ontario/ont_cal_2brks_ndt.R

In bbolker/McMasterPandemic: Pandemic Model

library(McMasterPandemic)

## second two breaks, but use Delta_t=0.1 to try to overcome extinction problems

## load("ontario_calibration.RData")  ## baseline calibration: ont_cal1 (calibrated object), bd (breakpoint dates)
## use hospitalization data only
print(unique(ont_all_sub$var))
print(opt_pars)  ## original parameter settings
opt_pars_2brks <- opt_pars
opt_pars_2brks$log_rel_beta0 <- rep(-1,2)  ## only two breakpoints (hosp data doesn't even start until after brk 1)
bd2 <- bd[-1]  ## drop first breakpoint
ont_cal_2brks_ndt <- update(ont_cal1
                         ,  opt_pars=opt_pars_2brks
                         , time_args=list(break_dates=bd2),
                         , sim_args = list(ndt=10))

# rdsave("ont_cal_2brks_ndt")