,
initializeAfib=initializeAfib)
self._white_male_plus_waist = Person(
age=self.baseAge + 1,
gender=NHANESGender.MALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_WHITE,
sbp=self.baseSBP,
dbp=80,
a1c=6,
hdl=50,
totChol=213,
ldl=90,
trig=150,
bmi=22,
waist=36,
anyPhysicalActivity=0,
education=Education.COLLEGEGRADUATE,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.NONE,
antiHypertensiveCount=0,
statin=0,
otherLipidLoweringMedicationCount=0,
initializeAfib=initializeAfib)
self._white_male_plus_activity = Person(
age=self.baseAge + 1,
gender=NHANESGender.MALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_WHITE,
sbp=self.baseSBP,
dbp=80,
a1c=6,
hdl=50,
totChol=213,
ldl=90,
trig=150,
bmi=22,
waist=34,
anyPhysicalActivity=1,
education=Education.COLLEGEGRADUATE,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.NONE,
antiHypertensiveCount=0,
statin=0,
otherLipidLoweringMedicationCount=0,
initializeAfib=initializeAfib)
self._white_male_minus_edudcation = Person(
age=self.baseAge + 1,
gender=NHANESGender.MALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_WHITE,
sbp=self.baseSBP,
dbp=80,
a1c=6,
hdl=50,
totChol=213,
ldl=90,
trig=150,
bmi=22,
waist=34,
anyPhysicalActivity=1,
education=Education.HIGHSCHOOLGRADUATE,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.NONE,
antiHypertensiveCount=0,
statin=0,
otherLipidLoweringMedicationCount=0,
initializeAfib=initializeAfib)
self._white_male_plus_smoking = Person(
age=self.baseAge + 1,
gender=NHANESGender.MALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_WHITE,
sbp=self.baseSBP,
dbp=80,
a1c=6,
hdl=50,
totChol=213,
ldl=90,
trig=150,
bmi=22,
waist=34,
anyPhysicalActivity=1,
education=Education.COLLEGEGRADUATE,
smokingStatus=SmokingStatus.CURRENT,
alcohol=AlcoholCategory.NONE,
antiHypertensiveCount=0,
statin=0,
otherLipidLoweringMedicationCount=0,
initializeAfib=initializeAfib)
self._white_male_plus_bpMed = Person(
age=self.baseAge + 1,
gender=NHANESGender.MALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_WHITE,
sbp=self.baseSBP,
dbp=80,
a1c=6,
hdl=50,
totChol=213,
ldl=90,
trig=150,
bmi=22,
waist=34,
anyPhysicalActivity=0,
education=Education.COLLEGEGRADUATE,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.NONE,
antiHypertensiveCount=1,
statin=0,
otherLipidLoweringMedicationCount=0,
initializeAfib=initializeAfib)
self._white_male_plus_statin = Person(
age=self.baseAge + 1,
gender=NHANESGender.MALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_WHITE,
sbp=self.baseSBP,
dbp=80,
a1c=6,
hdl=50,
totChol=213,
ldl=90,
trig=150,
bmi=22,
waist=34,
anyPhysicalActivity=0,
education=Education.COLLEGEGRADUATE,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.NONE,
antiHypertensiveCount=0,
statin=1,
otherLipidLoweringMedicationCount=0,
initializeAfib=initializeAfib)
self._white_male_plus_lipid = Person(
age=self.baseAge + 1,
gender=NHANESGender.MALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_WHITE,
sbp=self.baseSBP,
dbp=80,
a1c=6,
hdl=50,
totChol=213,
ldl=90,
trig=150,
bmi=22,
waist=34,
anyPhysicalActivity=0,
education=Education.COLLEGEGRADUATE,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.NONE,
antiHypertensiveCount=0,
statin=0,
otherLipidLoweringMedicationCount=1,
initializeAfib=initializeAfib)
self._white_male_plus_afib = Person(
age=self.baseAge + 1,
gender=NHANESGender.MALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_WHITE,
sbp=self.baseSBP,
dbp=80,
a1c=6,
hdl=50,
totChol=213,
ldl=90,
trig=150,
bmi=22,
waist=34,
anyPhysicalActivity=0,
education=Education.COLLEGEGRADUATE,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.NONE,
antiHypertensiveCount=0,
statin=0,
otherLipidLoweringMedicationCount=0,
initializeAfib=initializeAfibAlwaysPositive)
self._baseline_stroke_person = Person(
age=self.baseAge,
gender=NHANESGender.MALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_WHITE,
sbp=self.baseSBP,
dbp=80,
a1c=6,
hdl=50,
totChol=213,
ldl=90,
trig=150,
bmi=22,
waist=34,
anyPhysicalActivity=0,
