Index

A

AbsoluteShift (class in vivarium_public_health.treatment.magic_wand) ACMR add_dwell_time_transition() (vivarium_public_health.disease.state.BaseDiseaseState method) add_proportion_transition() (vivarium_public_health.disease.state.BaseDiseaseState method) add_rate_transition() (vivarium_public_health.disease.state.BaseDiseaseState method) (vivarium_public_health.disease.state.DiseaseState method) (vivarium_public_health.disease.state.NonDiseasedState method) adjust_cause_specific_mortality_rate() (vivarium_public_health.disease.model.DiseaseModel method) (vivarium_public_health.disease.special_disease.RiskAttributableDisease method) adjust_mortality_rate() (vivarium_public_health.disease.special_disease.RiskAttributableDisease method) (vivarium_public_health.disease.state.DiseaseState method)

adjust_state_and_transitions() (vivarium_public_health.disease.special_disease.RiskAttributableDisease method) Age-Specific Fertility Rate age_bins (vivarium_public_health.results.stratification.ResultsStratifier attribute) AgeOutSimulants (class in vivarium_public_health.population.base_population) AgeValues (class in vivarium_public_health.population.data_transformations) aggregate_category_person_time() (vivarium_public_health.results.causal_factor.CategoricalCausalFactorObserver method) aggregate_state_person_time() (vivarium_public_health.results.disease.DiseaseObserver method) All-Cause Mortality Rate apply_scale_up() (vivarium_public_health.treatment.scale_up.LinearScaleUp method) assign_demographic_proportions() (in module vivarium_public_health.population.data_transformations)

B

BaseDiseaseState (class in vivarium_public_health.disease.state) BasePopulation (class in vivarium_public_health.population.base_population) Birth Prevalence build_birth_exposure_params_table() (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGDistribution method) build_exposure_params_table() (vivarium_public_health.causal_factor.distributions.PolytomousDistribution method) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGDistribution method)

build_exposure_table() (vivarium_public_health.causal_factor.distributions.DichotomousDistribution method) build_rr_lookup_table() (vivarium_public_health.causal_factor.effect.CausalFactorEffect method) (vivarium_public_health.risks.effect.NonLogLinearRiskEffect method) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRiskEffect method)

C

calculate_mortality_rate() (vivarium_public_health.population.mortality.Mortality method) calculate_ylls() (vivarium_public_health.results.mortality.MortalityObserver method) Calibration Constant CategoricalCausalFactorObserver (class in vivarium_public_health.results.causal_factor) CategoricalInterventionObserver (class in vivarium_public_health.results.causal_factor) CategoricalRiskObserver (class in vivarium_public_health.results.causal_factor) categories (vivarium_public_health.causal_factor.distributions.PolytomousDistribution property) (vivarium_public_health.results.causal_factor.CategoricalCausalFactorObserver attribute) (vivarium_public_health.results.causal_factor.CategoricalInterventionObserver attribute) (vivarium_public_health.results.causal_factor.CategoricalRiskObserver attribute) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGDistribution property) causal_factor (vivarium_public_health.results.causal_factor.CategoricalCausalFactorObserver attribute) (vivarium_public_health.results.causal_factor.CategoricalInterventionObserver attribute) (vivarium_public_health.results.causal_factor.CategoricalRiskObserver attribute) CausalFactor (class in vivarium_public_health.causal_factor.exposure) CausalFactorDistribution (class in vivarium_public_health.causal_factor.distributions) CausalFactorEffect (class in vivarium_public_health.causal_factor.effect) Cause-Deleted Mortality Cause-Specific Mortality Rate cause_type (vivarium_public_health.results.simple_cause.SimpleCause attribute) causes_of_death (vivarium_public_health.results.mortality.MortalityObserver attribute) causes_of_disability (vivarium_public_health.results.disability.DisabilityObserver attribute) CausesConfigurationParser (class in vivarium_public_health.plugins.parser) CausesParsingErrors clip() (in module vivarium_public_health.causal_factor.distributions) clock (vivarium_public_health.results.mortality.MortalityObserver attribute) compute_disability_weight() (vivarium_public_health.disease.special_disease.RiskAttributableDisease method) (vivarium_public_health.disease.state.DiseaseState method) compute_excess_mortality_rate() (vivarium_public_health.disease.special_disease.RiskAttributableDisease method) (vivarium_public_health.disease.state.DiseaseState method)

