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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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R0 vs Reff in vignettes #116

Closed jamesmbaazam closed 10 months ago

jamesmbaazam commented 11 months ago

In some of the vignettes, the epidemic starts off with more than one infected individual in a completely susceptible population, so I think the preferred terminology for the reproduction number should be Reff instead of R0.

pratikunterwegs commented 11 months ago

Thanks @jamesmbaazam - you're very welcome to make these edits.

jamesmbaazam commented 11 months ago

May be worth a broader discussion with @rozeggo and others. It might also require renaming the R0 arguments to something like "R" to keep it generic and open to the users' interpretation.

adamkucharski commented 11 months ago

Are we talking about the realised reproduction number over time (i.e. R0 x S, which would be better labelled Reff or Rt) or the input parameter (which should be defined as R0, because it's independent of the initial conditions of the model)?

pratikunterwegs commented 11 months ago

The r0 is a property of the <infection>, and is independent of the number of initial infections as @adamkucharski says, so it more properly refers to $R_0$. Happy to hear more thoughts on this, but it seems like the current usage is the correct one.

pratikunterwegs commented 10 months ago

Closing this following the above discussion.