Risk Data Transformations
This module contains tools for handling raw risk exposure and relative risk data and performing any necessary data transformations.
- vivarium_public_health.risks.data_transformations.pivot_categorical(data)[source]
Pivots data that is long on categories to be wide.
- vivarium_public_health.risks.data_transformations.get_distribution_data(builder, risk)[source]
- Parameters:
risk (EntityString) –
- vivarium_public_health.risks.data_transformations.get_exposure_post_processor(builder, risk)[source]
- Parameters:
risk (EntityString) –
- vivarium_public_health.risks.data_transformations.load_distribution_data(builder, risk)[source]
- Parameters:
risk (EntityString) –
- vivarium_public_health.risks.data_transformations.get_distribution_type(builder, risk)[source]
- Parameters:
risk (EntityString) –
- vivarium_public_health.risks.data_transformations.get_exposure_data(builder, risk)[source]
- Parameters:
risk (EntityString) –
- vivarium_public_health.risks.data_transformations.load_exposure_data(builder, risk)[source]
- Parameters:
risk (EntityString) –
- vivarium_public_health.risks.data_transformations.get_exposure_standard_deviation_data(builder, risk)[source]
- Parameters:
risk (EntityString) –
- vivarium_public_health.risks.data_transformations.get_exposure_distribution_weights(builder, risk)[source]
- Parameters:
risk (EntityString) –
- vivarium_public_health.risks.data_transformations.rebin_exposure_data(builder, risk, exposure_data)[source]
- Parameters:
risk (EntityString) –
exposure_data (DataFrame) –
- vivarium_public_health.risks.data_transformations.get_relative_risk_data(builder, risk, target)[source]
- Parameters:
risk (EntityString) –
target (TargetString) –
- vivarium_public_health.risks.data_transformations.load_relative_risk_data(builder, risk, target, source_type)[source]
- Parameters:
risk (EntityString) –
target (TargetString) –
source_type (str) –
- vivarium_public_health.risks.data_transformations.generate_relative_risk_from_distribution(random_state, parameters)[source]
- Parameters:
random_state (RandomState) –
parameters (dict) –
- Return type:
- vivarium_public_health.risks.data_transformations.rebin_relative_risk_data(builder, risk, relative_risk_data)[source]
When the polytomous risk is rebinned, matching relative risk needs to be rebinned. After rebinning, rr for both exposed and unexposed categories should be the weighted sum of relative risk of the component categories where weights are relative proportions of exposure of those categories. For example, if cat1, cat2, cat3 are exposed categories and cat4 is unexposed with exposure [0.1,0.2,0.3,0.4], for the matching rr = [rr1, rr2, rr3, 1], rebinned rr for the rebinned cat1 should be: (0.1 rr1 + 0.2 * rr2 + 0.3 rr3) / (0.1+0.2+0.3)
- Parameters:
risk (EntityString) –
relative_risk_data (DataFrame) –
- Return type:
- vivarium_public_health.risks.data_transformations.get_exposure_effect(builder, risk)[source]
- Parameters:
risk (EntityString) –
- vivarium_public_health.risks.data_transformations.get_population_attributable_fraction_data(builder, risk, target)[source]
- Parameters:
risk (EntityString) –
target (TargetString) –
- vivarium_public_health.risks.data_transformations.validate_distribution_data_source(builder, risk)[source]
Checks that the exposure distribution specification is valid.
- Parameters:
risk (EntityString) –
- vivarium_public_health.risks.data_transformations.validate_relative_risk_data_source(builder, risk, target)[source]
- Parameters:
risk (EntityString) –
target (TargetString) –
- vivarium_public_health.risks.data_transformations.validate_relative_risk_rebin_source(builder, risk, target, data)[source]
- Parameters:
risk (EntityString) –
target (TargetString) –
data (DataFrame) –
- vivarium_public_health.risks.data_transformations.validate_rebin_source(builder, risk, data)[source]
- Parameters:
risk (EntityString) –
data (DataFrame) –