library(stockassessment)
setwd("run")
load("data.RData")
conf<-loadConf(dat,"../conf/model.cfg", patch=TRUE)
par<-defpar(dat,conf)
par$logSdLogN[2]<-log(0.05)
set.seed(1337)
idx<-which((dat$aux[,2]==1)&(dat$aux[,1]%in%c(1990:1999)))
dat$logobs[idx]<-NA
fit<-sam.fit(dat,conf,par,map=list(logSdLogN=as.factor(c(1,NA))))

if(fit$opt$convergence!=0) stop("Model did not converge.")
save(fit, file="model.RData")