compute_transition_rate() (vivarium_public_health.disease.transition.RateTransition method) configuration_defaults (vivarium_public_health.causal_factor.effect.CausalFactorEffect property) (vivarium_public_health.causal_factor.exposure.CausalFactor property) (vivarium_public_health.disease.model.DiseaseModel property) (vivarium_public_health.disease.special_disease.RiskAttributableDisease property) (vivarium_public_health.disease.state.BaseDiseaseState property) (vivarium_public_health.disease.state.DiseaseState property) (vivarium_public_health.disease.transition.ProportionTransition property) (vivarium_public_health.disease.transition.RateTransition property) (vivarium_public_health.population.add_new_birth_cohorts.FertilityAgeSpecificRates property) CONFIGURATION_DEFAULTS (vivarium_public_health.population.add_new_birth_cohorts.FertilityCrudeBirthRate attribute) (vivarium_public_health.population.add_new_birth_cohorts.FertilityDeterministic attribute) (vivarium_public_health.population.base_population.BasePopulation attribute) configuration_defaults (vivarium_public_health.population.mortality.Mortality property) (vivarium_public_health.results.mortality.MortalityObserver property) (vivarium_public_health.risks.effect.NonLogLinearRiskEffect property) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRisk property) CONFIGURATION_DEFAULTS (vivarium_public_health.treatment.magic_wand.AbsoluteShift attribute) configuration_defaults (vivarium_public_health.treatment.magic_wand.AbsoluteShift property) CONFIGURATION_DEFAULTS (vivarium_public_health.treatment.scale_up.LinearScaleUp attribute) configuration_defaults (vivarium_public_health.treatment.scale_up.LinearScaleUp property) CONFIGURATION_DEFAULTS (vivarium_public_health.treatment.therapeutic_inertia.TherapeuticInertia attribute) configuration_key (vivarium_public_health.treatment.scale_up.LinearScaleUp property) Continuous Distribution ContinuousDistribution (class in vivarium_public_health.causal_factor.distributions) count_deaths() (vivarium_public_health.results.mortality.MortalityObserver method) coverage_effect() (vivarium_public_health.treatment.scale_up.LinearScaleUp method) create_from_specific_cause() (vivarium_public_health.results.simple_cause.SimpleCause class method) Crude Birth Rate CSMR current (vivarium_public_health.population.data_transformations.AgeValues attribute)

D

DEFAULT_MODEL_CONFIG (vivarium_public_health.plugins.parser.CausesConfigurationParser attribute) DEFAULT_STATE_CONFIG (vivarium_public_health.plugins.parser.CausesConfigurationParser attribute) DEFAULT_TRANSITION_CONFIG (vivarium_public_health.plugins.parser.CausesConfigurationParser attribute) Dichotomous Distribution DichotomousDistribution (class in vivarium_public_health.causal_factor.distributions) Disability (class in vivarium_public_health.population.base_population) Disability Weight disability_classes (vivarium_public_health.results.disability.DisabilityObserver property) disability_weight (vivarium_public_health.results.disability.DisabilityObserver attribute)

disability_weight_aggregator() (vivarium_public_health.results.disability.DisabilityObserver method) disability_weight_pipeline (vivarium_public_health.population.base_population.Disability attribute) DisabilityObserver (class in vivarium_public_health.results.disability) disease (vivarium_public_health.results.disease.DiseaseObserver attribute) disease_model (vivarium_public_health.results.disease.DiseaseObserver attribute) DiseaseModel (class in vivarium_public_health.disease.model) DiseaseModelError DiseaseObserver (class in vivarium_public_health.results.disease) DiseaseState (class in vivarium_public_health.disease.state) Dwell Time

E

EMR end_year (vivarium_public_health.results.stratification.ResultsStratifier attribute) EndpointValues (class in vivarium_public_health.population.data_transformations) Ensemble Distribution EnsembleDistribution (class in vivarium_public_health.causal_factor.distributions) entity (vivarium_public_health.results.disease.DiseaseObserver attribute) entity_type (vivarium_public_health.results.disease.DiseaseObserver attribute) EntityString (class in vivarium_public_health.utilities) Excess Mortality Rate ExcessMortalityState (class in vivarium_public_health.disease.state) exposed (vivarium_public_health.causal_factor.distributions.DichotomousDistribution property) EXPOSURE_CLASS (vivarium_public_health.causal_factor.effect.CausalFactorEffect attribute) (vivarium_public_health.risks.effect.RiskEffect attribute) (vivarium_public_health.treatment.intervention.InterventionEffect attribute)

