class __AffectedUnmodeledCauses(NamedTuple):
# Keys that will be loaded into the artifact. must have a colon type declaration
URI_CSMR: TargetString = TargetString(
'cause.upper_respiratory_infections.cause_specific_mortality_rate')
OTITIS_MEDIA_CSMR: TargetString = TargetString(
'cause.otitis_media.cause_specific_mortality_rate')
MENINGITIS_CSMR: TargetString = TargetString(
'cause.meningitis.cause_specific_mortality_rate')
ENCEPHALITIS_CSMR: TargetString = TargetString(
'cause.encephalitis.cause_specific_mortality_rate')
NEONATAL_PRETERM_BIRTH_CSMR: TargetString = TargetString(
'cause.neonatal_preterm_birth.cause_specific_mortality_rate')
NEONATAL_ENCEPHALOPATHY_CSMR: TargetString = TargetString(
'cause.neonatal_encephalopathy_due_to_birth_asphyxia_and_trauma.cause_specific_mortality_rate'
)
NEONATAL_SEPSIS_CSMR: TargetString = TargetString(
'cause.neonatal_sepsis_and_other_neonatal_infections.cause_specific_mortality_rate'
)
NEONATAL_JAUNDICE_CSMR: TargetString = TargetString(
'cause.hemolytic_disease_and_other_neonatal_jaundice.cause_specific_mortality_rate'
)
OTHER_NEONATAL_DISORDERS_CSMR: TargetString = TargetString(
'cause.other_neonatal_disorders.cause_specific_mortality_rate')
SIDS_CSMR: TargetString = TargetString(
'cause.sudden_infant_death_syndrome.cause_specific_mortality_rate')
# Useful keys not for the artifact - distinguished by not using the colon type declaration
@property
def name(self):
return 'affected_unmodeled_causes'
@property
def log_name(self):
return 'affected unmodeled causes'
class __SomeDisease(NamedTuple):
# Keys that will be loaded into the artifact. must have a colon type declaration
SOME_DISEASE_PREVALENCE: TargetString = TargetString(
'cause.some_disease.prevalence')
SOME_DISEASE_INCIDENCE_RATE: TargetString = TargetString(
'cause.some_disease.incidence_rate')
SOME_DISEASE_REMISSION_RATE: TargetString = TargetString(
'cause.some_disease.remission_rate')
DISABILITY_WEIGHT: TargetString = TargetString(
'cause.some_disease.disability_weight')
EMR: TargetString = TargetString(
'cause.some_disease.excess_mortality_rate')
CSMR: TargetString = TargetString(
'cause.some_disease.cause_specific_mortality_rate')
RESTRICTIONS: TargetString = TargetString(
'cause.some_disease.restrictions')
# Useful keys not for the artifact - distinguished by not using the colon type declaration
RAW_DISEASE_PREVALENCE = TargetString('sequela.raw_disease.prevalence')
RAW_DISEASE_INCIDENCE_RATE = TargetString(
'sequela.raw_disease.incidence_rate')
@property
def name(self):
return 'some_disease'
@property
def log_name(self):
return 'some disease'
def _get_additive_risk_keys(treatment_type: str) -> __AdditiveRisk:
return __AdditiveRisk(
EXPOSURE=TargetString(f'risk_factor.{treatment_type}.exposure'),
DISTRIBUTION=TargetString(
f'risk_factor.{treatment_type}.distribution'),
CATEGORIES=TargetString(f'risk_factor.{treatment_type}.categories'),
EXCESS_SHIFT=TargetString(
f'risk_factor.{treatment_type}.excess_shift'),
RISK_SPECIFIC_SHIFT=TargetString(
f'risk_factor.{treatment_type}.risk_specific_shift'),
)
def _get_wasting_treatment_keys(treatment_type: str) -> __WastingTreatment:
return __WastingTreatment(
EXPOSURE=TargetString(f'risk_factor.{treatment_type}.exposure'),
DISTRIBUTION=TargetString(
f'risk_factor.{treatment_type}.distribution'),
CATEGORIES=TargetString(f'risk_factor.{treatment_type}.categories'),
RELATIVE_RISK=TargetString(
f'risk_factor.{treatment_type}.relative_risk'),
PAF=TargetString(
f'risk_factor.{treatment_type}.population_attributable_fraction'),
)
class __LowerRespiratoryInfections(NamedTuple):
# Keys that will be loaded into the artifact. must have a colon type declaration
DURATION: TargetString = TargetString(
'cause.lower_respiratory_infections.duration')
PREVALENCE: TargetString = TargetString(
