Index

A

AbsoluteShift (class in vivarium_public_health.treatment.magic_wand) AcuteDisease (class in vivarium_public_health.mslt.disease) add_dwell_time_transition() (vivarium_public_health.disease.state.BaseDiseaseState method) (vivarium_public_health.disease.state.DiseaseState 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_inc_rate() (vivarium_public_health.mslt.intervention.TobaccoEradication method) adjust_mortality_rate() (vivarium_public_health.disease.special_disease.RiskAttributableDisease method) (vivarium_public_health.disease.state.DiseaseState method)

adjust_rate() (vivarium_public_health.mslt.intervention.ModifyDiseaseRate method) (vivarium_public_health.mslt.intervention.TobaccoFreeGeneration method) adjust_rem_rate() (vivarium_public_health.mslt.intervention.TobaccoEradication method) adjust_state_and_transitions() (vivarium_public_health.disease.special_disease.RiskAttributableDisease method) AgeOutSimulants (class in vivarium_public_health.population.base_population) AgeValues (class in vivarium_public_health.population.data_transformations) aggregate_risk_category_person_time() (vivarium_public_health.metrics.risk.CategoricalRiskObserver method) aggregate_state_person_time() (vivarium_public_health.metrics.disease.DiseaseObserver method) apply_scale_up() (vivarium_public_health.treatment.scale_up.LinearScaleUp method) assign_demographic_proportions() (in module vivarium_public_health.population.data_transformations) assign_initial_status_to_simulants() (vivarium_public_health.disease.model.DiseaseModel static method) AXES (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRisk attribute)

B

BaseDiseaseState (class in vivarium_public_health.disease.state) BasePopulation (class in vivarium_public_health.mslt.population) (class in vivarium_public_health.population.base_population)

birth_exposure_pipeline_name() (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRisk static method)