education=Education.COLLEGEGRADUATE,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.NONE,
antiHypertensiveCount=0,
statin=0,
otherLipidLoweringMedicationCount=0,
initializeAfib=initializeAfib,
selfReportStrokeAge=50)
self._baseline_stroke_person_copy_paste = Person(
age=self.baseAge,
gender=NHANESGender.MALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_WHITE,
sbp=self.baseSBP,
dbp=80,
a1c=6,
hdl=50,
totChol=213,
ldl=90,
trig=150,
bmi=22,
waist=34,
anyPhysicalActivity=0,
education=Education.COLLEGEGRADUATE,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.NONE,
antiHypertensiveCount=0,
statin=0,
otherLipidLoweringMedicationCount=0,
initializeAfib=initializeAfib,
selfReportStrokeAge=50)
def testResetBasicAttributes(self):
self._white_male.advance_year(TestRiskModelRepository(),
AlwaysNonFatalStrokeOutcomeRepository())
self._baseline_stroke_person.advance_year(
TestRiskModelRepository(), AlwaysFatalStrokeOutcomeRepository())
self.assertEqual(2, len(self._white_male._dbp))
self._white_male.reset_to_baseline()
self.assertEqual(1, len(self._white_male._dbp))
self.assertEqual(1, len(self._white_male._totChol))
self.assertEqual(1, len(self._white_male._trig))
self.assertEqual(1, len(self._white_male._trig))
self.assertEqual(1, len(self._white_male._sbp))
self.assertEqual(self.baseSBP, self._white_male._sbp[-1])
self.assertEqual(self.baseAge, self._white_male._age[-1])
def testResetOutcomes(self):
self._white_male.advance_year(TestRiskModelRepository(),
AlwaysNonFatalStrokeOutcomeRepository())
self._baseline_stroke_person.advance_year(
TestRiskModelRepository(), AlwaysFatalStrokeOutcomeRepository())
self.assertEqual(1,
len(self._white_male._outcomes[OutcomeType.STROKE]))
self._white_male.reset_to_baseline()
self.assertEqual(0,
len(self._white_male._outcomes[OutcomeType.STROKE]))
def testResetOutcomesPreservesPreSimOutcomes(self):
self._white_male.advance_year(TestRiskModelRepository(),
AlwaysNonFatalStrokeOutcomeRepository())
self._baseline_stroke_person.advance_year(
TestRiskModelRepository(), AlwaysFatalStrokeOutcomeRepository())
self.assertEqual(
2, len(self._baseline_stroke_person._outcomes[OutcomeType.STROKE]))
self._baseline_stroke_person.reset_to_baseline()
self.assertEqual(
1, len(self._baseline_stroke_person._outcomes[OutcomeType.STROKE]))
def testRollbackNonFatalEvent(self):
self._white_male.advance_year(TestRiskModelRepository(),
AlwaysNonFatalStrokeOutcomeRepository())
self._baseline_stroke_person.advance_year(
TestRiskModelRepository(), AlwaysFatalStrokeOutcomeRepository())
self.assertEqual(False,
self._white_male.has_stroke_prior_to_simulation())
self.assertEqual(True, self._white_male.has_stroke_during_simulation())
self.assertEqual(True, self._white_male.has_stroke_during_wave(1))
self._white_male.rollback_most_recent_event(OutcomeType.STROKE)
self.assertEqual(False,
self._white_male.has_stroke_prior_to_simulation())
self.assertEqual(False, self._white_male.has_stroke_during_wave(1))
self.assertEqual(False,
self._white_male.has_stroke_during_simulation())
def testRollbackFatalEvent(self):
self._white_male.advance_year(TestRiskModelRepository(),
AlwaysNonFatalStrokeOutcomeRepository())
self._baseline_stroke_person.advance_year(
TestRiskModelRepository(), AlwaysFatalStrokeOutcomeRepository())
self.assertEqual(
True, self._baseline_stroke_person.has_stroke_during_simulation())
self.assertEqual(
True,
self._baseline_stroke_person.has_stroke_prior_to_simulation())
self.assertEqual(
True, self._baseline_stroke_person.has_stroke_during_wave(1))
self.assertEqual(True, self._baseline_stroke_person.is_dead())
self._baseline_stroke_person.rollback_most_recent_event(
OutcomeType.STROKE)
self.assertEqual(
True,
self._baseline_stroke_person.has_stroke_prior_to_simulation())
self.assertEqual(
False, self._baseline_stroke_person.has_stroke_during_wave(1))
self.assertEqual(
False, self._baseline_stroke_person.has_stroke_during_simulation())
self.assertEqual(False, self._baseline_stroke_person.is_dead())
self.assertEqual(self.baseAge + 1,
