Disease Modeling Tools
- The Disease Model
DiseaseModelError
DiseaseModel
DiseaseModel.columns_created
DiseaseModel.columns_required
DiseaseModel.initialization_requirements
DiseaseModel.state_names
DiseaseModel.transition_names
DiseaseModel.setup()
DiseaseModel.load_cause_specific_mortality_rate_data()
DiseaseModel.on_initialize_simulants()
DiseaseModel.on_time_step()
DiseaseModel.on_time_step_cleanup()
DiseaseModel.adjust_cause_specific_mortality_rate()
DiseaseModel.get_state_weights()
DiseaseModel.assign_initial_status_to_simulants()
- The Model Menagerie
SI()
SIR()
SIS()
SIS_fixed_duration()
SIR_fixed_duration()
NeonatalSWC_without_incidence()
NeonatalSWC_with_incidence()
- “Special” Disease Models
RiskAttributableDisease
RiskAttributableDisease.CONFIGURATION_DEFAULTS
RiskAttributableDisease.name
RiskAttributableDisease.configuration_defaults
RiskAttributableDisease.columns_created
RiskAttributableDisease.columns_required
RiskAttributableDisease.initialization_requirements
RiskAttributableDisease.state_names
RiskAttributableDisease.transition_names
RiskAttributableDisease.setup()
RiskAttributableDisease.adjust_state_and_transitions()
RiskAttributableDisease.load_cause_specific_mortality_rate_data()
RiskAttributableDisease.load_excess_mortality_rate_data()
RiskAttributableDisease.get_exposure_filter()
RiskAttributableDisease.on_initialize_simulants()
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
BaseDiseaseState
BaseDiseaseState.columns_created
BaseDiseaseState.columns_required
BaseDiseaseState.initialization_requirements
BaseDiseaseState.on_initialize_simulants()
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()
NonDiseasedState
SusceptibleState
RecoveredState
DiseaseState
DiseaseState.setup()
DiseaseState.load_prevalence_data()
DiseaseState.get_prevalence()
DiseaseState.load_birth_prevalence_data()
DiseaseState.get_birth_prevalence()
DiseaseState.load_dwell_time_data()
DiseaseState.get_dwell_time_pipeline()
DiseaseState.load_disability_weight_data()
DiseaseState.get_base_disability_weight()
DiseaseState.get_disability_weight_pipeline()
DiseaseState.load_excess_mortality_rate_data()
DiseaseState.get_base_excess_mortality_rate()
DiseaseState.get_excess_mortality_rate_pipeline()
DiseaseState.get_joint_paf()
DiseaseState.get_randomness_prevalence()
DiseaseState.add_rate_transition()
DiseaseState.add_dwell_time_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
TransitionString
RateTransition
ProportionTransition