vivarium_public_health
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vivarium_public_health
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Index
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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)
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