exposure_distributions (vivarium_public_health.causal_factor.exposure.CausalFactor attribute) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRisk attribute) exposure_parameter_source() (vivarium_public_health.causal_factor.distributions.DichotomousDistribution method) exposure_pipeline (vivarium_public_health.results.causal_factor.CategoricalCausalFactorObserver attribute) (vivarium_public_health.results.causal_factor.CategoricalInterventionObserver attribute) (vivarium_public_health.results.causal_factor.CategoricalRiskObserver attribute) exposure_ppf() (vivarium_public_health.causal_factor.distributions.ContinuousDistribution method) (vivarium_public_health.causal_factor.distributions.DichotomousDistribution method) (vivarium_public_health.causal_factor.distributions.EnsembleDistribution method) (vivarium_public_health.causal_factor.distributions.PolytomousDistribution method) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGDistribution method)

F

FertilityAgeSpecificRates (class in vivarium_public_health.population.add_new_birth_cohorts) FertilityCrudeBirthRate (class in vivarium_public_health.population.add_new_birth_cohorts) FertilityDeterministic (class in vivarium_public_health.population.add_new_birth_cohorts) format() (vivarium_public_health.results.causal_factor.CategoricalCausalFactorObserver method) (vivarium_public_health.results.disability.DisabilityObserver method) (vivarium_public_health.results.disease.DiseaseObserver method) (vivarium_public_health.results.mortality.MortalityObserver method) (vivarium_public_health.results.observer.PublicHealthObserver method)

format_results() (vivarium_public_health.results.observer.PublicHealthObserver method)

G

generate_population() (in module vivarium_public_health.population.base_population) get_age_bins() (vivarium_public_health.results.stratification.ResultsStratifier static method) get_age_intervals() (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRiskEffect method) get_calibration_constant_data() (vivarium_public_health.causal_factor.effect.CausalFactorEffect method) get_calibration_constant_pipeline_name() (in module vivarium_public_health.causal_factor.calibration_constant) get_category_intervals() (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGDistribution method) get_cause_deleted_mortality_rate() (in module vivarium_public_health.population.data_transformations) get_clock() (vivarium_public_health.treatment.scale_up.LinearScaleUp method) get_configuration() (vivarium_public_health.causal_factor.distributions.CausalFactorDistribution method) get_configuration_name() (vivarium_public_health.results.causal_factor.CategoricalCausalFactorObserver method) (vivarium_public_health.results.disease.DiseaseObserver method) get_continuous_propensity_name() (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRisk static method) get_demographic_proportions_for_creation_time() (vivarium_public_health.population.base_population.BasePopulation static method) get_disability_weight_source() (vivarium_public_health.disease.state.DiseaseState method) get_distribution_definitions() (vivarium_public_health.causal_factor.distributions.EnsembleDistribution method) get_distribution_parameters() (vivarium_public_health.causal_factor.distributions.ContinuousDistribution method) get_distribution_type() (vivarium_public_health.causal_factor.effect.CausalFactorEffect method) (vivarium_public_health.causal_factor.exposure.CausalFactor method) get_dwell_time() (vivarium_public_health.disease.state.BaseDiseaseState method) get_endpoint_value_from_data() (vivarium_public_health.treatment.scale_up.LinearScaleUp method) get_entity_column() (vivarium_public_health.results.causal_factor.CategoricalCausalFactorObserver method) (vivarium_public_health.results.disability.DisabilityObserver method) (vivarium_public_health.results.disease.DiseaseObserver method) (vivarium_public_health.results.mortality.MortalityObserver method) (vivarium_public_health.results.observer.PublicHealthObserver method) get_entity_type_column() (vivarium_public_health.results.causal_factor.CategoricalCausalFactorObserver method) (vivarium_public_health.results.disability.DisabilityObserver method) (vivarium_public_health.results.disease.DiseaseObserver method) (vivarium_public_health.results.mortality.MortalityObserver method) (vivarium_public_health.results.observer.PublicHealthObserver method) get_excess_mortality_rate_source() (vivarium_public_health.disease.state.DiseaseState method) get_exposure() (vivarium_public_health.risks.base_risk.Risk method) get_exposure_data() (vivarium_public_health.causal_factor.distributions.CausalFactorDistribution method) (vivarium_public_health.causal_factor.distributions.DichotomousDistribution method) get_exposure_distribution() (vivarium_public_health.causal_factor.exposure.CausalFactor method)