self._baseline_stroke_person._age[-1])
def testBasePatientEquals(self):
self.assertTrue(self._white_male == self._white_male_copy_paste)
self.assertEqual(self._white_male, self._white_male_copy_paste)
self.assertNotEqual(self._white_male, self._white_female)
self.assertNotEqual(self._white_female, self._black_female)
self.assertNotEqual(self._white_male,
self._white_male_minus_edudcation)
self.assertNotEqual(self._white_male, self._white_male_plus_a1c)
self.assertNotEqual(self._white_male, self._white_male_plus_activity)
self.assertNotEqual(self._white_male, self._white_male_plus_afib)
self.assertNotEqual(self._white_male, self._white_male_plus_bmi)
self.assertNotEqual(self._white_male, self._white_male_plus_dbp)
self.assertNotEqual(self._white_male, self._white_male_plus_hdl)
self.assertNotEqual(self._white_male, self._white_male_plus_ldl)
self.assertNotEqual(self._white_male, self._white_male_plus_lipid)
self.assertNotEqual(self._white_male, self._white_male_plus_one_year)
self.assertNotEqual(self._white_male, self._white_male_plus_sbp)
self.assertNotEqual(self._white_male, self._white_male_plus_smoking)
self.assertNotEqual(self._white_male, self._white_male_plus_statin)
self.assertNotEqual(self._white_male, self._white_male_plus_totChol)
self.assertNotEqual(self._white_male, self._white_male_plus_trig)
self.assertNotEqual(self._white_male, self._white_male_plus_waist)
def testBaselineEqualityAfterAdvancingAYear(self):
self._white_male.advance_year(TestRiskModelRepository(),
NothingHappensRepository())
self._white_male_copy_paste.advance_year(TestRiskModelRepository(),
NothingHappensRepository())
self.assertEqual(self._white_male, self._white_male_copy_paste)
def testBasePatientWithBaselineStroke(self):
self.assertNotEqual(self._white_male, self._baseline_stroke_person)
self.assertEqual(self._baseline_stroke_person,
self._baseline_stroke_person_copy_paste)
self._baseline_stroke_person.advance_year(TestRiskModelRepository(),
NothingHappensRepository())
self._baseline_stroke_person_copy_paste.advance_year(
TestRiskModelRepository(), NothingHappensRepository())
self.assertEqual(self._baseline_stroke_person,
self._baseline_stroke_person_copy_paste)
def testBasePatientWithCVEvents(self):
self.assertEqual(self._white_male_copy_paste, self._white_male)
self._white_male.advance_year(TestRiskModelRepository(),
AlwaysNonFatalStrokeOutcomeRepository())
self.assertNotEqual(self._white_male, self._white_male_copy_paste)
self._white_male_copy_paste.advance_year(
TestRiskModelRepository(), AlwaysNonFatalStrokeOutcomeRepository())
self.assertEqual(self._white_male_copy_paste, self._white_male)
def testBasePatientWithNonCVDeath(self):
self.assertEqual(self._white_male_copy_paste, self._white_male)
self._white_male.advance_year(TestRiskModelRepository(),
AlwaysNonCVDeathRepository())
self.assertNotEqual(self._white_male, self._white_male_copy_paste)
self._white_male_copy_paste.advance_year(TestRiskModelRepository(),
NothingHappensRepository())
self.assertNotEqual(self._white_male_copy_paste, self._white_male)
def testBasePatientWithNonCVDeathOtherWay(self):
self.assertEqual(self._white_male_copy_paste, self._white_male)
self._white_male.advance_year(TestRiskModelRepository(),
AlwaysNonCVDeathRepository())
self.assertNotEqual(self._white_male, self._white_male_copy_paste)
self._white_male_copy_paste.advance_year(TestRiskModelRepository(),
AlwaysNonCVDeathRepository())
self.assertEqual(self._white_male_copy_paste, self._white_male)
def testDeepCopy(self):
self.assertEqual(self._white_male, copy.deepcopy(self._white_male))
self._white_male.advance_year(TestRiskModelRepository(),
NothingHappensRepository())
self.assertEqual(self._white_male, copy.deepcopy(self._white_male))
self._white_male.advance_year(TestRiskModelRepository(),
AlwaysNonFatalStrokeOutcomeRepository())
self.assertEqual(self._white_male, copy.deepcopy(self._white_male))
self._white_male.advance_year(TestRiskModelRepository(),
AlwaysNonCVDeathRepository())
