require(R2jags)

skate_BUGS_fit <- function(data,n.iter=175000,n.chains=1,n.burnin=100000,n.thin=30) {

  inits1 <-list(q=rep(.9,3),sdobs=rep(.65,3),sdpro=rep(1,3),theta=c(0.2,0.25),recrate=2,N69=c(1,0.3),Nad=rep(4,5),N= (t(data[,-1])),z=matrix(0.3,ncol=3,nrow=3))
  par.save <- c("theta","recrate", "z","Im","logIpred")
   
data2 <-list(Iobs=t(data[,-1]))

      tfit_jags <-    jags(data=(data2), inits=list(inits1), parameters.to.save=par.save, model.file="skate_bugs.txt", n.chains=n.chains, n.iter=n.iter, n.burnin=n.burnin, n.thin=n.thin, DIC=TRUE, working.directory=NULL, refresh = n.iter/50, progress.bar = "text")
#browser()
#tfit_jags <- jags(model="skate_bugs.txt",
#                  data=c(as.list(data)),
#                  parameters.to.save=c("q","theta","recrate", "z"),
#                  n.chains=1,
#                  n.iter=20000,
#                  inits=list(chain1))
}