'cause.lower_respiratory_infections.prevalence')
INCIDENCE_RATE: TargetString = TargetString(
'cause.lower_respiratory_infections.incidence_rate')
REMISSION_RATE: TargetString = TargetString(
'cause.lower_respiratory_infections.remission_rate')
DISABILITY_WEIGHT: TargetString = TargetString(
'cause.lower_respiratory_infections.disability_weight')
EMR: TargetString = TargetString(
'cause.lower_respiratory_infections.excess_mortality_rate')
CSMR: TargetString = TargetString(
'cause.lower_respiratory_infections.cause_specific_mortality_rate')
RESTRICTIONS: TargetString = TargetString(
'cause.lower_respiratory_infections.restrictions')
# Useful keys not for the artifact - distinguished by not using the colon type declaration
@property
def name(self):
return 'lower_respiratory_infections'
@property
def log_name(self):
return 'lower respiratory infections'
def __init__(self, intervention_name: str, target: str):
self.intervention_name = intervention_name
self.target = TargetString(target)
self.configuration_defaults = {"interventions": {
f"{self.intervention_name}_intervention": {
f'effect_on_{self.target.name}':
InterventionEffect.configuration_defaults['interventions']['specific_intervention']['effect']}}}
def load_relative_risk_data(self, builder):
if self.target.measure == 'incidence_rate':
return super().load_relative_risk_data(builder)
elif self.target.measure == 'relapse_rate':
hacked_target = TargetString(
f'{self.target.type}.{self.target.name}.incidence_rate')
return get_relative_risk_data(builder, self.risk, hacked_target,
self.randomness)
def __init__(self, target: str):
"""
Parameters
----------
target :
Type, name, and target rate of entity to be affected by risk factor,
supplied in the form "entity_type.entity_name.measure"
where entity_type should be singular (e.g., cause instead of causes).
"""
self.risk = EntityString(
f'risk_factor.low_birth_weight_and_short_gestation')
self.target = TargetString(target)
class __ProteinEnergyMalnutrition(NamedTuple):
# Keys that will be loaded into the artifact. must have a colon type declaration
MAM_DISABILITY_WEIGHT: TargetString = TargetString(
'sequela.moderate_acute_malnutrition.disability_weight')
SAM_DISABILITY_WEIGHT: TargetString = TargetString(
'sequela.severe_acute_malnutrition.disability_weight')
EMR: TargetString = TargetString(
'cause.protein_energy_malnutrition.excess_mortality_rate')
CSMR: TargetString = TargetString(
'cause.protein_energy_malnutrition.cause_specific_mortality_rate')
RESTRICTIONS: TargetString = TargetString(
'cause.protein_energy_malnutrition.restrictions')
# Useful keys not for the artifact - distinguished by not using the colon type declaration
@property
def name(self):
return 'protein_energy_malnutrition'
@property
def log_name(self):
return 'protein energy malnutrition'
def __init__(self, target: str):
"""
Parameters
----------
target :
Type, name, and target rate of entity to be affected by risk factor,
supplied in the form "entity_type.entity_name.measure"
where entity_type should be singular (e.g., cause instead of causes).
"""
self.risk = EntityString(
'risk_factor.low_birth_weight_and_short_gestation')
self.target = TargetString(target)
self.configuration_defaults = {
f'effect_of_{self.risk.name}_on_{self.target.name}': {
self.target.measure:
RiskEffect.configuration_defaults['effect_of_risk_on_target']
['measure']
}
}
def __init__(self, risk: str, target: str):
"""
Parameters
----------
risk :
Type and name of risk factor, supplied in the form
"risk_type.risk_name" where risk_type should be singular (e.g.,
risk_factor instead of risk_factors).
target :
Type, name, and target rate of entity to be affected by risk factor,
supplied in the form "entity_type.entity_name.measure"
where entity_type should be singular (e.g., cause instead of causes).