self.assertEqual(self._white_male, copy.deepcopy(self._white_male))
class TestPersonAdvanceOutcomes(unittest.TestCase):
def setUp(self):
self.joe = Person(
42,
NHANESGender.MALE,
NHANESRaceEthnicity.NON_HISPANIC_BLACK,
140,
90,
5.5,
50,
200,
25,
90,
150,
45,
0,
Education.COLLEGEGRADUATE,
SmokingStatus.NEVER,
AlcoholCategory.NONE,
0,
0,
0,
0,
initializeAFib,
)
self.joe_with_mi = copy.deepcopy(self.joe)
self.joe_with_mi.add_outcome_event(Outcome(OutcomeType.MI, False))
self.joe_with_stroke = copy.deepcopy(self.joe)
self.joe_with_stroke.add_outcome_event(Outcome(OutcomeType.STROKE, False))
self._population_dataframe = init_vectorized_population_dataframe(
[self.joe, self.joe_with_mi, self.joe_with_stroke],
with_base_gcp=True,
)
self._always_positive_repository = AlwaysPositiveOutcomeRepository()
self._always_negative_repository = AlwaysNegativeOutcomeRepository()
self.cvDeterminer = CVOutcomeDetermination(self._always_positive_repository)
def test_dead_is_dead_advance_year(self):
self.joe._alive[-1] = False
with self.assertRaises(RuntimeError, msg="Person is dead. Can not advance year"):
self.joe.advance_year(None, None)
def test_dead_is_dead_advance_risk_factors(self):
self.joe._alive[-1] = False
with self.assertRaises(RuntimeError, msg="Person is dead. Can not advance risk factors"):
self.joe.advance_risk_factors(None)
def test_dead_is_dead_advance_outcomes(self):
self.joe._alive[-1] = False
with self.assertRaises(RuntimeError, msg="Person is dead. Can not advance outcomes"):
self.joe.advance_outcomes(None)
def test_will_have_fatal_mi(self):
joe_data = self._population_dataframe.iloc[0]
is_max_prob_mi_fatal = self.cvDeterminer._will_have_fatal_mi(
joe_data,
vectorized=True,
overrideMIProb=1.0,
)
is_min_prob_mi_fatal = self.cvDeterminer._will_have_fatal_mi(
joe_data,
vectorized=True,
overrideMIProb=0.0,
)
self.assertTrue(is_max_prob_mi_fatal)
self.assertFalse(is_min_prob_mi_fatal)
def test_fatal_mi_secondary_prob(self):
self.cvDeterminer.mi_secondary_case_fatality = 1.0
self.cvDeterminer.mi_case_fatality = 0.0
joe_data = self._population_dataframe.iloc[0]
joe_with_mi_data = self._population_dataframe.iloc[1] # same as joe_data plus 1 MI
will_have_fatal_first_mi = self.cvDeterminer._will_have_fatal_mi(
joe_data,
vectorized=True,
overrideMIProb=0.0,
)
will_have_fatal_second_mi = self.cvDeterminer._will_have_fatal_mi(
joe_with_mi_data,
vectorized=True,
overrideMIProb=0.0,
)
self.assertFalse(will_have_fatal_first_mi)
# even though the passed fatality rate is zero, it should be overriden by the
# secondary rate given that joe had a prior MI
self.assertTrue(will_have_fatal_second_mi)
def test_fatal_stroke_secondary_prob(self):
self.cvDeterminer.stroke_secondary_case_fatality = 1.0
self.cvDeterminer.stroke_case_fatality = 0.0
joe_data = self._population_dataframe.iloc[0]
joe_with_stroke_data = self._population_dataframe.iloc[2] # same as joe_data plus 1 stroke
will_have_fatal_first_stroke = self.cvDeterminer._will_have_fatal_stroke(
joe_data,
vectorized=True,
overrideStrokeProb=0.0,
)
will_have_fatal_second_stroke = self.cvDeterminer._will_have_fatal_stroke(
joe_with_stroke_data,
vectorized=True,
overrideStrokeProb=0.0,
)
self.assertFalse(will_have_fatal_first_stroke)
# even though the passed fatality rate is zero, it shoudl be overriden by the
# secondary rate given that joeclone had a prior stroke
self.assertTrue(will_have_fatal_second_stroke)
def test_will_have_fatal_stroke(self):
joe_data = self._population_dataframe.iloc[0]
is_max_prob_stroke_fatal = self.cvDeterminer._will_have_fatal_stroke(
joe_data,
vectorized=True,
overrideStrokeProb=1.0,
)
is_min_prob_stroke_fatal = self.cvDeterminer._will_have_fatal_stroke(
joe_data,
vectorized=True,
overrideStrokeProb=0.0,
)
self.assertTrue(is_max_prob_stroke_fatal)
self.assertFalse(is_min_prob_stroke_fatal)
def test_has_mi_vs_stroke(self):
joe_data = self._population_dataframe.iloc[0]
has_mi_max_manual_prob = self.cvDeterminer._will_have_mi(
joe_data,
outcome_model_repository=None,
