library(stockassessment)
setwd("run")
load("data.RData")

#dat$fleetTypes[2] <- 3  #### ADDED TO FIX a PROBLEM OF AGE 99
conf<-defcon(dat)
conf$keyLogFsta[1,] <- c(0,1,2,3,4,5,6,7,7,7,7,7,7)
conf$keyVarObs[4,]      <- c(-1,-1,-1, 3,4,4,4,4,4,4,4,4,-1)
conf$fbarRange <- c(4,8)
conf$corFlag <- 0
conf$fixVarToWeight<-1
conf$obsCorStruct[] <- c("ID", "ID", "ID", "AR", "ID")
conf$keyCorObs[4,]<-0
saveConf(conf,file="../conf/model.cfg")

par<-defpar(dat,conf)

# model fitting
fit <-sam.fit(dat,conf,par, newtonsteps=0)



#conf<-loadConf(dat,"../conf/model.cfg")
#par<-defpar(dat,conf)
#fit<-sam.fit(dat,conf,par)

save(fit, file="model.RData")