get_exposure_filter() (vivarium_public_health.disease.special_disease.RiskAttributableDisease method) get_exposure_name() (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRisk static method) get_exposure_parameters() (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGDistribution method) get_exposure_post_processor() (in module vivarium_public_health.causal_factor.utilities) get_exposure_value_columns() (vivarium_public_health.causal_factor.distributions.PolytomousDistribution method) get_filtered_data() (vivarium_public_health.causal_factor.effect.CausalFactorEffect method) get_initial_event_times() (vivarium_public_health.disease.state.BaseDiseaseState method) (vivarium_public_health.disease.state.DiseaseState method) get_initialization_parameters() (vivarium_public_health.disease.state.BaseDiseaseState method) get_interpolator() (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRiskEffect method) get_is_intervention_scenario() (vivarium_public_health.treatment.scale_up.LinearScaleUp method) get_live_births_per_year() (in module vivarium_public_health.population.data_transformations) get_measure_column() (vivarium_public_health.results.causal_factor.CategoricalCausalFactorObserver method) (vivarium_public_health.results.disease.DiseaseObserver method) (vivarium_public_health.results.observer.PublicHealthObserver method) get_name() (vivarium_public_health.causal_factor.effect.CausalFactorEffect static method) get_paf_data() (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRiskEffect method) get_prevalence_source() (vivarium_public_health.disease.state.DiseaseState method) get_randomness_prevalence() (vivarium_public_health.disease.state.DiseaseState method) get_randomness_stream() (vivarium_public_health.causal_factor.exposure.CausalFactor method) (vivarium_public_health.population.mortality.Mortality method) get_randomness_streams() (vivarium_public_health.population.base_population.BasePopulation method) get_relative_risk_column_name() (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRiskEffect method) get_relative_risk_source() (vivarium_public_health.causal_factor.effect.CausalFactorEffect method) (vivarium_public_health.risks.effect.NonLogLinearRiskEffect method) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRiskEffect method) get_required_pipelines() (vivarium_public_health.treatment.scale_up.LinearScaleUp method) get_risk_distribution_parameter() (in module vivarium_public_health.causal_factor.distributions) get_scale_up_dates() (vivarium_public_health.treatment.scale_up.LinearScaleUp method) get_scale_up_values() (vivarium_public_health.treatment.scale_up.LinearScaleUp method) get_sub_entity_column() (vivarium_public_health.results.causal_factor.CategoricalCausalFactorObserver method) (vivarium_public_health.results.disability.DisabilityObserver method) (vivarium_public_health.results.disease.DiseaseObserver method) (vivarium_public_health.results.mortality.MortalityObserver method) (vivarium_public_health.results.observer.PublicHealthObserver method) get_transition_names() (vivarium_public_health.disease.state.BaseDiseaseState method)

H

has_dwell_time (vivarium_public_health.disease.state.BaseDiseaseState property) has_excess_mortality() (vivarium_public_health.disease.state.ExcessMortalityState method)

has_initialization_weights() (vivarium_public_health.disease.state.DiseaseState method) (vivarium_public_health.disease.state.SusceptibleState method)

I

Incidence Rate initialize_birth_time_and_parent_id() (vivarium_public_health.population.add_new_birth_cohorts.FertilityAgeSpecificRates method) initialize_categorical_and_continuous_propensities() (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRisk method) initialize_disease() (vivarium_public_health.disease.special_disease.RiskAttributableDisease method) initialize_ensemble_propensity() (vivarium_public_health.causal_factor.distributions.EnsembleDistribution method) initialize_event_time_and_count() (vivarium_public_health.disease.state.BaseDiseaseState method) initialize_exposure() (vivarium_public_health.risks.base_risk.Risk method) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRisk method) initialize_is_aged_out() (vivarium_public_health.population.base_population.AgeOutSimulants method) initialize_mortality() (vivarium_public_health.population.mortality.Mortality method)

initialize_population() (vivarium_public_health.population.base_population.BasePopulation method) initialize_previous_state() (vivarium_public_health.results.disease.DiseaseObserver method) initialize_propensity() (vivarium_public_health.causal_factor.exposure.CausalFactor method) initialize_relative_risk() (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRiskEffect method) initialize_state() (vivarium_public_health.disease.model.DiseaseModel method) initialize_therapeutic_inertia() (vivarium_public_health.treatment.therapeutic_inertia.TherapeuticInertia method) Intervention (class in vivarium_public_health.treatment.intervention) intervention_effect() (vivarium_public_health.treatment.magic_wand.AbsoluteShift method) InterventionEffect (class in vivarium_public_health.treatment.intervention) is_exposure_categorical (vivarium_public_health.causal_factor.effect.CausalFactorEffect property) is_non_zero() (in module vivarium_public_health.utilities)