C

calculate_LE() (vivarium_public_health.mslt.observer.MorbidityMortality method) calculate_mortality_rate() (vivarium_public_health.population.mortality.Mortality method) calculate_ylls() (vivarium_public_health.metrics.mortality.MortalityObserver method) CategoricalRiskObserver (class in vivarium_public_health.metrics.risk) CausesConfigurationParser (class in vivarium_public_health.plugins.parser) CausesParsingErrors clip() (in module vivarium_public_health.risks.distributions) columns_created (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.metrics.disease.DiseaseObserver property) (vivarium_public_health.mslt.delay.DelayedRisk property) (vivarium_public_health.mslt.disease.Disease property) (vivarium_public_health.mslt.population.BasePopulation property) (vivarium_public_health.population.add_new_birth_cohorts.FertilityAgeSpecificRates property) (vivarium_public_health.population.base_population.BasePopulation property) (vivarium_public_health.population.mortality.Mortality property) (vivarium_public_health.risks.base_risk.Risk property) (vivarium_public_health.risks.distributions.EnsembleSimulation property) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRisk property) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRiskEffect property) columns_required (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.metrics.disease.DiseaseObserver property) (vivarium_public_health.metrics.mortality.MortalityObserver property) (vivarium_public_health.metrics.risk.CategoricalRiskObserver property) (vivarium_public_health.mslt.delay.DelayedRisk property) (vivarium_public_health.mslt.disease.Disease property) (vivarium_public_health.mslt.observer.Disease property) (vivarium_public_health.mslt.observer.MorbidityMortality property) (vivarium_public_health.mslt.observer.TobaccoPrevalence property) (vivarium_public_health.mslt.population.BasePopulation property) (vivarium_public_health.mslt.population.Disability property) (vivarium_public_health.mslt.population.Mortality property) (vivarium_public_health.population.add_new_birth_cohorts.FertilityAgeSpecificRates property) (vivarium_public_health.population.base_population.AgeOutSimulants property) (vivarium_public_health.population.mortality.Mortality property) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRiskEffect property) (vivarium_public_health.treatment.magic_wand.AbsoluteShift property) 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.disease.special_disease.RiskAttributableDisease attribute) configuration_defaults (vivarium_public_health.disease.special_disease.RiskAttributableDisease property) CONFIGURATION_DEFAULTS (vivarium_public_health.metrics.disability.DisabilityObserver attribute) (vivarium_public_health.metrics.disease.DiseaseObserver attribute) configuration_defaults (vivarium_public_health.metrics.disease.DiseaseObserver property) CONFIGURATION_DEFAULTS (vivarium_public_health.metrics.mortality.MortalityObserver attribute) (vivarium_public_health.metrics.risk.CategoricalRiskObserver attribute) configuration_defaults (vivarium_public_health.metrics.risk.CategoricalRiskObserver property) (vivarium_public_health.mslt.delay.DelayedRisk property) (vivarium_public_health.mslt.disease.Disease property) (vivarium_public_health.mslt.intervention.ModifyAcuteDiseaseIncidence property) (vivarium_public_health.mslt.intervention.ModifyAcuteDiseaseMorbidity property) (vivarium_public_health.mslt.intervention.ModifyAcuteDiseaseMortality property) (vivarium_public_health.mslt.intervention.ModifyAllCauseMortality property) (vivarium_public_health.mslt.intervention.ModifyDiseaseRate property) (vivarium_public_health.mslt.intervention.TobaccoEradication property) (vivarium_public_health.mslt.intervention.TobaccoFreeGeneration property) (vivarium_public_health.mslt.magic_wand_components.ModifyAcuteDiseaseMortality property) (vivarium_public_health.mslt.magic_wand_components.ModifyAcuteDiseaseYLD property) CONFIGURATION_DEFAULTS (vivarium_public_health.mslt.population.BasePopulation attribute) (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) (vivarium_public_health.population.mortality.Mortality attribute) (vivarium_public_health.risks.base_risk.Risk attribute) configuration_defaults (vivarium_public_health.risks.base_risk.Risk property) CONFIGURATION_DEFAULTS (vivarium_public_health.risks.effect.RiskEffect attribute) configuration_defaults (vivarium_public_health.risks.effect.RiskEffect property) CONFIGURATION_DEFAULTS (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGDistribution attribute) (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) ContinuousDistribution (class in vivarium_public_health.risks.distributions) count_deaths() (vivarium_public_health.metrics.mortality.MortalityObserver method) coverage_effect() (vivarium_public_health.treatment.scale_up.LinearScaleUp method) 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) DelayedRisk (class in vivarium_public_health.mslt.delay) DichotomousDistribution (class in vivarium_public_health.risks.distributions) Disability (class in vivarium_public_health.mslt.population) disability_adjustment() (vivarium_public_health.mslt.disease.AcuteDisease method) (vivarium_public_health.mslt.disease.Disease method) (vivarium_public_health.mslt.intervention.ModifyAcuteDiseaseMorbidity method) (vivarium_public_health.mslt.magic_wand_components.ModifyAcuteDiseaseYLD method) (vivarium_public_health.mslt.magic_wand_components.YLDShift method)

disability_weight_aggregator() (vivarium_public_health.metrics.disability.DisabilityObserver method) DisabilityObserver (class in vivarium_public_health.metrics.disability) Disease (class in vivarium_public_health.mslt.disease) (class in vivarium_public_health.mslt.observer) disease_classes (vivarium_public_health.metrics.disability.DisabilityObserver property) DiseaseModel (class in vivarium_public_health.disease.model) DiseaseModelError DiseaseObserver (class in vivarium_public_health.metrics.disease) DiseaseState (class in vivarium_public_health.disease.state)

E

EndpointValues (class in vivarium_public_health.population.data_transformations) EnsembleSimulation (class in vivarium_public_health.risks.distributions)

EntityString (class in vivarium_public_health.utilities) exposure() (vivarium_public_health.risks.distributions.DichotomousDistribution method) exposure_column_name() (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRisk static 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)

