Disease

The vivarium_public_health disease package provides components for modeling disease progression in a population of simulants. It builds on vivarium’s Machine framework to represent diseases as state machines where simulants move between health states according to epidemiological rates.

The package is organized around three cooperating concerns:

1. Disease models — the orchestrator that composes states and transitions into a complete disease simulation component, integrating with mortality and the broader vivarium framework. States represent the health conditions a simulant can occupy (susceptible, infected, recovered, transient), while transitions define the rules governing movement between them (rate-based, proportion-based, or dwell-time-based). See Disease Model.

2. Risk attributable disease — an alternative modeling approach where disease state is derived directly from risk factor exposure rather than explicit state transitions. See Risk Attributable Disease.