TRANSVIR model fitting for wave_1 (pre-delta) - Githubissues

dchodge / serojump

GNU General Public License v3.0

1 stars 2 forks source link

TRANSVIR model fitting for wave_1 (pre-delta) #2

Open dchodge opened 6 months ago

dchodge commented 6 months ago

Exposure rate

Multimodal peaks (empirical)

Correlate of protection

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 []
Observational model is normal

dchodge commented 6 months ago

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