I'm trying to run his model code with JAGS:
model{
## priors
b0 ~ dnorm(0, 5)
b1 ~ dnorm(0, 5)
b2 ~ dnorm(0, 5)
b3 ~ dnorm(0, 5)
b4 ~ dnorm(0, 5)
b5 ~ dnorm(0, 5)
b6 ~ dnorm(0, 5)
sigmayear ~ dt(0, 1, 2) I(0, )
## likelihood
for(i in 1:nind){
for(t in 2:last[i]){
y[i,t] ~ dbern(prop[i, t - 1])
prop[i, t - 1] <- y[i, t - 1] * (1 - d[i, t - 1])
logit(d[i, t - 1]) <-
b0 + b1 * temp[i, t] + b2 * sex[i] + b3 * day[t] +
b4 * strat[i] + b5 * temp[i, t] * sex[i] +
b6 * temp[i, t] * strat[i] + sigmayear * ryear[years[i]]
} # close t
} # close i
for(k in 1:nyears){
ryear[k] ~ dnorm(0, 1)
} #close k
}
The data-matrix I created should be fine:
> str(bugs.data)
List of 9
$ y : num [1:124, 1:203] 1 1 1 1 1 1 1 1 1 1 ...
$ nind : int 124
$ last : num [1:124] 98 98 78 91 78 98 87 88 98 111 ...
$ temp : num [1:124, 1:203] 1.33 1.33 1.33 1.33 1.33 ...
$ sex : num [1:124] 1 0 1 1 1 0 0 0 0 1 ...
$ day : num [1:203] -1.72 -1.7 -1.69 -1.67 -1.65 ...
$ strat : num [1:124] 0 0 0 0 0 0 0 0 0 0 ...
$ years : num [1:124] 7 7 7 7 7 7 7 7 7 1 ...
$ nyears: int 8
The actual call with these parameters has been working before...
ni <- 5000 #number of sims
nt <- 1 #get rid of
nb <- 2000 #warm in
nc <- 3 # number of chains
But for some reason, when i want to call it this happens:
> ms <- jags(bugs.data, inits, parameters, "knownfateSurvivalfat.txt", n.chains = nc, n.thin = nt, n.iter = ni, n.burnin = nb, working.directory = getwd())
Compiling model graph
Resolving undeclared variables
Deleting model
Fehler in jags.model(model.file, data = data, inits = init.values, n.chains = n.chains, :
RUNTIME ERROR:
Compilation error on line 14.
Index out of range taking subset of y
Somebody has any ideas why "y" should be out of range?
"i" should always go from 1 to 124 which fits to the matrix(bugs.data) and "t" goes from 2 to 203 which is also fine....
Make sure in your data list, it looks like list("y"=y,...) and not list(y="y"...).
Just a hunch.
Matt