vectorized=False,
manualMIProb=1.0,
)
has_mi_min_manual_prob = self.cvDeterminer._will_have_mi(
joe_data,
outcome_model_repository=None,
vectorized=False,
manualMIProb=0.0,
)
self.assertTrue(has_mi_max_manual_prob)
self.assertFalse(has_mi_min_manual_prob)
def test_advance_outcomes_fatal_mi(self):
self._always_positive_repository.stroke_case_fatality = 1.0
self._always_positive_repository.mi_case_fatality = 1.0
self._always_positive_repository.manualStrokeMIProbability = 1.0
self.joe.advance_outcomes(self._always_positive_repository)
self.assertTrue(self.joe.has_mi_during_simulation())
self.assertFalse(self.joe.has_stroke_during_simulation())
self.assertTrue(self.joe.is_dead())
def test_advance_outcomes_fatal_stroke(self):
self._always_positive_repository.stroke_case_fatality = 1.0
self._always_positive_repository.mi_case_fatality = 1.0
self._always_positive_repository.manualStrokeMIProbability = 0.0
self.joe.advance_outcomes(self._always_positive_repository)
self.assertFalse(self.joe.has_mi_during_simulation())
self.assertTrue(self.joe.has_stroke_during_simulation())
self.assertTrue(self.joe.is_dead())
def test_advance_outcomes_nonfatal_mi(self):
self.assertEqual(0, self.joe.is_dead())
self._always_positive_repository.stroke_case_fatality = 0.0
self._always_positive_repository.mi_case_fatality = 0.0
self._always_positive_repository.manualStrokeMIProbability = 1.0
self.joe.advance_outcomes(self._always_positive_repository)
self.assertTrue(self.joe.has_mi_during_simulation())
self.assertFalse(self.joe.has_stroke_during_simulation())
def test_advance_outcomes_nonfatal_stroke(self):
self._always_positive_repository.stroke_case_fatality = 0.0
self._always_positive_repository.mi_case_fatality = 0.0
self._always_positive_repository.manualStrokeMIProbability = 0.0
self.joe.advance_outcomes(self._always_positive_repository)
self.assertFalse(self.joe.has_mi_during_simulation())
self.assertTrue(self.joe.has_stroke_during_simulation())
class TestGCPModel(unittest.TestCase):
def initializeAfib(person):
return None
def setUp(self):
self._test_case_one = Person(
age=65 - 0.828576318 * 10,
gender=NHANESGender.FEMALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_WHITE,
sbp=120 + 0.45 * 10,
dbp=80,
# guessingon the centering standard for glucose...may have to check
a1c=Person.convert_fasting_glucose_to_a1c(100 - 1.1 * 10),
hdl=50,
totChol=127 - 3.64 * 10,
ldl=90,
trig=150,
bmi=26.6 + 15.30517532,
waist=94 + 19.3,
anyPhysicalActivity=1,
education=Education.COLLEGEGRADUATE,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.ONETOSIX,
antiHypertensiveCount=1,
statin=0,
otherLipidLoweringMedicationCount=0,
initializeAfib=TestGCPModel.initializeAfib)
self._test_case_two = Person(
age=65 - 0.458555784 * 10,
gender=NHANESGender.MALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_WHITE,
sbp=120 + 0.3 * 10,
dbp=80,
# guessingon the centering standard for glucose...may have to check
a1c=Person.convert_fasting_glucose_to_a1c(100 + 0.732746529 * 10),
hdl=50,
totChol=127 + 1.18 * 10,
ldl=90,
trig=150,
bmi=26.6 + 0.419305619,
waist=94 - 2.5,
anyPhysicalActivity=1,
education=Education.SOMEHIGHSCHOOL,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.ONETOSIX,
antiHypertensiveCount=0,
statin=0,
otherLipidLoweringMedicationCount=0,
initializeAfib=TestGCPModel.initializeAfib)
self._test_case_three = Person(
age=65 - 0.358692676 * 10,
gender=NHANESGender.FEMALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_BLACK,
sbp=120 + 2.3 * 10,
dbp=80,
# guessingon the centering standard for glucose...may have to check
a1c=Person.convert_fasting_glucose_to_a1c(100 + 0.8893 * 10),
hdl=50,
totChol=127 + 4.7769 * 10,
ldl=90,
trig=150,
bmi=26.6 + 2.717159247,
waist=94 + 9,
anyPhysicalActivity=1,
education=Education.LESSTHANHIGHSCHOOL,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.NONE,
antiHypertensiveCount=1,
statin=0,
otherLipidLoweringMedicationCount=0,
initializeAfib=TestGCPModel.initializeAfib)
def test_baseline_gcp(self):
