fn<-function(id,ts=NULL,...){
print(id)
args=list(...)
inp=subset(ts,assessid==id)
inp=inp[order(inp$year),]
inp=with(inp,list(obsC=catch,
timeC=year,
obsI =biomass,
timeI=year))
parNm=c("log"=c("logn","logm","logK","logq"),
"par"=c("n", "m", "K", "q"))
#n: Parameter determining the shape of the production curve as in the generalised form of Pella & Tomlinson (1969).
#m: Log of maximum sustainable yield.
#K: Log of carrying capacity.
#q: Log of catchability vector.
#sdb: Log of standard deviation of biomass process error.
#sdf: Log of standard deviation of fishing mortality process error.
#sdi: Log of standard deviation of index observation error.
#sdc: Log of standard deviation of catch observation error.
print(names(args))
for (i in names(args)){
inp$priors[[i]]=c(args[[i]],1e-3)
inp$phase[[i]] =-1}
res=try(fit.spict(inp))
return(res)}
fnFLQuant<-function(x,val="logB"){
dat=data.frame(year =c(rep(seq(x$inp$timerange[1],x$inp$timerange[2]),each=16)),
season=c(rep(seq(16),x$inp$timerange[2]-x$inp$timerange[1]+1)),
data =exp(x$report[[val]])[-length(x$report[[val]])])
as.FLQuant(dat)}
fnMSY<-function(x){
with(x$report,FLPar(msy=MSY,bmsy=Bmsy,fmsy=Fmsy))}
fnKobe<-function(x){
FLQuants(stock =fnFLQuant(x,"logBBmsy"),
harvest=fnFLQuant(x,"logFFmsy"))}
fnPf<-function(x){
FLPar(r=x$value["r"],K=x$value["K"],p=x$value["p"])}
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