G

generate_population() (in module vivarium_public_health.population.base_population) generate_relative_risk_from_distribution() (in module vivarium_public_health.risks.data_transformations) get_age_bins() (vivarium_public_health.metrics.stratification.ResultsStratifier static method) get_age_intervals() (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRiskEffect method) get_all_cause_mortality_rate() (vivarium_public_health.population.mortality.Mortality method) get_base_disability_weight() (vivarium_public_health.disease.state.DiseaseState method) get_base_excess_mortality_rate() (vivarium_public_health.disease.state.DiseaseState method) get_bin_names() (vivarium_public_health.mslt.delay.DelayedRisk method) (vivarium_public_health.mslt.observer.TobaccoPrevalence method) get_birth_exposure() (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRisk method) get_birth_exposure_pipelines() (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRisk method) get_birth_prevalence() (vivarium_public_health.disease.state.DiseaseState method) get_categories() (vivarium_public_health.risks.distributions.PolytomousDistribution method) 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_cause_specific_mortality_rate() (vivarium_public_health.population.mortality.Mortality method) get_clock() (vivarium_public_health.treatment.scale_up.LinearScaleUp method) get_current_exposure() (vivarium_public_health.risks.base_risk.Risk method) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRisk method) get_demographic_proportions_for_creation_time() (vivarium_public_health.population.base_population.BasePopulation static method) get_disability_weight_pipeline() (vivarium_public_health.disease.state.DiseaseState method) (vivarium_public_health.metrics.disability.DisabilityObserver method) get_distribution() (in module vivarium_public_health.risks.distributions) get_distribution_data() (in module vivarium_public_health.risks.data_transformations) get_distribution_type() (in module vivarium_public_health.risks.data_transformations) (vivarium_public_health.risks.effect.RiskEffect method) get_dwell_time_pipeline() (vivarium_public_health.disease.state.DiseaseState method) get_endpoint_value_from_data() (vivarium_public_health.treatment.scale_up.LinearScaleUp method) get_excess_mortality_rate_pipeline() (vivarium_public_health.disease.state.DiseaseState method) get_exposure_data() (in module vivarium_public_health.risks.data_transformations) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGDistribution method) get_exposure_distribution() (vivarium_public_health.risks.base_risk.Risk method) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRisk method) get_exposure_distribution_weights() (in module vivarium_public_health.risks.data_transformations) get_exposure_effect() (in module vivarium_public_health.risks.data_transformations) get_exposure_filter() (vivarium_public_health.disease.special_disease.RiskAttributableDisease method) get_exposure_parameters() (vivarium_public_health.risks.distributions.PolytomousDistribution method) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGDistribution method) get_exposure_pipeline() (vivarium_public_health.risks.base_risk.Risk method) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRisk method)

get_exposure_post_processor() (in module vivarium_public_health.risks.data_transformations) get_exposure_standard_deviation_data() (in module vivarium_public_health.risks.data_transformations) 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_joint_paf() (vivarium_public_health.disease.state.DiseaseState method) get_life_expectancy() (vivarium_public_health.population.mortality.Mortality method) get_live_births_per_year() (in module vivarium_public_health.population.data_transformations) get_mortality_rate() (vivarium_public_health.population.mortality.Mortality method) get_parameters() (vivarium_public_health.risks.distributions.ContinuousDistribution method) (vivarium_public_health.risks.distributions.EnsembleSimulation method) get_population_attributable_fraction_data() (in module vivarium_public_health.risks.data_transformations) get_population_attributable_fraction_source() (vivarium_public_health.risks.effect.RiskEffect method) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRiskEffect method) get_prevalence() (vivarium_public_health.disease.state.DiseaseState method) get_propensity_pipeline() (vivarium_public_health.risks.base_risk.Risk method) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRisk method) get_randomness_prevalence() (vivarium_public_health.disease.state.DiseaseState method) get_randomness_stream() (vivarium_public_health.population.mortality.Mortality method) (vivarium_public_health.risks.base_risk.Risk method) get_randomness_streams() (vivarium_public_health.population.base_population.BasePopulation static method) get_raw_unmodeled_csmr() (vivarium_public_health.population.mortality.Mortality method) get_relative_risk() (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRiskEffect method) get_relative_risk_data() (in module vivarium_public_health.risks.data_transformations) get_relative_risk_source() (vivarium_public_health.risks.effect.RiskEffect 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_exposure() (vivarium_public_health.risks.effect.RiskEffect method) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRiskEffect method) get_rr_column_names() (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRiskEffect method) 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_state_weights() (vivarium_public_health.disease.model.DiseaseModel method) get_target_modifier() (vivarium_public_health.risks.effect.RiskEffect method) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRiskEffect method) get_transition_names() (vivarium_public_health.disease.state.BaseDiseaseState method) get_unmodeled_csmr() (vivarium_public_health.population.mortality.Mortality method) get_unmodeled_csmr_paf() (vivarium_public_health.population.mortality.Mortality method) get_unmodeled_csmr_source() (vivarium_public_health.population.mortality.Mortality method)

