Disease Models
This module contains tools for modeling diseases in multi-state lifetable simulations.
- class vivarium_public_health.mslt.disease.AcuteDisease(disease)[source]
An acute disease has a sufficiently short duration, relative to the time-step size, that it is not meaningful to talk about prevalence. Instead, it simply contributes an excess mortality rate, and/or a disability rate.
Interventions may affect these rates:
<disease>_intervention.excess_mortality
<disease>_intervention.yld_rate
where <disease> is the name as provided to the constructor.
- Parameters:
disease (str) – The disease name (referred to as <disease> here).
- setup(builder)[source]
Load the morbidity and mortality data.
- Parameters:
builder (Builder) –
- Return type:
None
- class vivarium_public_health.mslt.disease.Disease(disease)[source]
This component characterises a chronic disease.
It defines the following rates, which may be affected by interventions:
<disease>_intervention.incidence
<disease>_intervention.remission
<disease>_intervention.mortality
<disease>_intervention.morbidity
where <disease> is the name as provided to the constructor.
- Parameters:
disease (str) – The disease name (referred to as <disease> here).
- property configuration_defaults: Dict[str, Any]
Provides a dictionary containing the defaults for any configurations managed by this component.
These default values will be stored at the component_configs layer of the simulation’s ConfigTree.
- Returns:
A dictionary containing the defaults for any configurations managed by this component.
- Return type:
Dict[str, Any]
- property columns_created: List[str]
Provides names of columns created by the component.
- Returns:
Names of the columns created by this component, or an empty list if none.
- Return type:
List[str]
- property columns_required: List[str] | None
Provides names of columns required by the component.
- Returns:
Names of required columns not created by this component. An empty list means all available columns are needed. None means no additional columns are necessary.
- Return type:
Optional[List[str]]
- property initialization_requirements: Dict[str, List[str]]
Provides the names of all values required by this component during simulant initialization.
- setup(builder)[source]
Load the disease prevalence and rates data.
- Parameters:
builder (Builder) –
- Return type:
None
- on_initialize_simulants(pop_data)[source]
Initialize the test population for which this disease is modeled.
- Parameters:
pop_data (SimulantData) –
- Return type:
None
- on_time_step_prepare(event)[source]
Update the disease status for both the BAU and intervention scenarios.
- Parameters:
event (Event) –
- Return type:
None