L

LBWSGDistribution (class in vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation) LBWSGRisk (class in vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation) LBWSGRiskEffect (class in vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation) left (vivarium_public_health.population.data_transformations.EndpointValues attribute) Linear Scale-Up LinearScaleUp (class in vivarium_public_health.treatment.scale_up) load_age_specific_fertility_rate_data() (vivarium_public_health.population.add_new_birth_cohorts.FertilityAgeSpecificRates method) load_cause_specific_mortality_rate() (vivarium_public_health.disease.model.DiseaseModel method)

load_cause_specific_mortality_rate_data() (vivarium_public_health.disease.special_disease.RiskAttributableDisease method) load_excess_mortality_rate_data() (vivarium_public_health.disease.special_disease.RiskAttributableDisease method) load_exposure_data() (in module vivarium_public_health.causal_factor.utilities) load_population_structure() (in module vivarium_public_health.population.data_transformations) load_relative_risk() (vivarium_public_health.causal_factor.effect.CausalFactorEffect method) (vivarium_public_health.risks.effect.NonLogLinearRiskEffect method) load_unmodeled_csmr() (vivarium_public_health.population.mortality.Mortality method) Log-Linear Model

M

map_age_groups() (vivarium_public_health.results.stratification.ResultsStratifier method) map_transitions() (vivarium_public_health.results.disease.DiseaseObserver method) map_year() (vivarium_public_health.results.stratification.ResultsStratifier static method) measure (vivarium_public_health.utilities.TargetString property) MissingDataError model (vivarium_public_health.results.simple_cause.SimpleCause attribute) module vivarium_public_health vivarium_public_health.causal_factor vivarium_public_health.causal_factor.calibration_constant vivarium_public_health.causal_factor.distributions vivarium_public_health.causal_factor.effect vivarium_public_health.causal_factor.exposure vivarium_public_health.causal_factor.utilities vivarium_public_health.disease vivarium_public_health.disease.exceptions vivarium_public_health.disease.model vivarium_public_health.disease.models vivarium_public_health.disease.special_disease vivarium_public_health.disease.state vivarium_public_health.disease.transition vivarium_public_health.plugins vivarium_public_health.plugins.parser vivarium_public_health.population vivarium_public_health.population.add_new_birth_cohorts vivarium_public_health.population.base_population vivarium_public_health.population.data_transformations vivarium_public_health.population.mortality vivarium_public_health.results vivarium_public_health.results.causal_factor vivarium_public_health.results.disability vivarium_public_health.results.disease vivarium_public_health.results.mortality vivarium_public_health.results.observer vivarium_public_health.results.simple_cause vivarium_public_health.results.stratification vivarium_public_health.risks vivarium_public_health.risks.base_risk vivarium_public_health.risks.effect vivarium_public_health.risks.implementations vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation vivarium_public_health.treatment vivarium_public_health.treatment.intervention vivarium_public_health.treatment.magic_wand vivarium_public_health.treatment.scale_up vivarium_public_health.treatment.therapeutic_inertia vivarium_public_health.utilities

Mortality (class in vivarium_public_health.population.mortality) Mortality Rate MortalityObserver (class in vivarium_public_health.results.mortality)

N

name (vivarium_public_health.causal_factor.effect.CausalFactorEffect property) (vivarium_public_health.causal_factor.exposure.CausalFactor property) (vivarium_public_health.disease.special_disease.RiskAttributableDisease property) (vivarium_public_health.results.causal_factor.CategoricalInterventionObserver property) (vivarium_public_health.results.causal_factor.CategoricalRiskObserver property) (vivarium_public_health.risks.effect.NonLogLinearRiskEffect property) (vivarium_public_health.risks.effect.RiskEffect property) (vivarium_public_health.treatment.intervention.InterventionEffect property) (vivarium_public_health.utilities.EntityString property) (vivarium_public_health.utilities.TargetString property)

NeonatalSWC_with_incidence() (in module vivarium_public_health.disease.models) NeonatalSWC_without_incidence() (in module vivarium_public_health.disease.models) next_state() (vivarium_public_health.disease.state.DiseaseState method) NonDiseasedState (class in vivarium_public_health.disease.state) NonLogLinearRiskEffect (class in vivarium_public_health.risks.effect)