I

incidence_adjustment() (vivarium_public_health.mslt.delay.DelayedRisk method) (vivarium_public_health.mslt.magic_wand_components.IncidenceShift method) IncidenceShift (class in vivarium_public_health.mslt.magic_wand_components) initialization_requirements (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.mslt.delay.DelayedRisk property) (vivarium_public_health.mslt.disease.Disease property) (vivarium_public_health.population.add_new_birth_cohorts.FertilityAgeSpecificRates property) (vivarium_public_health.risks.base_risk.Risk property) (vivarium_public_health.risks.distributions.EnsembleSimulation property) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRiskEffect property)

initialize_therapeutic_inertia() (vivarium_public_health.treatment.therapeutic_inertia.TherapeuticInertia method) intervention_effect() (vivarium_public_health.treatment.magic_wand.AbsoluteShift method) 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) LinearScaleUp (class in vivarium_public_health.treatment.scale_up) load() (vivarium_public_health.testing.mock_artifact.MockArtifact method) (vivarium_public_health.testing.mock_artifact.MockArtifactManager method) load_age_specific_fertility_rate_data() (vivarium_public_health.population.add_new_birth_cohorts.FertilityAgeSpecificRates method) load_birth_prevalence_data() (vivarium_public_health.disease.state.DiseaseState method) load_cause_specific_mortality_rate_data() (vivarium_public_health.disease.model.DiseaseModel method) (vivarium_public_health.disease.special_disease.RiskAttributableDisease method)

load_disability_weight_data() (vivarium_public_health.disease.state.DiseaseState method) load_distribution_data() (in module vivarium_public_health.risks.data_transformations) load_dwell_time_data() (vivarium_public_health.disease.state.DiseaseState method) load_excess_mortality_rate_data() (vivarium_public_health.disease.special_disease.RiskAttributableDisease method) (vivarium_public_health.disease.state.DiseaseState method) load_exposure_data() (in module vivarium_public_health.risks.data_transformations) load_population_data() (in module vivarium_public_health.mslt.population) load_population_structure() (in module vivarium_public_health.population.data_transformations) load_prevalence_data() (vivarium_public_health.disease.state.DiseaseState method) load_relative_risk_data() (in module vivarium_public_health.risks.data_transformations) load_transition_rate_data() (vivarium_public_health.disease.transition.RateTransition method)