# check that all of the random elements have been removed for testing...
self.assertEqual(
GCPModel().calc_linear_predictor(person=self._test_case_one,
test=True),
GCPModel().calc_linear_predictor(person=self._test_case_one,
test=True))
# this is for the first person in teh spreadsheet (1569nomas)...comparator is GCP + backing out the cohort effect (NOMAS)
self.assertAlmostEqual(64.45419405 - 2.7905,
GCPModel().calc_linear_predictor(
person=self._test_case_one, test=True),
places=1)
# this is for the 2nd person in the spreadhsheet (204180409594cardia)...comparabor is GCP margin + backing out the cohort effect (cardia)
self.assertAlmostEqual(50.01645213 + 1.3320,
GCPModel().calc_linear_predictor(
person=self._test_case_two, test=True),
places=1)
# this is for the the first black person in the spreadsheet (J150483aric)...comparator is GCP + no cohort effect (ARIC)
self.assertAlmostEqual(42.99471241,
GCPModel().calc_linear_predictor(
person=self._test_case_three, test=True),
places=1)
def test_gcp_after_one_year(self):
# this is for the first person in teh spreadsheet (1569nomas)...comparator is GCP + backing out the cohort effect (NOMAS)
self._test_case_one.advance_year(
DoNotChangeRiskFactorsModelRepository(),
AlwaysNegativeOutcomeRepository())
# account for the difference between the actual mean systolic change
self.assertAlmostEqual(64.28862964 - 2.7905,
GCPModel().calc_linear_predictor(
person=self._test_case_one, test=True),
places=1)
def test_gcp_random_effect(self):
self._test_case_one._randomEffects['gcp'] = 5
self.assertAlmostEqual(64.45419405 - 2.7905 + 5,
GCPModel().get_risk_for_person(
person=self._test_case_one,
years=1,
test=True),
places=1)
class TestPersonAdvanceOutcomes(unittest.TestCase):
def setUp(self):
self.joe = Person(42, NHANESGender.MALE,
NHANESRaceEthnicity.NON_HISPANIC_BLACK, 140, 90, 5.5,
50, 200, 25, 90, 150, 45, 0,
Education.COLLEGEGRADUATE, SmokingStatus.NEVER,
AlcoholCategory.NONE, 0, 0, 0, initializeAFib)
self._always_positive_repository = AlwaysPositiveOutcomeRepository()
self._always_negative_repository = AlwaysNegativeOutcomeRepository()
self.cvDeterminer = CVOutcomeDetermination(
self._always_positive_repository)
def test_dead_is_dead_advance_year(self):
self.joe._alive[-1] = False
with self.assertRaises(RuntimeError,
msg="Person is dead. Can not advance year"):
self.joe.advance_year(None, None)
def test_dead_is_dead_advance_risk_factors(self):
self.joe._alive[-1] = False
with self.assertRaises(
RuntimeError,
msg="Person is dead. Can not advance risk factors"):
self.joe.advance_risk_factors(None)
def test_dead_is_dead_advance_outcomes(self):
self.joe._alive[-1] = False
with self.assertRaises(RuntimeError,
msg="Person is dead. Can not advance outcomes"):
self.joe.advance_outcomes(None)
def test_will_have_fatal_mi(self):
self.assertEqual(self.cvDeterminer._will_have_fatal_mi(self.joe, 1.0),
1)
self.assertEqual(self.cvDeterminer._will_have_fatal_mi(self.joe, 0.0),
0)
def test_fatal_mi_secondary_prob(self):
self.cvDeterminer.mi_secondary_case_fatality = 1.0
self.cvDeterminer.mi_case_fatality = 0.0
joeClone = copy.deepcopy(self.joe)
self.assertEqual(self.cvDeterminer._will_have_fatal_mi(joeClone, 0.0),
0)
joeClone._outcomes[OutcomeType.MI] = (joeClone._age,
Outcome(OutcomeType.MI, False))
