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mrc-ide / squire

SEIR transmission model of COVID-19. Documentation at:
https://mrc-ide.github.io/squire/
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Understanding the difference between "infections", "ICase", and "IMild" in format_output #182

Open zterner-mitre opened 5 months ago

zterner-mitre commented 5 months ago

Hi @richfitz and @OJWatson,

When running format_output on my simulation, I am trying to grab the number of new infections that occur every day. I have tried to do this two ways:

format_output(out, var_select = c("ICase","IMild")) and format_output(out, var_select = "infections").

These give vastly different outputs for the number of infections each day. I would imagine that infections = ICase + IMild, but that is clearly not the case:

This is ICase and IMild:

image

This is infections:

image

Can someone explain the difference between these two and what they are enumerating? It is unclear to what they refer. I understand that "infections" is labeled as "daily infections" on the documentation site, but if that is the case, what do ICase and IMild refer to?

This also seems related to this Github issue, though I do not think it answers my question: https://github.com/mrc-ide/squire/issues/130

Thanks for your time and consideration.

OJWatson commented 1 month ago

Hi @zterner-mitre

So sorry for the delay. Infections is the incidence of infections (i.e. number of people being infected each day). And ICase and IMild is just the number of individuals in these infection compartments on that time step.

Hope that help,

OJ