notes/spline_shape_calib.R

In bbolker/McMasterPandemic: Pandemic Model

library(McMasterPandemic)
library(tidyverse)
library(zoo)
library(parallel)
library(furrr)
library(future.batchtools)
library(splines)

source("makestuff/makeRfuns.R")
commandEnvironments()
makeGraphics()

objects()

start_date <- first_date
end_date <- start_date -1 + fitmax
obs_disp <- 50
proc_disp <- 1

params <- read_params(matchFile(".csv$"))

print(bb)

params <- fix_pars(params, target=c(R0=Rt[[1]]))

params["obs_disp"] <- obs_disp
params["proc_disp"] <- proc_disp
# params["obs_disp_report"] <- obs_disp
# params["obs_disp_death"] <- obs_disp


opt_pars_beta0less <- list()

sim_calib <- function(x){
	set.seed(x)

ddfull_sim<- (forecast_sim(p = unlist(opt_pars)
	, opt_pars = opt_pars
	, base_params = params
	, stoch = list(obs=TRUE,proc=TRUE)
	, stoch_start = c(proc=min(dd),obs=min(dd))
	, time_args = list(X_date=dd, X=X,extra_pars=list(time_beta=bb))
	, start_date = min(dd)
	, end_date = max(dd)
	, sim_fun = run_sim_loglin
	)
	%>% filter(var %in% c("report"))
#	%>% mutate(value = ifelse(is.na(value),0,value))
)


dd_sim <- (ddfull_sim
	%>% filter(date <= end_date)
	)

ff <- calibrate_comb(params = params
	, debug_plot=FALSE
	, use_DEoptim=TRUE
	, DE_cores = 6
	, opt_pars = opt_pars
	, use_spline = TRUE
	, spline_df = ndf
	, spline_type = "bs"
	, spline_int = FALSE
	, data= dd_sim
	, start_date = min(dd_sim$date)
	, start_date_offset = 0
)

ff2 <- calibrate_comb(params = params
							, debug_plot=FALSE
							, use_DEoptim=TRUE
							, DE_cores = 6
							, opt_pars = opt_pars
							, use_spline = TRUE
							, spline_df = ndf
							, spline_pen = 5
							, spline_type = "bs"
							, spline_int=FALSE
							, data= dd_sim
							, start_date = min(dd_sim$date)
							, start_date_offset = 0
)

ff_list <- list(fit=ff, fitpen=ff2, fitdat=dd_sim, full_dat=ddfull_sim)

saveRDS(object=ff_list, file=paste0("./cachestuff/spline_shape_calib.",x,".RDS"))
}

batch_setup()

future_map(1:10,function(x)sim_calib(x))