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mrc-ide / helios

Simulating far UVC for pathogen control
https://mrc-ide.github.io/helios/
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external FOI functionality in to stabilise and facilitate simulation of endemic pathogens #79

Closed cwhittaker1000 closed 5 months ago

cwhittaker1000 commented 6 months ago

We've been struggling with stochastic extinction of endemic pathogens during the establishment of endemicity (when oscillations in active infection prevalence are quite significant). A principled and reasonable way around this is to assume a background, baseline FOI to keeps the number of infectious individuals very slightly > 0 during periods of very low incidence. This PR implements this functionality.

@tbreweric could you have a look at this when you get a chance please? I think I've captured the principle of what we need, but you're way better at infrastructure design than I am! :)

tbreweric commented 6 months ago

Another thing we might want to add is a step rendering the number of cases in each timestep that arise through this new mechanism?

tbreweric commented 6 months ago

Another thing we might want to add is a step rendering the number of cases in each timestep that arise through this new mechanism?

I have pushed a version with the number of individuals that get infected through this mechanism in each time step when endemic model setting is used. I've also added some unit tests for the rendering process.