"""
self.risk = EntityString(risk)
self.target = TargetString(target)
self.configuration_defaults = {
f'effect_of_{self.risk.name}_on_{self.target.name}': {
self.target.measure: RiskEffect.configuration_defaults['effect_of_risk_on_target']['measure']
}
}
def setup(self, builder: 'Builder'):
self.randomness_key = self.get_randomness_key(builder)
self.randomness = builder.randomness.get_stream(self.name)
self.correlation = self.load_correlation_data(builder)
columns_created = project_globals.CORRELATED_PROPENSITY_COLUMNS
self.population_view = builder.population.get_view(columns_created + ['age'])
builder.population.initializes_simulants(self.on_initialize_simulants,
creates_columns=columns_created,
requires_columns=['age'],
requires_streams=[self.name])
for target, rate in project_globals.RATE_TARGET_MAP.items():
population_attributable_fraction_data = self.load_population_attributable_fraction_data(builder, rate)
population_attributable_fraction = builder.lookup.build_table(population_attributable_fraction_data,
key_columns=['sex'],
parameter_columns=['age', 'year'])
target = TargetString(target)
builder.value.register_value_modifier(f'{target.name}.{target.measure}.paf',
modifier=population_attributable_fraction,
requires_columns=['age', 'sex'])
class __LowBirthWeightShortGestation(NamedTuple):
# Keys that will be loaded into the artifact. must have a colon type declaration
EXPOSURE: TargetString = 'risk_factor.low_birth_weight_and_short_gestation.exposure'
DISTRIBUTION: TargetString = 'risk_factor.low_birth_weight_and_short_gestation.distribution'
CATEGORIES: TargetString = 'risk_factor.low_birth_weight_and_short_gestation.categories'
RELATIVE_RISK: TargetString = 'risk_factor.low_birth_weight_and_short_gestation.relative_risk'
RELATIVE_RISK_INTERPOLATOR: TargetString = 'risk_factor.low_birth_weight_and_short_gestation.relative_risk_interpolator'
PAF: TargetString = 'risk_factor.low_birth_weight_and_short_gestation.population_attributable_fraction'
# Useful keys not for the artifact - distinguished by not using the colon type declaration
BIRTH_WEIGHT_EXPOSURE = TargetString(
'risk_factor.low_birth_weight.birth_exposure')
@property
def name(self):
return 'low_birth_weight_and_short_gestation'
@property
def log_name(self):
return 'low birth weight and short gestation'
class __Measles(NamedTuple):
# Keys that will be loaded into the artifact. must have a colon type declaration
PREVALENCE: TargetString = TargetString('cause.measles.prevalence')
INCIDENCE_RATE: TargetString = TargetString('cause.measles.incidence_rate')
DISABILITY_WEIGHT: TargetString = TargetString(
'cause.measles.disability_weight')
EMR: TargetString = TargetString('cause.measles.excess_mortality_rate')
CSMR: TargetString = TargetString(
'cause.measles.cause_specific_mortality_rate')
RESTRICTIONS: TargetString = TargetString('cause.measles.restrictions')
# Useful keys not for the artifact - distinguished by not using the colon type declaration
@property
def name(self):
return 'measles'
@property
def log_name(self):
return 'measles'
def __init__(self, target):
self.target = TargetString(target)
self.configuration_defaults = {
f'intervention_on_{self.target.name}':
AbsoluteShift.configuration_defaults['intervention']
}
def test_TargetString_pass(s):
target_type, target_name, target_measure = s.split('.')
