[R] BRugs

[Uwe Ligges]

Perhaps a better idea is to ask on a BUGS mailing list. BRugs is just an 
interface to OpenBUGS and is not involved in handling the BUGS language....

I'd also suggest to strat trying your problem witht BRugs but in 
OpenBUGS directly in order to avoid confusion caused by the interface.

Best wishes,
Uwe Ligges

On 19.04.2010 18:04, N S Ha wrote:
>
> Thanks for the reply Bob, but it still does not work, you see. I ran this
> model, just with the main effects and it ran fine.
>
> n=length(bi.bmi)
>
> Lgen=2
> Lrace=5
> Lagegp=13
> Lstra=15
> Lpsu=2
>
> bi.bmi.model=function(){
> # likelihood
> for(i in 1:n){
> 	bi.bmi[i]~ dbern(p[i])
> 	logit(p[i])<- a0 + a1[agegp[i]]+a2[gen[i]]+a3[race[i]]
> 			    + g[stra[i]]+ u[psu[i],stra[i]]
> 		}
> # constraints for a1, a2, a3
> a1[1]<-0.0
> a2[1]<-0.0
> a3[1]<-0.0
> # priors
> a0~ dnorm(0.0, 1.0E-4)
> for(j in 2:Lagegp){a1[j]~ dnorm(0.0, 1.0E-4)}
> for(j in 2:Lgen){ a2[j]~ dnorm(0.0, 1.0E-4)}
> for(k in 2:Lrace){ a3[k]~ dnorm(0.0, 1.0E-4)}
>
> for(l in 1:Lstra){
> 	g[l]~dunif(0, 100)
> 	}
> for( m in 1:Lpsu){
> 	for(l in 1:Lstra){
> 		u[m,l]~ dnorm(0.0, tau.u)
> 		}}
> tau.u<-pow(sigma.u, -2)
> sigma.u~ dunif(0.0,100)
> }
>
> library(BRugs)
> writeModel(bi.bmi.model, con='bi.bmi.model.txt')
> model.data=list( 'n','Lagegp', 'Lgen', 'Lrace', 'Lstra', 'Lpsu',				
> 				'bi.bmi','agegp', 'gen', 'race','stra', 'psu')
> model.init=function(){
> 	list( sigma.u=runif(1),
> 		a0=rnorm(1), a1=c(NA, rep(0,12)),
> 		a2=c(NA, rep(0, 1)),
> 		a3=c(NA, rep(0, 4)),
>   		g=rep(0,Lstra), u=matrix(rep(0, 30), nrow=2)	)
> 	}
> model.parameters=c( 'a0', 'a1', 'a2', 'a3')
> model.bugs=BRugsFit(modelFile='bi.bmi.model.txt',
> 				   data=model.data,
> 				   inits=model.init,
> 				   numChains=1,
> 				   para=model.parameters,
> 				   nBurnin=50, nIter=100)
>
> This is just with the main effects, and this does not give me any problems,
> and I also ran the following model with interaction term between gen and
> race, and it also ran fine.
> for (i in 1:n){
> 	bi.bmi[i]~ dbern(p[i])
> 	logit(p[i])<- a0 + a1[agegp[i]]+a2[gen[i]]+a3[race[i]]
> 			   + a23[gen[i], race[i]]
> 			  + gam[stra[i]]+ u[psu[i],stra[i]]
> 		}
> # constraints for a2, a3, a12 and a13
> a1[1]<-0.0
> a2[1]<-0.0
> a3[1]<-0.0
> a23[1,1]<-0.0
>
> #gen x race
> for(j in 2:Lrace){ a23[1,j]<-0.0}
> for(k in 2:Lgen){ a23[k,1]<-0.0}
> # priors
> a0~ dnorm(0.0, 1.0E-4)
> for(i in 2:Lagegp){a1[i]~dnorm(0.0, 1.0E-4)}
> for(i in 2:Lgen){ a2[i]~ dnorm(0.0, 1.0E-4)}
> for(i in 2:Lrace){ a3[i]~ dnorm(0.0, 1.0E-4)}
> for(i in 2:Lgen){
> 	for(j in 2:Lrace){
> 		a23[i,j]~ dnorm(0.0, 1.0E-4)
> 	}}
> for(i in 1:Lstra){
> 	gam[i]~dunif(0, 1000)
> 	}
> for( i in 1:Lpsu){
> 	for(j in 1:Lstra){
> 		u[i,j]~ dnorm(0.0, tau.u)
> 		}}
> tau.u<-pow(sigma.u, -2)
> sigma.u~ dunif(0.0,100)
> }
>
> So, the error happens only when I try to plug in interaction with the agegp.
> I still don't know how to correct it.
> Thanks
>