O

old (vivarium_public_health.population.data_transformations.AgeValues attribute) on_post_setup() (vivarium_public_health.disease.model.DiseaseModel method) on_time_step() (vivarium_public_health.disease.special_disease.RiskAttributableDisease method) (vivarium_public_health.population.add_new_birth_cohorts.FertilityAgeSpecificRates method) (vivarium_public_health.population.add_new_birth_cohorts.FertilityCrudeBirthRate method) (vivarium_public_health.population.add_new_birth_cohorts.FertilityDeterministic method) (vivarium_public_health.population.base_population.BasePopulation method) (vivarium_public_health.population.mortality.Mortality method)

on_time_step_cleanup() (vivarium_public_health.population.base_population.AgeOutSimulants method) (vivarium_public_health.population.base_population.BasePopulation method) on_time_step_prepare() (vivarium_public_health.results.disease.DiseaseObserver method) (vivarium_public_health.risks.base_risk.Risk method)

P

PAF parse_component_config() (vivarium_public_health.plugins.parser.CausesConfigurationParser method) Percent-Point Function pivot_categorical() (in module vivarium_public_health.causal_factor.utilities) PolytomousDistribution (class in vivarium_public_health.causal_factor.distributions) Population Attributable Fraction

PPF Prevalence previous_state_column_name (vivarium_public_health.results.disease.DiseaseObserver attribute) process_categorical_data() (vivarium_public_health.causal_factor.effect.CausalFactorEffect method) Propensity ProportionTransition (class in vivarium_public_health.disease.transition) PublicHealthObserver (class in vivarium_public_health.results.observer)

R

RateTransition (class in vivarium_public_health.disease.transition) rebin_relative_risk_data() (vivarium_public_health.causal_factor.effect.CausalFactorEffect method) RecoveredState (class in vivarium_public_health.disease.state) register_adding_observation() (vivarium_public_health.results.observer.PublicHealthObserver method) register_birth_exposure_pipeline() (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRisk method) register_calibration_constant_modifier() (vivarium_public_health.causal_factor.effect.CausalFactorEffect method) register_cause_specific_mortality_rate() (vivarium_public_health.population.mortality.Mortality method) register_disability_weight_pipeline() (vivarium_public_health.disease.state.DiseaseState method) register_disease_state_stratification() (vivarium_public_health.results.disease.DiseaseObserver method) register_excess_mortality_rate_pipeline() (vivarium_public_health.disease.state.DiseaseState method) register_exposure_params_pipeline() (vivarium_public_health.causal_factor.distributions.ContinuousDistribution method) (vivarium_public_health.causal_factor.distributions.DichotomousDistribution method) (vivarium_public_health.causal_factor.distributions.PolytomousDistribution method) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGDistribution method) register_exposure_pipeline() (vivarium_public_health.causal_factor.exposure.CausalFactor method) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRisk method) register_exposure_ppf_pipeline() (vivarium_public_health.causal_factor.distributions.CausalFactorDistribution method) (vivarium_public_health.causal_factor.distributions.ContinuousDistribution method) (vivarium_public_health.causal_factor.distributions.DichotomousDistribution method) (vivarium_public_health.causal_factor.distributions.EnsembleDistribution method) (vivarium_public_health.causal_factor.distributions.PolytomousDistribution method) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGDistribution method) register_intervention_modifiers() (vivarium_public_health.treatment.scale_up.LinearScaleUp method) register_mortality_rate() (vivarium_public_health.population.mortality.Mortality method)

register_observations() (vivarium_public_health.results.causal_factor.CategoricalCausalFactorObserver method) (vivarium_public_health.results.disability.DisabilityObserver method) (vivarium_public_health.results.disease.DiseaseObserver method) (vivarium_public_health.results.mortality.MortalityObserver method) register_person_time_observation() (vivarium_public_health.results.disease.DiseaseObserver method) register_relative_risk_pipeline() (vivarium_public_health.causal_factor.effect.CausalFactorEffect method) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRiskEffect method) register_risk_affected_attribute_producer() (in module vivarium_public_health.causal_factor.calibration_constant) register_risk_affected_rate_producer() (in module vivarium_public_health.causal_factor.calibration_constant) register_stratifications() (vivarium_public_health.results.stratification.ResultsStratifier method) register_target_modifier() (vivarium_public_health.causal_factor.effect.CausalFactorEffect method) register_transition_count_observation() (vivarium_public_health.results.disease.DiseaseObserver method) register_transition_stratification() (vivarium_public_health.results.disease.DiseaseObserver method) register_unmodeled_csmr() (vivarium_public_health.population.mortality.Mortality method) Relative Risk Remission Rate rename_deprecated_categories() (vivarium_public_health.causal_factor.distributions.DichotomousDistribution method) rescale_binned_proportions() (in module vivarium_public_health.population.data_transformations) rescale_final_age_bin() (in module vivarium_public_health.population.data_transformations) ResultsStratifier (class in vivarium_public_health.results.stratification) right (vivarium_public_health.population.data_transformations.EndpointValues attribute) Risk (class in vivarium_public_health.risks.base_risk) RiskAttributableDisease (class in vivarium_public_health.disease.special_disease) RiskEffect (class in vivarium_public_health.risks.effect) rr_column_names (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRiskEffect property)

