setUp<-function(year,name,jbinput,key){
if (is.null(name))
key[key$year>year,"value"]=NA
else
key[!(!(key$name%in%name)|(key$name%in%name&key$year<=year)),"value"]=NA
Is =seq(dim(jbinput$data$cpue)[2]-1)
names(Is)=dimnames(jbinput$data$cpue)[[2]][-1]
dat=cast(key,year~name)
dimnames(dat)[[1]]=dat[,1]-jbinput$data$cpue[1,1]+1
dat=dat[,-1]
jbinput$jagsdata$I[as.numeric(dimnames(dat)[[1]]),Is[dimnames(dat)[[2]]]][]=as.matrix(dat)
jbinput}
hcstJabba<-function(year,name,jb,key,K,r,q){
jb$settings$scenario = paste0("hc",year,paste(name,collapse="."))
jb=setUp(year,name,jb,key)
fit_jabba(jb,init.values=TRUE,
init.K=K,
init.r=r,
init.q=q,
ni =5500,
nt =1,
nb =500,
nc =2)$diags}
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