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mrc-ide / helios

Simulating far UVC for pathogen control
https://mrc-ide.github.io/helios/
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[DEPRECATED] specification of all disease state initial conditions (plus a small bug fix) #114

Closed cwhittaker1000 closed 4 months ago

cwhittaker1000 commented 4 months ago

This PR initially started off as extending the current functionality we offer to specify the initial conditions from just the number initially in the E state to requiring manual specification of the number of individuals in each of the disease states (i.e. S, E, I and R).

I also spotted a small bug in the way we had specified the draws from the gamma distribution for the duration of the latent, infectious and immunity loss periods. I had got the shape and rate arguments muddled up. It doesn't change the mean of the distribution, but previously the variance was very low (too low).

par(mfrow = c(2, 1))
hist(rgamma(10000, 2 * 365, 2), breaks = 50) ## this is what we had before
hist(rgamma(n = 10000, shape = 2, rate = 2/365), breaks = 50) ### this is what we do now
cwhittaker1000 commented 4 months ago

Closing as merged into july-report branch via https://github.com/mrc-ide/helios/pull/118