# even though the passed fatality rate is zero, it shoudl be overriden by the
# secondary rate given that joeclone had a prior MI
self.assertEqual(self.cvDeterminer._will_have_fatal_mi(joeClone, 0.0),
1)
def test_fatal_stroke_secondary_prob(self):
self.cvDeterminer.stroke_secondary_case_fatality = 1.0
self.cvDeterminer.stroke_case_fatality = 0.0
joeClone = copy.deepcopy(self.joe)
self.assertEqual(
self.cvDeterminer._will_have_fatal_stroke(joeClone, 0.0), 0)
joeClone._outcomes[OutcomeType.STROKE] = (joeClone._age,
Outcome(
OutcomeType.STROKE,
False))
# even though the passed fatality rate is zero, it shoudl be overriden by the
# secondary rate given that joeclone had a prior stroke
self.assertEqual(
self.cvDeterminer._will_have_fatal_stroke(joeClone, 0.0), 1)
def test_will_have_fatal_stroke(self):
self.assertEqual(
self.cvDeterminer._will_have_fatal_stroke(self.joe, 1.0), 1)
self.assertEqual(
self.cvDeterminer._will_have_fatal_stroke(self.joe, 0.0), 0)
def test_has_mi_vs_stroke(self):
self.assertEqual(self.cvDeterminer._will_have_mi(self.joe, None, 1.0),
1)
self.assertEqual(self.cvDeterminer._will_have_mi(self.joe, None, 0.0),
0)
def test_advance_outcomes_fatal_mi(self):
self._always_positive_repository.stroke_case_fatality = 1.0
self._always_positive_repository.mi_case_fatality = 1.0
self._always_positive_repository.manualStrokeMIProbability = 1.0
self.joe.advance_outcomes(self._always_positive_repository)
self.assertTrue(self.joe.has_mi_during_simulation())
self.assertFalse(self.joe.has_stroke_during_simulation())
self.assertTrue(self.joe.is_dead())
def test_advance_outcomes_fatal_stroke(self):
self._always_positive_repository.stroke_case_fatality = 1.0
self._always_positive_repository.mi_case_fatality = 1.0
self._always_positive_repository.manualStrokeMIProbability = 0.0
self.joe.advance_outcomes(self._always_positive_repository)
self.assertFalse(self.joe.has_mi_during_simulation())
self.assertTrue(self.joe.has_stroke_during_simulation())
self.assertTrue(self.joe.is_dead())
def test_advance_outcomes_nonfatal_mi(self):
self.assertEqual(0, self.joe.is_dead())
self._always_positive_repository.stroke_case_fatality = 0.0
self._always_positive_repository.mi_case_fatality = 0.0
self._always_positive_repository.manualStrokeMIProbability = 1.0
self.joe.advance_outcomes(self._always_positive_repository)
self.assertTrue(self.joe.has_mi_during_simulation())
self.assertFalse(self.joe.has_stroke_during_simulation())
def test_advance_outcomes_nonfatal_stroke(self):
self._always_positive_repository.stroke_case_fatality = 0.0
self._always_positive_repository.mi_case_fatality = 0.0
self._always_positive_repository.manualStrokeMIProbability = 0.0
self.joe.advance_outcomes(self._always_positive_repository)
self.assertFalse(self.joe.has_mi_during_simulation())
self.assertTrue(self.joe.has_stroke_during_simulation())
class TestPersonWaveStatus(unittest.TestCase):
def setUp(self):
self.oldJoe = Person(
age=60,
gender=NHANESGender.MALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_BLACK,
sbp=140,
dbp=90,
a1c=5.5,
hdl=50,
totChol=200,
bmi=25,
ldl=90,
trig=150,
waist=45,
anyPhysicalActivity=0,
education=Education.COLLEGEGRADUATE,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.NONE,
antiHypertensiveCount=0,
statin=0,
otherLipidLoweringMedicationCount=0,
initializeAfib=initializeAFib)
self.youngJoe = Person(
age=40,
gender=NHANESGender.MALE,
raceEthnicity=NHANESRaceEthnicity.NON_HISPANIC_BLACK,