t = TargetString(s)
assert t.type == target_type
assert t.name == target_name
assert t.measure == target_measure
@property
def disability_weights(self):
return [
self.CAT_1_DISABILITY_WEIGHT,
self.CAT_2_DISABILITY_WEIGHT,
self.CAT_3_DISABILITY_WEIGHT,
self.CAT_4_DISABILITY_WEIGHT,
]
IKF = __ImpairedKidneyFunction()
RATE_TARGET_MAP = {
'sequela.acute_myocardial_infarction.incidence_rate':
TargetString(IHD.ACUTE_MI_INCIDENCE_RATE),
'sequela.post_myocardial_infarction_to_acute_myocardial_infarction.transition_rate':
TargetString(IHD.ACUTE_MI_INCIDENCE_RATE),
'sequela.acute_ischemic_stroke.incidence_rate':
TargetString(ISCHEMIC_STROKE.ACUTE_STROKE_INCIDENCE_RATE),
'sequela.post_ischemic_stroke_to_acute_ischemic_stroke.transition_rate':
TargetString(ISCHEMIC_STROKE.ACUTE_STROKE_INCIDENCE_RATE),
}
MAKE_ARTIFACT_KEY_GROUPS = [
POPULATION,
IHD,
ISCHEMIC_STROKE,
DIABETES_MELLITUS,
LDL_C,
SBP,
class __MultipleMyeloma(NamedTuple):
# Keys that will be loaded into the artifact. must have a colon type declaration
PREVALENCE: TargetString = TargetString(
'cause.multiple_myeloma.prevalence')
INCIDENCE_RATE: TargetString = TargetString(
'cause.multiple_myeloma.incidence_rate')
DISABILITY_WEIGHT: TargetString = TargetString(
'cause.multiple_myeloma.disability_weight')
CSMR: TargetString = TargetString(
'cause.multiple_myeloma.cause_specific_mortality_rate')
RESTRICTIONS: TargetString = TargetString(
'cause.multiple_myeloma.restrictions')
LINE_1_PREVALENCE: TargetString = TargetString(
'cause.multiple_myeloma_1.prevalence')
LINE_1_DISABILITY_WEIGHT: TargetString = TargetString(
'cause.multiple_myeloma_1.disability_weight')
LINE_1_EMR: TargetString = TargetString(
'cause.multiple_myeloma_1.excess_mortality_rate')
LINE_2_PREVALENCE: TargetString = TargetString(
'cause.multiple_myeloma_2.prevalence')
LINE_2_DISABILITY_WEIGHT: TargetString = TargetString(
'cause.multiple_myeloma_2.disability_weight')
LINE_2_EMR: TargetString = TargetString(
'cause.multiple_myeloma_2.excess_mortality_rate')
LINE_3_PREVALENCE: TargetString = TargetString(
'cause.multiple_myeloma_3.prevalence')
LINE_3_DISABILITY_WEIGHT: TargetString = TargetString(
'cause.multiple_myeloma_3.disability_weight')
LINE_3_EMR: TargetString = TargetString(
'cause.multiple_myeloma_3.excess_mortality_rate')
LINE_4_PREVALENCE: TargetString = TargetString(
'cause.multiple_myeloma_4.prevalence')
LINE_4_DISABILITY_WEIGHT: TargetString = TargetString(
'cause.multiple_myeloma_4.disability_weight')
LINE_4_EMR: TargetString = TargetString(
'cause.multiple_myeloma_4.excess_mortality_rate')
LINE_5_PREVALENCE: TargetString = TargetString(
'cause.multiple_myeloma_5.prevalence')
LINE_5_DISABILITY_WEIGHT: TargetString = TargetString(
'cause.multiple_myeloma_5.disability_weight')
LINE_5_EMR: TargetString = TargetString(
'cause.multiple_myeloma_5.excess_mortality_rate')
GBD_CSMR: TargetString = TargetString(
'cause.multiple_myeloma_gbd.cause_specific_mortality_rate')
SUSCEPTIBLE_EMR: TargetString = TargetString(
'cause.susceptible_to_multiple_myeloma.excess_mortality_rate')
@property
def name(self):
return 'multiple_myeloma'
@property
def log_name(self):
return 'multiple myeloma'
def test_TargetString_fail(s):
with pytest.raises(ValueError):
TargetString(s)
