def setup(self, builder):
self.config = builder.configuration.metrics.mortality
self.clock = builder.time.clock()
self.step_size = builder.time.step_size()
self.start_time = self.clock()
self.initial_pop_entrance_time = self.start_time - self.step_size()
self.age_bins = get_age_bins(builder)
diseases = builder.components.get_components_by_type(
(DiseaseState, RiskAttributableDisease))
self.causes = [c.state_id for c in diseases] + ['other_causes']
life_expectancy_data = builder.data.load(
"population.theoretical_minimum_risk_life_expectancy")
self.life_expectancy = builder.lookup.build_table(
life_expectancy_data, key_columns=[], parameter_columns=['age'])
columns_required = [
'tracked', 'alive', 'entrance_time', 'exit_time', 'cause_of_death',
'years_of_life_lost', 'age'
]
if self.config.by_sex:
columns_required += ['sex']
self.population_view = builder.population.get_view(columns_required)
builder.event.register_listener('time_step__prepare',
self.on_time_step_prepare)
builder.value.register_value_modifier('metrics', self.metrics)
def setup(self, builder: 'Builder'):
self.config = builder.configuration['metrics'][
f'{self.disease}_observer'].to_dict()
self.clock = builder.time.clock()
self.age_bins = get_age_bins(builder)
self.counts = Counter()
self.person_time = Counter()
self.states = project_globals.DISEASE_MODEL_MAP[self.disease]['states']
self.transitions = project_globals.DISEASE_MODEL_MAP[
self.disease]['transitions']
self.previous_state_column = f'previous_{self.disease}'
builder.population.initializes_simulants(
self.on_initialize_simulants,
creates_columns=[self.previous_state_column])
columns_required = [
'alive', f'{self.disease}', self.previous_state_column
]
if self.config['by_age']:
columns_required += ['age']
if self.config['by_sex']:
columns_required += ['sex']
self.population_view = builder.population.get_view(columns_required)
builder.value.register_value_modifier('metrics', self.metrics)
# FIXME: The state table is modified before the clock advances.
# In order to get an accurate representation of person time we need to look at
# the state table before anything happens.
builder.event.register_listener('time_step__prepare',
self.on_time_step_prepare)
builder.event.register_listener('collect_metrics',
self.on_collect_metrics)
def setup(self, builder):
self.clock = builder.time.clock()
self.config = builder.configuration['metrics']['medication']
self.counts = Counter()
self.never_treated = pd.DataFrame(columns=HYPERTENSION_DRUGS,
dtype=bool)
age_sex_filter, (self.ages,
self.sexes) = get_age_sex_filter_and_iterables(
self.config, get_age_bins(builder))
self.base_filter = age_sex_filter
columns_required = ['alive', 'last_prescription_date'
] + DOSAGE_COLUMNS + SINGLE_PILL_COLUMNS
if self.config.by_age:
columns_required += ['age']
if self.config.by_sex:
columns_required += ['sex']
self.population_view = builder.population.get_view(columns_required)
builder.population.initializes_simulants(
self.on_initialize_simulants, requires_columns=columns_required)
builder.value.register_value_modifier('metrics', self.metrics)
builder.event.register_listener('collect_metrics',
self.on_collect_metrics)
def setup(self, builder):
super().setup(builder)
self.age_bins = get_age_bins(builder)
self.anemia_counts = Counter()
self.anemia_thresholds = builder.lookup.build_table(
get_anemia_thresholds(),
key_columns=[],
parameter_columns=[('age', 'age_group_start', 'age_group_end')],
value_columns=[
'severe_threshold', 'moderate_threshold', 'mild_threshold'
])
self._disability_weight_data = builder.lookup.build_table(
get_iron_deficiency_disability_weight(builder))
self.disability_weight = builder.value.register_value_producer(
'iron_deficiency.disability_weight',
source=self.compute_disability_weight)
builder.value.register_value_modifier('disability_weight',
modifier=self.disability_weight)
self.pop_view = builder.population.get_view(['alive', 'age', 'sex'])
self.data = {}
self.observer_config = builder.configuration['metrics'][
'anemia_observer']
self.clock = builder.time.clock()
builder.value.register_value_modifier('metrics', self.metrics)
builder.event.register_listener('collect_metrics',
self.on_collect_metrics)
def test_get_age_bins(builder, base_config, age_start, exit_age,
result_age_end_values, result_age_start_values):
base_config.update(
{'population': {
'age_start': age_start,
'exit_age': exit_age
}}, **metadata(__file__))
builder.configuration = base_config
df = get_age_bins(builder)
assert set(df.age_end) == result_age_end_values
assert set(df.age_start) == result_age_start_values
def setup(self, builder):
self.schedule = builder.configuration.shigellosis_vaccine.schedule
self.config = builder.configuration['metrics'][self.name].to_dict()
self.age_bins = get_age_bins(builder)
self.counts = Counter()
columns_required = ['alive', f'vaccine_dose', f'vaccine_event_time']
if self.config['by_age']:
columns_required += ['age']
if self.config['by_sex']:
columns_required += ['sex']
self.population_view = builder.population.get_view(columns_required)