M

make_age_bins() (in module vivarium_public_health.testing.utils) make_uniform_pop_data() (in module vivarium_public_health.testing.utils) map_age_groups() (vivarium_public_health.metrics.stratification.ResultsStratifier method) map_year() (vivarium_public_health.metrics.stratification.ResultsStratifier static method) measure (vivarium_public_health.utilities.TargetString property) MissingDataError MockArtifact (class in vivarium_public_health.testing.mock_artifact) MockArtifactManager (class in vivarium_public_health.testing.mock_artifact) ModifyAcuteDiseaseIncidence (class in vivarium_public_health.mslt.intervention) ModifyAcuteDiseaseMorbidity (class in vivarium_public_health.mslt.intervention) ModifyAcuteDiseaseMortality (class in vivarium_public_health.mslt.intervention) (class in vivarium_public_health.mslt.magic_wand_components) ModifyAcuteDiseaseYLD (class in vivarium_public_health.mslt.magic_wand_components) ModifyAllCauseMortality (class in vivarium_public_health.mslt.intervention) ModifyDiseaseIncidence (class in vivarium_public_health.mslt.intervention) ModifyDiseaseMorbidity (class in vivarium_public_health.mslt.intervention) ModifyDiseaseMortality (class in vivarium_public_health.mslt.intervention) ModifyDiseaseRate (class in vivarium_public_health.mslt.intervention) module vivarium_public_health vivarium_public_health.disease 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.metrics vivarium_public_health.metrics.disability vivarium_public_health.metrics.disease vivarium_public_health.metrics.mortality vivarium_public_health.metrics.risk vivarium_public_health.metrics.stratification vivarium_public_health.mslt vivarium_public_health.mslt.delay vivarium_public_health.mslt.disease vivarium_public_health.mslt.intervention vivarium_public_health.mslt.magic_wand_components vivarium_public_health.mslt.observer vivarium_public_health.mslt.population 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.risks vivarium_public_health.risks.base_risk vivarium_public_health.risks.data_transformations vivarium_public_health.risks.distributions vivarium_public_health.risks.effect vivarium_public_health.risks.implementations vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation vivarium_public_health.testing vivarium_public_health.testing.mock_artifact vivarium_public_health.testing.utils vivarium_public_health.treatment vivarium_public_health.treatment.magic_wand vivarium_public_health.treatment.scale_up vivarium_public_health.treatment.therapeutic_inertia vivarium_public_health.utilities

MorbidityMortality (class in vivarium_public_health.mslt.observer) Mortality (class in vivarium_public_health.mslt.population) (class in vivarium_public_health.population.mortality) mortality_adjustment() (vivarium_public_health.mslt.disease.AcuteDisease method) (vivarium_public_health.mslt.disease.Disease method) (vivarium_public_health.mslt.intervention.ModifyAcuteDiseaseMortality method) (vivarium_public_health.mslt.intervention.ModifyAllCauseMortality method) (vivarium_public_health.mslt.magic_wand_components.ModifyAcuteDiseaseMortality method) (vivarium_public_health.mslt.magic_wand_components.MortalityShift method) MortalityObserver (class in vivarium_public_health.metrics.mortality) MortalityShift (class in vivarium_public_health.mslt.magic_wand_components)

N

name (vivarium_public_health.disease.special_disease.RiskAttributableDisease property) (vivarium_public_health.testing.mock_artifact.MockArtifactManager 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)

O

old (vivarium_public_health.population.data_transformations.AgeValues attribute) on_collect_metrics() (vivarium_public_health.mslt.observer.Disease method) (vivarium_public_health.mslt.observer.MorbidityMortality method) (vivarium_public_health.mslt.observer.TobaccoPrevalence method) on_initialize_simulants() (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.metrics.disease.DiseaseObserver method) (vivarium_public_health.mslt.delay.DelayedRisk method) (vivarium_public_health.mslt.disease.Disease method) (vivarium_public_health.mslt.population.BasePopulation method) (vivarium_public_health.population.add_new_birth_cohorts.FertilityAgeSpecificRates method) (vivarium_public_health.population.base_population.BasePopulation method) (vivarium_public_health.population.mortality.Mortality method) (vivarium_public_health.risks.base_risk.Risk method) (vivarium_public_health.risks.distributions.EnsembleSimulation 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)

