Syntax error when trying to parse Bayesian model using RJAGS

Question

I'm running the following code to attempt Bayesian modelling using rjags but coming up with the syntax error below.

Error in jags.model(file = "RhoModeldef.txt", data = ModelData, inits = ModelInits, : Error parsing model file: syntax error on line 4 near "~"

RhoModel.def <- function() {
  for (s in 1:S) {
    log(rhohat[s]) ~ dnorm(log(rho[s]),log(rhovar[s]))
    rho[s] ~ dgamma(Kappa,Beta)
  }
  Kappa ~ dt(0,2.5,1) # dt(0, pow(2.5,-2), 1) https://stackoverflow.com/questions/34935606/cauchy-prior-in-jags https://arxiv.org/pdf/0901.4011.pdf 
  sig.k <- abs(Kappa)
  Beta ~ dt(0,2.5,1)
  sig.b <- abs(Beta)
}

S <- length(africasad21)-1 # integer
Rhohat <- afzip30$Rho # vector
Rhovar <- afzip30$RhoVar # vector

ModelData <-list(S=S,rhohat=Rhohat,rhovar=Rhovar)

ModelInits <-  list(list(rho = rep(1,S),Kappa=0.1,Beta=0.1))

Model.1 <- jags.model(file = 'RhoModeldef.txt',data = ModelData,inits=ModelInits,
                              n.chains = 4, n.adapt = 100)

Does anyone have any ideas how I might be able to fix this? I'm thinking it might have something to do with my attempts to fit a logged model? Please let me know if more details are needed.

Thanks!

Thanks for the idea - I fixed the indentation (and edited the code above accordingly) but still get the same error — Dexoryte, Oct 02 '22 at 21:41

score 1 · Accepted Answer · answered Oct 04 '22 at 10:09

Line 4 of the file 'RhoModeldef.txt' is most likely this one:

log(rhohat[s]) ~ dnorm(log(rho[s]),log(rhovar[s]))

JAGS does not allow log transformations on the left hand side of stochastic relations, only deterministic ones. Given that you are providing rhohat as data, the easiest solution is to do the log transformation in R and drop that part in JAGS i.e.:

log_rhohat[s] ~ dnorm(log(rho[s]), log(rhovar[s]))

ModelData <-list(S=S, log_rhohat=log(Rhohat), rhovar=Rhovar)

Alternatively, you could use dlnorm rather than dnorm in JAGS.

Does that solve your problem? Your example is not self-contained so I can't check myself, but I guess it should work now.

Thanks Matt! That has indeed solved the syntax error. Now coming up with 'node logrhohat[x] inconsistent with parents' and 'node logrhohat[x] inconsistent parent values' errors instead but I guess that's a function of the data I'm inputting.. — Dexoryte, Oct 05 '22 at 13:47

Syntax error when trying to parse Bayesian model using RJAGS

1 Answers1