ontario/ont_cal_HD_2brks.R

In bbolker/McMasterPandemic: Pandemic Model

library(McMasterPandemic)

## load("ontario_calibration.RData")  ## baseline calibration: ont_cal1 (calibrated object), bd (breakpoint dates)
print(unique(ont_all_sub$var))
print(opt_pars)  ## original parameter settings
ont_HD <- dplyr::filter(ont_all_sub, var %in% c("H","death"))
opt_pars_2brks <- opt_pars
opt_pars_2brks$logit_rel_beta0 <- rep(-1,2)  ## only two breakpoints (hosp data doesn't even start until after brk 1)
bd2 <- bd[-1]  ## drop first breakpoint
priors <- list(~dnorm(qlogis(rel_beta0[1]),mean=1,sd=1.5))
ont_cal_HD_2brks <- update(ont_cal1
                        , opt_pars=opt_pars_2brks
                        , time_args=list(break_dates=bd2)
                        , data=ont_HD
                        , priors=priors
                        , use_DEoptim=TRUE
                        , DE_cores=6
)

# rdsave("ont_cal_HD_2brks")