on_simulation_end() (vivarium_public_health.mslt.observer.Disease method) (vivarium_public_health.mslt.observer.MorbidityMortality method) (vivarium_public_health.mslt.observer.TobaccoPrevalence method) on_time_step() (vivarium_public_health.disease.model.DiseaseModel method) (vivarium_public_health.disease.special_disease.RiskAttributableDisease method) (vivarium_public_health.mslt.population.Disability method) (vivarium_public_health.mslt.population.Mortality 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.disease.model.DiseaseModel method) (vivarium_public_health.population.base_population.AgeOutSimulants method) on_time_step_prepare() (vivarium_public_health.metrics.disease.DiseaseObserver method) (vivarium_public_health.mslt.delay.DelayedRisk method) (vivarium_public_health.mslt.disease.Disease method) (vivarium_public_health.mslt.population.BasePopulation method) output_file() (in module vivarium_public_health.mslt.observer)

P

parse_component_config() (vivarium_public_health.plugins.parser.CausesConfigurationParser method) pivot_categorical() (in module vivarium_public_health.risks.data_transformations) pivot_load() (in module vivarium_public_health.mslt.delay) PolytomousDistribution (class in vivarium_public_health.risks.distributions) ppf() (vivarium_public_health.risks.distributions.ContinuousDistribution method) (vivarium_public_health.risks.distributions.DichotomousDistribution method) (vivarium_public_health.risks.distributions.EnsembleSimulation method) (vivarium_public_health.risks.distributions.PolytomousDistribution method) (vivarium_public_health.risks.distributions.SimulationDistribution method) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGDistribution method)

ProportionTransition (class in vivarium_public_health.disease.transition)

R

rate_adjustment() (vivarium_public_health.mslt.intervention.ModifyAcuteDiseaseIncidence method) RateTransition (class in vivarium_public_health.disease.transition) rebin_exposure_data() (in module vivarium_public_health.risks.data_transformations) rebin_relative_risk_data() (in module vivarium_public_health.risks.data_transformations) RecoveredState (class in vivarium_public_health.disease.state) register_intervention_modifiers() (vivarium_public_health.treatment.scale_up.LinearScaleUp method) register_modifier() (vivarium_public_health.mslt.delay.DelayedRisk method) register_paf_modifier() (vivarium_public_health.risks.effect.RiskEffect method) register_stratifications() (vivarium_public_health.metrics.stratification.ResultsStratifier method)

register_target_modifier() (vivarium_public_health.risks.effect.RiskEffect method) (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRiskEffect method) relative_risk_column_name() (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGRiskEffect 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.metrics.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)

