API Reference

vivarium.public_health

Components for modeling diseases, risks, and interventions with vivarium.

Part of the vivarium-suite monorepo; the previously-standalone ihmeuw/vivarium_public_health GitHub repository has been archived. The import path changed from vivarium_public_health to vivarium.public_health; update your imports accordingly.

• Utilities
• EntityString
  • EntityString.type
  • EntityString.name
  • EntityString.split_entity()
• TargetString
  • TargetString.type
  • TargetString.name
  • TargetString.measure
  • TargetString.split_target()
• to_snake_case()
• to_time_delta()
• to_years()
• is_non_zero()
• Causal Factor Framework
  • Calibration Constant
  • get_calibration_constant_pipeline_name()
  • register_risk_affected_attribute_producer()
  • register_risk_affected_rate_producer()
  • Risk Exposure Distribution Models
  • MissingDataError
  • CausalFactorDistribution
  • EnsembleDistribution
  • ContinuousDistribution
  • PolytomousDistribution
  • DichotomousDistribution
  • clip()
  • get_risk_distribution_parameter()
  • CausalFactor Effect Models
  • CausalFactorEffect
  • Exposure Model
  • CausalFactor
  • Utilities
  • pivot_categorical()
  • get_exposure_post_processor()
  • load_exposure_data()
• Disease Modeling Tools
  • DiseaseModelError
  • The Disease Model
  • DiseaseModel
  • The Model Menagerie
  • SI()
  • SIR()
  • SIS()
  • SIS_fixed_duration()
  • SIR_fixed_duration()
  • NeonatalSWC_without_incidence()
  • NeonatalSWC_with_incidence()
  • “Special” Disease Models
  • RiskAttributableDisease
  • Disease States
  • BaseDiseaseState
  • NonDiseasedState
  • SusceptibleState
  • RecoveredState
  • ExcessMortalityState
  • DiseaseState
  • TransientDiseaseState
  • Disease Transitions
  • TransitionString
  • RateTransition
  • ProportionTransition
• Manager Plugins
  • Component Configuration Parsers
  • CausesParsingErrors
  • CausesConfigurationParser
• Population
  • Fertility Models
  • FertilityDeterministic
  • FertilityCrudeBirthRate
  • FertilityAgeSpecificRates
  • The Core Population Model
  • BasePopulation
  • ScaledPopulation
  • AgeOutSimulants
  • generate_population()
  • Disability
  • Population Data Transformations
  • add_age_midpoint()
  • assign_demographic_proportions()
  • rescale_binned_proportions()
  • AgeValues
  • EndpointValues
  • smooth_ages()
  • get_cause_deleted_mortality_rate()
  • The Core Mortality Model
  • Mortality
• Simulation Observers and Results
  • Disability Observers
  • DisabilityObserver
  • Disease Observers
  • DiseaseObserver
  • Mortality Observers
  • MortalityObserver
  • Basic Observers
  • PublicHealthObserver
  • Risk Observers
  • CategoricalCausalFactorObserver
  • CategoricalRiskObserver
  • CategoricalInterventionObserver
  • Simple Cause
  • SimpleCause
  • Results Stratifier
  • ResultsStratifier
• Risk Modeling Tools
  • Risk Exposure Model
  • Risk
  • Risk Effect Models
  • RiskEffect
  • NonLogLinearRiskEffect
  • Special Risk Implementations
• Treatment Modeling Tools
  • Treatment Modeling Tools
  • Intervention Exposure Model
  • Intervention
  • InterventionEffect
  • Simple Intervention Models
  • AbsoluteShift
  • Linear Scale-Up Model
  • LinearScaleUp
  • Therapeutic Inertia Model
  • TherapeuticInertia