S

ScaledPopulation (class in vivarium_public_health.population.base_population) scaling_factor (vivarium_public_health.population.base_population.ScaledPopulation attribute) set_causes_of_death() (vivarium_public_health.results.mortality.MortalityObserver method) set_causes_of_disability() (vivarium_public_health.results.disability.DisabilityObserver method) setup() (vivarium_public_health.causal_factor.distributions.CausalFactorDistribution method) (vivarium_public_health.causal_factor.distributions.ContinuousDistribution method) (vivarium_public_health.causal_factor.distributions.DichotomousDistribution method) (vivarium_public_health.causal_factor.distributions.EnsembleDistribution method) (vivarium_public_health.causal_factor.distributions.PolytomousDistribution method) (vivarium_public_health.causal_factor.effect.CausalFactorEffect method) (vivarium_public_health.causal_factor.exposure.CausalFactor method) (vivarium_public_health.disease.model.DiseaseModel method) (vivarium_public_health.disease.special_disease.RiskAttributableDisease method) (vivarium_public_health.disease.state.BaseDiseaseState method) (vivarium_public_health.disease.state.DiseaseState method) (vivarium_public_health.disease.transition.ProportionTransition method) (vivarium_public_health.disease.transition.RateTransition method) (vivarium_public_health.population.add_new_birth_cohorts.FertilityAgeSpecificRates method) (vivarium_public_health.population.add_new_birth_cohorts.FertilityCrudeBirthRate method) (vivarium_public_health.population.add_new_birth_cohorts.FertilityDeterministic method) (vivarium_public_health.population.base_population.AgeOutSimulants method) (vivarium_public_health.population.base_population.BasePopulation method) (vivarium_public_health.population.base_population.Disability method) (vivarium_public_health.population.mortality.Mortality method) (vivarium_public_health.results.causal_factor.CategoricalCausalFactorObserver method) (vivarium_public_health.results.disability.DisabilityObserver method) (vivarium_public_health.results.disease.DiseaseObserver method) (vivarium_public_health.results.mortality.MortalityObserver method) (vivarium_public_health.results.stratification.ResultsStratifier method) (vivarium_public_health.risks.base_risk.Risk method) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGDistribution method) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRisk method) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRiskEffect method) (vivarium_public_health.treatment.magic_wand.AbsoluteShift method) (vivarium_public_health.treatment.scale_up.LinearScaleUp method) (vivarium_public_health.treatment.therapeutic_inertia.TherapeuticInertia method)

SI() (in module vivarium_public_health.disease.models) SimpleCause (class in vivarium_public_health.results.simple_cause) SIR() (in module vivarium_public_health.disease.models) SIR_fixed_duration() (in module vivarium_public_health.disease.models) SIS() (in module vivarium_public_health.disease.models) SIS_fixed_duration() (in module vivarium_public_health.disease.models) smooth_ages() (in module vivarium_public_health.population.data_transformations) split_entity() (vivarium_public_health.utilities.EntityString method) split_target() (vivarium_public_health.utilities.TargetString method) standard_lookup_tables (vivarium_public_health.population.mortality.Mortality property) start_year (vivarium_public_health.results.stratification.ResultsStratifier attribute) state_id (vivarium_public_health.results.simple_cause.SimpleCause attribute) state_names (vivarium_public_health.disease.model.DiseaseModel property) (vivarium_public_health.disease.special_disease.RiskAttributableDisease property) step_size (vivarium_public_health.results.causal_factor.CategoricalCausalFactorObserver attribute) (vivarium_public_health.results.causal_factor.CategoricalInterventionObserver attribute) (vivarium_public_health.results.causal_factor.CategoricalRiskObserver attribute) (vivarium_public_health.results.disability.DisabilityObserver attribute) (vivarium_public_health.results.disease.DiseaseObserver attribute) SusceptibleState (class in vivarium_public_health.disease.state)

