From the start of the epidemic so the assumption is everyone has no baseline immunity and therefore, titre. This means there is no correlate of protection model running (100% infection rate given exposure).
Likelihood
Infer one infection per individual and maybe vaccination)
Use Ancestral titre values (one for infection one for vaccination [if needed])
Linear boost and then exponential wane to set point as highlighted in Svajanaet []
Code to run this is in rjmc_transvir_wave1.Rmd. Current issues:
I run into identifiability problems between those who are i) not infected and ii) those infected in the first wave and experience 300+ days of waning. To try and get around this, I've added a strong prior for standard deviation in the case where someone has a very low titre but I might need to think a bit more about how best to model this with a better observational model?
Need to make more post-processing figures for plotting
Exposure rate
Correlate of protection
Likelihood