model natural immunity with ab titre

[slwu89]

Instead of using the R compartment to model 100% immunizing infection for a period, we want to allow natural infection to boost ab titre and then allow it to decay naturally. It should be converted into protection from infection/severe disease according to current functional forms. The ab boost from natural infection should be equal to the "best" vaccine product for starters, but this should be a default parameter value, rather than hardcoded (allow user input).

One thing to change is to make the dwell time in R deterministically equal to 1 time step, so we don't have people still in R: https://github.com/mrc-ide/safir/blob/main/R/events.R#L328

This takes precedence over #7

[slwu89]

new files:

• events_naturalimmunity.R: sets up logic upon recovery to update ab titre and increment the number of infection bouts this person experienced
• variables_naturalimmunity.R: just adds the 2 variables necessary for the additional functionality
• efficacy_naturalimmunity.R: modifies somewhat the daily ab titre calculation to correctly calculate for those with vaccine, prior infection, or both.

remaining tasks:

• add parameter parameters$mu_ab_infection giving the boost each infection bout to ab titre
• confirm that calculation of efficacies from ab titre will work with existing infection process and hospitalization outcomes
• test the simulation

[slwu89]

closed with #40