T

TargetString (class in vivarium_public_health.utilities) Theoretical Minimum Risk Life Expectancy Theoretical Minimum-Risk Exposure Distribution Theoretical Minimum-Risk Exposure Level Therapeutic Inertia TherapeuticInertia (class in vivarium_public_health.treatment.therapeutic_inertia) time_step_cleanup_priority (vivarium_public_health.population.base_population.BasePopulation property) time_step_priority (vivarium_public_health.population.base_population.BasePopulation property) (vivarium_public_health.population.mortality.Mortality property) TMRED TMREL TMREL_BIRTH_WEIGHT_INTERVAL (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRiskEffect attribute) TMREL_GESTATIONAL_AGE_INTERVAL (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRiskEffect attribute)

TMRLE to_snake_case() (in module vivarium_public_health.utilities) to_time_delta() (in module vivarium_public_health.utilities) to_years() (in module vivarium_public_health.utilities) TransientDiseaseState (class in vivarium_public_health.disease.state) transition_names (vivarium_public_health.disease.model.DiseaseModel property) (vivarium_public_health.disease.special_disease.RiskAttributableDisease property) transition_rate_pipeline (vivarium_public_health.disease.transition.RateTransition property) transition_side_effect() (vivarium_public_health.disease.state.BaseDiseaseState method) transition_stratification_name (vivarium_public_health.results.disease.DiseaseObserver attribute) TransitionString (class in vivarium_public_health.disease.transition) type (vivarium_public_health.utilities.EntityString property) (vivarium_public_health.utilities.TargetString property)

U

unexposed (vivarium_public_health.causal_factor.distributions.DichotomousDistribution property) Unmodeled Cause

update_exit_times() (vivarium_public_health.population.base_population.AgeOutSimulants method) (vivarium_public_health.population.mortality.Mortality method)

V

VALID_ENTITY_TYPES (vivarium_public_health.causal_factor.exposure.CausalFactor attribute) (vivarium_public_health.risks.base_risk.Risk attribute) (vivarium_public_health.treatment.intervention.Intervention attribute) validate_crude_birth_rate_data() (in module vivarium_public_health.population.data_transformations) validate_rebin_source() (vivarium_public_health.causal_factor.distributions.DichotomousDistribution method) validate_rr_data() (vivarium_public_health.risks.effect.NonLogLinearRiskEffect method) vivarium_public_health module vivarium_public_health.causal_factor module vivarium_public_health.causal_factor.calibration_constant module vivarium_public_health.causal_factor.distributions module vivarium_public_health.causal_factor.effect module vivarium_public_health.causal_factor.exposure module vivarium_public_health.causal_factor.utilities module vivarium_public_health.disease module vivarium_public_health.disease.exceptions module vivarium_public_health.disease.model module vivarium_public_health.disease.models module vivarium_public_health.disease.special_disease module vivarium_public_health.disease.state module vivarium_public_health.disease.transition module vivarium_public_health.plugins module vivarium_public_health.plugins.parser module vivarium_public_health.population module vivarium_public_health.population.add_new_birth_cohorts module vivarium_public_health.population.base_population module

vivarium_public_health.population.data_transformations module vivarium_public_health.population.mortality module vivarium_public_health.results module vivarium_public_health.results.causal_factor module vivarium_public_health.results.disability module vivarium_public_health.results.disease module vivarium_public_health.results.mortality module vivarium_public_health.results.observer module vivarium_public_health.results.simple_cause module vivarium_public_health.results.stratification module vivarium_public_health.risks module vivarium_public_health.risks.base_risk module vivarium_public_health.risks.effect module vivarium_public_health.risks.implementations module vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation module vivarium_public_health.treatment module vivarium_public_health.treatment.intervention module vivarium_public_health.treatment.magic_wand module vivarium_public_health.treatment.scale_up module vivarium_public_health.treatment.therapeutic_inertia module vivarium_public_health.utilities module

W

with_condition() (vivarium_public_health.disease.special_disease.RiskAttributableDisease method) (vivarium_public_health.disease.state.DiseaseState method)

Y

Years Lived with Disability Years of Life Lost

YLD YLL young (vivarium_public_health.population.data_transformations.AgeValues attribute)