[R] Error message R2Jags

[alexB]

Hi, 

I'm trying to generate a GLMM for Y following a negative binomial
distribution. The first step I'm taking as a beginner in the use of R2Jags
is to generate a GLM for Y following a Poisson distribution (I heard it's
good in order to get used to the coding language), so here I am and here I
face the first error message for which I can't find any mistake of spelling.
Could you please give me your opinion about it?

I'm modelling the abundance of Thersitina parasites as a response to the
standard size of the host fish (=Standard), the type of site where it was
sampled (Site, two levelled factor: C, E) month of sampling (Month, 3
levelled factor: May, June, July). 

Here's what I did:

MM1 <- model.matrix(~ Site * Month + Standard, data = Data)
head(MM1)

#
#  (Intercept) SiteE MonthJune MonthJuly Standard SiteE:MonthJune
SiteE:MonthJuly
#1           1              0         0         0     5.14                       
0                        0
#2           1              1         0         0     5.49                       
0                        0
#3           1              1         0         0     5.20                       
0                        0
#4           1              1         0         0     5.57                       
0                        0
#5           1              0         0         0     4.90                       
0                        0
#6           1              0         0         0     5.99                       
0                        0
#

win.data1 <- list(Y       = Data$Thersitina,
                  Eut     = MM1[,2],  # SiteE
                  M2      = MM1[,3],  # Month2_June
                  M3      = MM1[,4],  # Month3_July
                  Std     = MM1[,5],  # Standard
                  I2      = MM1[,6],  # SiteE:Month2_June
                  I3      = MM1[,7],  # SiteE:Month3_July
                  N       = nrow(Data))


sink("GLM.txt")
cat("
model {
    #Likelihood(data | parameters)
    for (i in 1:N) {                                    # N is the sample
size
      Y[i]  ~  dpois(mu[i])    
      eta[i]  <- b[1]  +
		 b[2] * Eut[i] + 
                 b[3] * M2[i]  +
                 b[4] * M3[i]  +
                 b[5] * Std[i] +
                 b[6] * I2[i]  +
                 b[7] * I3[i]
      log(mu[i]) <-  max(-20, min(20, eta[i]))  
      PRes[i] <- (Y[i] - mu[i]) / sqrt(mu[i])   #estimate residuals (=
observed - expected / sqrt(variance))
     #Discrepancy measures (used for checking overdispersion)
     YNew[i]    ~ dpois(mu[i])                   #New data   
     PResNew[i] <- (YNew[i] - mu[i]) / sqrt(mu[i])
     D[i]       <- pow(PRes[i], 2)
     DNew[i]    <- pow(PResNew[i], 2)
    }     

#   Add up discrepancy measures
    fit <- sum(D[1:N])
    fit.new <- sum(DNew[1:N])
    for (i in 1:6) { b[i] ~ dnorm(0.0, 0.01)
                  #  b[i] ~ dunif(-20, +20)          
    }                                           

}
",fill = TRUE)
sink()

inits1 <- function () {
  list(b = rnorm(7, 0, 0.01))}  

out1 <- jags(data = win.data1, 
             inits = inits1,
             parameters = params1,
             model.file = "GLM.txt",  
             n.thin = nt,
             n.chains = nc,
             n.burnin = nb,
             n.iter = ni)




That's when R returns this error message:

#
#Compiling model graph
#   Resolving undeclared variables
#   Allocating nodes
#Deleting model
#
#Error in jags.model(model.file, data = data, inits = init.values, n.chains
= n.chains,  : 
#  RUNTIME ERROR:
#Compilation error on line 13.
#Subset out of range: b[7]
#

So I guess there's a problem with line 13 of the code (i.e. b[7] * I3[i])
causing the problem, but why... I really don't see the problem :(

Any guess?

Thanks in advance,

aB


 



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