builder.value.register_value_modifier('metrics', self.metrics)
builder.event.register_listener('collect_metrics',
self.on_collect_metrics)
def setup(self, builder):
self.clock = builder.time.clock()
self.age_bins = get_age_bins(builder)
required_columns = [
'registry_evaluation_status', 'registry_evaluation_date', 'age',
'sex', 'alive', *data_values.RISKS
]
self.population_view = builder.population.get_view(required_columns)
builder.value.register_value_modifier('metrics', self.metrics)
builder.event.register_listener('collect_metrics',
self.on_collect_metrics)
self.registry_entrances = Counter()
self.registry_prevalence = Counter()
def setup(self, builder):
self.data = {}
self.config = builder.configuration[f'metrics'][
f'{self.risk.name}_observer']
self.clock = builder.time.clock()
self.categories = self.config.categories
self.age_bins = get_age_bins(builder)
self.category_counts = Counter()
self.population_view = builder.population.get_view(
['alive', 'age', 'sex'], query='alive == "alive"')
self.exposure = builder.value.get_value(f'{self.risk.name}.exposure')
builder.value.register_value_modifier('metrics', self.metrics)
builder.event.register_listener('collect_metrics',
self.on_collect_metrics)
def setup(self, builder):
self.config = builder.configuration.metrics.supplemented_days
self.step_size = builder.time.step_size()
self.age_bins = get_age_bins(builder)
self.lack_of_vitamin_a_supplementation = builder.value.get_value(
"lack_of_vitamin_a_supplementation.exposure")
self.supplemented_days = Counter()
columns_required = ['tracked', 'alive']
if self.config.by_age:
columns_required += ['age']
if self.config.by_sex:
columns_required += ['sex']
self.population_view = builder.population.get_view(columns_required)
builder.event.register_listener('collect_metrics',
self.on_collect_metrics)
builder.value.register_value_modifier('metrics', self.metrics)
def setup(self, builder):
self.age_bins = get_age_bins(builder)
treatment_cols = [
'treatment_start_date', 'last_visit_date', 'last_visit_type',
'high_systolic_blood_pressure_measurement'
]
disease_event_cols = [
f'{disease}_event_time' for disease in self.diseases
]
death_cols = ['alive', 'exit_time', 'cause_of_death']
self.population_view = builder.population.get_view(treatment_cols +
disease_event_cols +
death_cols)
builder.population.initializes_simulants(self.on_initialize_simulants)
builder.value.register_value_modifier('metrics', self.metrics)
builder.event.register_listener('collect_metrics',
self.on_collect_metrics)
def setup(self, builder: 'Builder'):
self.config = builder.configuration['metrics'][
'anemia_observer'].to_dict()
self.clock = builder.time.clock()
self.age_bins = get_age_bins(builder)
self.person_time = Counter()
self.anemia_severity = builder.value.get_value('anemia_severity')
self.states = project_globals.ANEMIA_SEVERITY_GROUPS
columns_required = ['alive']
if self.config['by_age']:
columns_required += ['age']
if self.config['by_sex']:
columns_required += ['sex']
self.population_view = builder.population.get_view(columns_required)
builder.value.register_value_modifier('metrics', self.metrics)
# FIXME: The state table is modified before the clock advances.
# In order to get an accurate representation of person time we need to look at
# the state table before anything happens.
builder.event.register_listener('time_step__prepare',
self.on_time_step_prepare)
def setup(self, builder):
self.config = builder.configuration['metrics'][
f'{self.disease}_observer']
self.clock = builder.time.clock()
self.age_bins = get_age_bins(builder)
self.counts = Counter()
model = builder.components.get_component(
f'disease_model.{self.disease}')
self.disease_states = [s.name.split('.')[-1] for s in model.states]
columns_required = ['alive'] + [
f'{state}_event_time' for state in self.disease_states
]
if self.config.by_age:
columns_required += ['age']
if self.config.by_sex:
columns_required += ['sex']
self.population_view = builder.population.get_view(columns_required)
builder.value.register_value_modifier('metrics', self.metrics)
builder.event.register_listener('collect_metrics',
self.on_collect_metrics)
def setup(self, builder: 'Builder'):
self.config = builder.configuration.metrics.miscellaneous_observer.to_dict(
)
self.age_bins = get_age_bins(builder)
columns_required = [
project_globals.TREATMENT.name, 'age', 'sex', 'alive',
'initial_treatment_proportion_reduction'
]
self.population_view = builder.population.get_view(columns_required)
self.fpg = builder.value.get_value(
f'{project_globals.FPG.name}.exposure')
self.ldlc = builder.value.get_value(
f'{project_globals.LDL_C.name}.exposure')
self.sbp = builder.value.get_value(
f'{project_globals.SBP.name}.exposure')
self.is_adherent = builder.value.get_value('ldlc_treatment_adherence')
self.cvd_risk_score = builder.value.get_value('cvd_risk_score')
self.results = Counter()
builder.value.register_value_modifier('metrics', self.metrics)
builder.event.register_listener('collect_metrics',
self.on_collect_metrics)
def _get_age_bins(self, builder: Builder) -> pd.DataFrame:
return utilities.get_age_bins(builder)