In FPRgroup/FPEM: FPEM

ptm <- proc.time()
#### to be replaced with current run
proc.time() - ptm
res$mod$BUGSoutput$summary
bugs_15000 <- res$mod$BUGSoutput
mcmc.array <- bugs_15000$sims.array
library(coda)
invlogit <- function(x){
  exp(x)/(1+exp(x))
}
# "mod.ct", 
# "unmet.ct", 
# "trad.ct", 
# " mu.jn", 
# "logitratio.yunmet.hat.j",
# "logitRmax.c",
# "logitomega.c",
# "logitpmax.c",
# "logitRomega.c",
# "setlevel.c",
# "RT.c",
# "unmet.intercept.c"
par <- res$mod$BUGSoutput$sims.list$unmet.ct %>% invlogit()
unmet <- c()
for (i in 1:dim(par)[3]) {
unmet[i] <- effectiveSize(par[,,i]) %>% round()
}
par <- res$mod$BUGSoutput$sims.list$mod.ct %>% invlogit()
mod <- c()
for (i in 1:dim(par)[3]) {
mod[i] <- effectiveSize(par[,,i]) %>% round()
}
par <- res$mod$BUGSoutput$sims.list$trad.ct %>% invlogit()
trad <- c()
for (i in 1:dim(par)[3]) {
trad[i] <- effectiveSize(par[,,i]) %>% round
}
temp <- data.frame(unmet = unmet, mod = mod, trad = trad)
write.table(temp, "neff_logit.txt")



# checking some parameters
PlotTrace <- function(#Traceplot for one parameter
  ### Trace plot for one parameter and add loess smoother for each chain
  parname, mcmc.array,##<< needs to be 3-dimensional array!
  n.chains= NULL, n.sim= NULL, main = NULL){
  if (is.null(main)) main <- parname
  if (is.null(n.sim)) n.sim <- dim(mcmc.array)[1]
  if (is.null(n.chains)) n.chains <- dim(mcmc.array)[2]
  plot(c(mcmc.array[,1,parname]), type = "l", ylab = parname,  main = main,
       ylim = c(min(mcmc.array[,,parname]),max(mcmc.array[,,parname])))
  for (chain in 1:n.chains){
    lines(c(mcmc.array[,chain,parname]), type = "l", col = chain)
  }
  for (chain in 1:n.chains){
    curve(predict(loess(c(mcmc.array[,chain,parname])~seq(1,n.sim)),x), lty = 2, lwd = 3, add = TRUE, type = "l", col = chain)
  }
}

pdf("traceplots_lowneffpars.pdf")
PlotTrace("logitRomega.c", mcmc.array)
PlotTrace("mu.jn[4,1]", mcmc.array)
for (t in 1:length(first_year:last_year)) PlotTrace(paste0("trad.ct[1,",t,"]"), mcmc.array)
for (j in 1:6) PlotTrace(paste0("logitratio.yunmet.hat.j[",j,"]"), mcmc.array)
for (t in 1:length(first_year:last_year)) PlotTrace(paste0("unmet.ct[1,",t,"]"), mcmc.array)
dev.off()