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canmod / macpan2

Rebuilding https://github.com/mac-theobio/McMasterPandemic/
https://canmod.github.io/macpan2/
GNU General Public License v3.0
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look into incorporating `AutomaticR0`? #120

Open papsti opened 10 months ago

papsti commented 10 months ago

a colleague of mine shared this work, which could potentially be incorporated as a feature of macpan2 in some form, though i haven't looked at it in any depth: https://github.com/asimard1/automaticR0

it's supposed to compute R0 and Rt in compartmental models based off of a model specification via a JSON file. apparently it works in cases where the next-generation matrix approach fails.

bbolker commented 10 months ago

We did originally have a lot of ideas/machinery for different ways to compute metrics such as r, R0, generation time (based on pushing a single infected individual through all the compartments and measuring FOI(t), or based on linear algebra); it's something that hasn't made it back into canmod yet ...

Without spending a little more time than I have right now, it's hard to tell exactly how AutomaticR0 works ... (when does the next-gen matrix approach fail ... ?)

papsti commented 10 months ago

Without spending a little more time than I have right now, it's hard to tell exactly how AutomaticR0 works ... (when does the next-gen matrix approach fail ... ?)

yeah, i have no clue. just wanted to flag it before i forgot.