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epiverse-trace / epidemics

A library of published compartmental epidemic models, and classes to represent demographic structure, non-pharmaceutical interventions, and vaccination regimes, to compose epidemic scenarios.
https://epiverse-trace.github.io/epidemics/
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Infection should hold rates only #58

Closed pratikunterwegs closed 1 year ago

pratikunterwegs commented 1 year ago

This issue is in reference to this comment on PR #54, and is to suggest that infection class objects should only hold conversion rates between compartments, such $\beta$ the transmission rate/force of infection, or $\gamma$ the recovery rate.

These could be created from comprehensible parameters such as $R_0$ and the infectious period using helper functions.

infection objects could be passed directly to calls to the epidemic functions, allowing fewer separate calls (e.g. .epidemic_default_cpp() and .epidemic_vacamole_cpp().

If beta, alpha, gamma were part of a parameters class, we could standardize the function signature to function(population, parameters, intervention, vaccination, time_end, increment). Then like the other classes in this package infection, intervention, population and vaccination. We can then keep all checks and functions related to parameters in one place for easier maintenance.

_Originally posted by @bahadzie in https://github.com/epiverse-trace/epidemics/pull/54#discussion_r1210037921_

pratikunterwegs commented 1 year ago

Closing as superseded by #133