sbp=140,
dbp=90,
a1c=5.5,
hdl=50,
totChol=200,
bmi=25,
ldl=90,
trig=150,
waist=45,
anyPhysicalActivity=0,
education=Education.COLLEGEGRADUATE,
smokingStatus=SmokingStatus.NEVER,
alcohol=AlcoholCategory.NONE,
antiHypertensiveCount=0,
statin=0,
otherLipidLoweringMedicationCount=0,
initializeAfib=initializeAFib)
def testStatusAfterFatalStroke(self):
self.youngJoe.advance_year(TestRiskModelRepository(),
AgeOver50CausesFatalStroke())
self.assertEqual(41, self.youngJoe._age[-1])
self.assertEqual(False, self.youngJoe.is_dead())
self.assertEqual(False, self.youngJoe._stroke)
self.assertEqual(True, self.youngJoe.alive_at_start_of_wave(1))
self.assertEqual(True, self.youngJoe.alive_at_start_of_wave(2))
with self.assertRaises(Exception):
self.youngJoe.alive_at_start_of_wave(3)
self.youngJoe.advance_year(TestRiskModelRepository(),
AgeOver50CausesFatalStroke())
self.assertEqual(True, self.youngJoe.alive_at_start_of_wave(3))
self.oldJoe.advance_year(TestRiskModelRepository(),
AgeOver50CausesFatalStroke())
self.assertEqual(60, self.oldJoe._age[-1])
self.assertEqual(True, self.oldJoe.is_dead())
self.assertEqual(True, self.oldJoe._stroke)
self.assertEqual(True, self.oldJoe.alive_at_start_of_wave(1))
self.assertEqual(False, self.oldJoe.alive_at_start_of_wave(2))
# this is called to verify that it DOES NOT throw an excepiotn
self.oldJoe.alive_at_start_of_wave(3)
def testNonCVMortalityLeadsToCorrectStatus(self):
self.youngJoe.advance_year(TestRiskModelRepository(),
AgeOver50CausesNonCVMortality())
self.assertEqual(41, self.youngJoe._age[-1])
self.assertEqual(False, self.youngJoe.is_dead())
self.assertEqual(False, self.youngJoe._stroke)
self.assertEqual(True, self.youngJoe.alive_at_start_of_wave(1))
self.assertEqual(True, self.youngJoe.alive_at_start_of_wave(2))
with self.assertRaises(Exception):
self.youngJoe.alive_at_start_of_wave(3)
self.youngJoe.advance_year(TestRiskModelRepository(),
AgeOver50CausesNonCVMortality())
self.assertEqual(True, self.youngJoe.alive_at_start_of_wave(3))
self.oldJoe.advance_year(TestRiskModelRepository(),
AgeOver50CausesNonCVMortality())
self.assertEqual(60, self.oldJoe._age[-1])
self.assertEqual(True, self.oldJoe.is_dead())
self.assertEqual(False, self.oldJoe._stroke)
self.assertEqual(True, self.oldJoe.alive_at_start_of_wave(1))
self.assertEqual(False, self.oldJoe.alive_at_start_of_wave(2))
# this is called to verify that it DOES NOT throw an excepiotn
self.oldJoe.alive_at_start_of_wave(3)
def testHasFatalStrokeInWaveIsCaptured(self):
self.oldJoe.advance_year(TestRiskModelRepository(),
AgeOver50CausesFatalStroke())
self.assertEqual(True, self.oldJoe.has_stroke_during_simulation())
self.assertEqual(True, self.oldJoe.has_stroke_during_wave(1))
with self.assertRaises(Exception):
self.oldJoe.has_stroke_during_wave(0)
# calling to make sure it does NOT raise an exception...you should
# be able to ask whether somebody has a stroke in a wave after they are dead, the answer is
# "No"
self.assertEqual(False, self.oldJoe.has_stroke_during_wave(2))
def testNonFatalStrokeInWaveWithNonCVDeathIsCaptured(self):
self.oldJoe.advance_year(TestRiskModelRepository(),
NonFatalStrokeAndNonCVMortality())
self.assertEqual(True, self.oldJoe.has_stroke_during_simulation())
self.assertEqual(True, self.oldJoe.has_stroke_during_wave(1))
self.assertEqual(True, self.oldJoe.is_dead())