Changed model specifications

NegBinomBreedMolt.txt

@@ -15,7 +15,7 @@ model{
 	}
 
 
-tau.eps.year ~ dgamma(1,1) #dunif(0,10) might be better
+tau.eps.year ~ dgamma(1,1) 
 tau.eps.pair ~ dgamma(1,1)
 tau.eps.psu ~ dgamma(1,1)
 beta.bss.0~dnorm(0, 0.01)
@@ -44,9 +44,10 @@ beta.chl~dnorm(0, 0.1)
 beta.BM~dnorm(0,0.1)
 beta.offshore~dnorm(0,0.1)
 alpha~dnorm(0,.1)
-sigma0~dunif(0,300)
+sigma0~dunif(0, 7)
 sigma.eps.year <- 1/sqrt(tau.eps.year)
 sigma.eps.pair <- 1/sqrt(tau.eps.pair)
+sigma.eps.psu <- 1/sqrt(tau.eps.psu)
 
 r.N~dunif(0,100)
 

SS HDS model final.R

@@ -323,7 +323,7 @@ dataCovs<-list(nG=nG, xg=dist.breaks[-1]-13.5, nsites=nSites, Year = Year, pair
 ### initial values for N
 N.in<-t(seals.sum)+3
 
-initsCovs<-function(){list(N=as.vector(N.in), alpha = runif(1,1, 3), sigma0 = runif(1, 110, 130),
+initsCovs<-function(){list(N=as.vector(N.in), alpha = runif(1,1, 3), sigma0 = runif(1, 0, 7),
                            beta.bss.1=rnorm(1, 0, 0.1),
                            beta.bss.2=rnorm(1, 0, 0.1),
                            beta.bss.3=rnorm(1, 0, 0.1),
@@ -363,10 +363,11 @@ covs.mod<-run.jags(model = modelFileCovs,
                    monitor = params.Covs,
                    data = dataCovs,
                    n.chains = 3,
-                   burnin = 50000,
-                   sample = 100000,
+                   adapt = 2000,
+                   burnin = 10000,
+                   sample = 50000,
                    inits = initsCovs,
-                   thin = 2)
+                   thin = 1)
 
 
 #Diagnostics