S

setup() (vivarium_public_health.disease.model.DiseaseModel method) (vivarium_public_health.disease.special_disease.RiskAttributableDisease 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.metrics.disability.DisabilityObserver method) (vivarium_public_health.metrics.disease.DiseaseObserver method) (vivarium_public_health.metrics.mortality.MortalityObserver method) (vivarium_public_health.metrics.risk.CategoricalRiskObserver method) (vivarium_public_health.metrics.stratification.ResultsStratifier method) (vivarium_public_health.mslt.delay.DelayedRisk method) (vivarium_public_health.mslt.disease.AcuteDisease method) (vivarium_public_health.mslt.disease.Disease method) (vivarium_public_health.mslt.intervention.ModifyAcuteDiseaseIncidence method) (vivarium_public_health.mslt.intervention.ModifyAcuteDiseaseMorbidity method) (vivarium_public_health.mslt.intervention.ModifyAcuteDiseaseMortality method) (vivarium_public_health.mslt.intervention.ModifyAllCauseMortality method) (vivarium_public_health.mslt.intervention.ModifyDiseaseRate method) (vivarium_public_health.mslt.intervention.TobaccoEradication method) (vivarium_public_health.mslt.intervention.TobaccoFreeGeneration method) (vivarium_public_health.mslt.magic_wand_components.IncidenceShift method) (vivarium_public_health.mslt.magic_wand_components.ModifyAcuteDiseaseMortality method) (vivarium_public_health.mslt.magic_wand_components.ModifyAcuteDiseaseYLD method) (vivarium_public_health.mslt.magic_wand_components.MortalityShift method) (vivarium_public_health.mslt.magic_wand_components.YLDShift method) (vivarium_public_health.mslt.observer.Disease method) (vivarium_public_health.mslt.observer.MorbidityMortality method) (vivarium_public_health.mslt.observer.TobaccoPrevalence method) (vivarium_public_health.mslt.population.BasePopulation method) (vivarium_public_health.mslt.population.Disability method) (vivarium_public_health.mslt.population.Mortality 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.mortality.Mortality method) (vivarium_public_health.risks.base_risk.Risk method) (vivarium_public_health.risks.distributions.ContinuousDistribution method) (vivarium_public_health.risks.distributions.DichotomousDistribution method) (vivarium_public_health.risks.distributions.EnsembleSimulation method) (vivarium_public_health.risks.distributions.PolytomousDistribution method) (vivarium_public_health.risks.distributions.SimulationDistribution method) (vivarium_public_health.risks.effect.RiskEffect 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.testing.mock_artifact.MockArtifactManager 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) SimulationDistribution (class in vivarium_public_health.risks.distributions) single_axis_ppf() (vivarium_public_health.risks.implementations.low_birth_weight_and_short_gestation.LBWSGDistribution method) 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) state_names (vivarium_public_health.disease.model.DiseaseModel property) (vivarium_public_health.disease.special_disease.RiskAttributableDisease property) SusceptibleState (class in vivarium_public_health.disease.state)

T

TargetString (class in vivarium_public_health.utilities) TherapeuticInertia (class in vivarium_public_health.treatment.therapeutic_inertia) time_step_priority (vivarium_public_health.population.base_population.BasePopulation property) (vivarium_public_health.population.mortality.Mortality property) 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) 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)

TobaccoEradication (class in vivarium_public_health.mslt.intervention) TobaccoFreeGeneration (class in vivarium_public_health.mslt.intervention) TobaccoPrevalence (class in vivarium_public_health.mslt.observer) 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_side_effect() (vivarium_public_health.disease.state.BaseDiseaseState method) TransitionString (class in vivarium_public_health.disease.transition) type (vivarium_public_health.utilities.EntityString property) (vivarium_public_health.utilities.TargetString property)

V

validate_crude_birth_rate_data() (in module vivarium_public_health.population.data_transformations) validate_distribution_data_source() (in module vivarium_public_health.risks.data_transformations) validate_rebin_source() (in module vivarium_public_health.risks.data_transformations) validate_relative_risk_data_source() (in module vivarium_public_health.risks.data_transformations) validate_relative_risk_rebin_source() (in module vivarium_public_health.risks.data_transformations) vivarium_public_health module vivarium_public_health.disease 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.metrics module vivarium_public_health.metrics.disability module vivarium_public_health.metrics.disease module vivarium_public_health.metrics.mortality module vivarium_public_health.metrics.risk module vivarium_public_health.metrics.stratification module vivarium_public_health.mslt module vivarium_public_health.mslt.delay module vivarium_public_health.mslt.disease module vivarium_public_health.mslt.intervention module vivarium_public_health.mslt.magic_wand_components module vivarium_public_health.mslt.observer module vivarium_public_health.mslt.population 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.risks module vivarium_public_health.risks.base_risk module vivarium_public_health.risks.data_transformations module vivarium_public_health.risks.distributions 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.testing module vivarium_public_health.testing.mock_artifact module vivarium_public_health.testing.utils module vivarium_public_health.treatment 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)

write() (vivarium_public_health.testing.mock_artifact.MockArtifact method) (vivarium_public_health.testing.mock_artifact.MockArtifactManager method)

Y

YLDShift (class in vivarium_public_health.mslt.magic_wand_components)

young (vivarium_public_health.population.data_transformations.AgeValues attribute)