Disease Modeling Tools
Disease modeling tools for vivarium simulations.
This package provides components for building state machine-based disease models, including disease states, transitions, and pre-built model parameterizations.
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
RiskAttributableDiseaseRiskAttributableDisease.nameRiskAttributableDisease.configuration_defaultsRiskAttributableDisease.state_namesRiskAttributableDisease.transition_namesRiskAttributableDisease.setup()RiskAttributableDisease.adjust_state_and_transitions()RiskAttributableDisease.load_cause_specific_mortality_rate_data()RiskAttributableDisease.load_excess_mortality_rate_data()RiskAttributableDisease.get_exposure_filter()RiskAttributableDisease.initialize_disease()RiskAttributableDisease.on_time_step()RiskAttributableDisease.compute_disability_weight()RiskAttributableDisease.compute_excess_mortality_rate()RiskAttributableDisease.adjust_cause_specific_mortality_rate()RiskAttributableDisease.adjust_mortality_rate()RiskAttributableDisease.with_condition()
- Disease States
BaseDiseaseStateBaseDiseaseState.configuration_defaultsBaseDiseaseState.has_dwell_timeBaseDiseaseState.setup()BaseDiseaseState.get_dwell_time()BaseDiseaseState.initialize_event_time_and_count()BaseDiseaseState.get_initialization_parameters()BaseDiseaseState.get_initial_event_times()BaseDiseaseState.transition_side_effect()BaseDiseaseState.get_transition_names()BaseDiseaseState.add_rate_transition()BaseDiseaseState.add_proportion_transition()BaseDiseaseState.add_dwell_time_transition()
NonDiseasedStateSusceptibleStateRecoveredStateExcessMortalityStateDiseaseStateDiseaseState.configuration_defaultsDiseaseState.setup()DiseaseState.get_prevalence_source()DiseaseState.get_disability_weight_source()DiseaseState.register_disability_weight_pipeline()DiseaseState.get_excess_mortality_rate_source()DiseaseState.register_excess_mortality_rate_pipeline()DiseaseState.get_randomness_prevalence()DiseaseState.has_initialization_weights()DiseaseState.add_rate_transition()DiseaseState.next_state()DiseaseState.compute_disability_weight()DiseaseState.compute_excess_mortality_rate()DiseaseState.adjust_mortality_rate()DiseaseState.get_initial_event_times()DiseaseState.with_condition()
TransientDiseaseState- Disease Transitions
TransitionStringRateTransitionProportionTransition