nbin_ri.bug

##
## negative binomial mixed effects model for the effect of treatment and day in the cycle on y
##
## Author: Pawel Gajer
## Sept 26, 2014
##
model
{
    eps <- pow(10,-13)
    for(i in 1:length(y))
    {
        y[i] ~ dnegbin(p[i],r[i])
        p[i] <- r[i]/(r[i] + lambda[i]) + eps
        log(lambda[i]) <- a[treatment[i],day[i]] + d[animal[i]]
        log(r[i]) <-  mur[treatment[i]]
        ## standardized residuals
        stRes[i] <- (y[i] - lambda[i])/sqrt(lambda[i] * (lambda[i] + r[i]) )
    }

    ## fixed effects
    prec <- 1.0E-6

    ## interaction between treatment and day
    for ( i in 1:12 )
    {
        a[1,i] ~ dnorm(0.0, prec)
        a[2,i] ~ dnorm(0.0, prec)
        a[3,i] ~ dnorm(0.0, prec)
    }

    for ( i in 1:3 )
    {
        mur[i] ~ dnorm(0.0, prec)
    }

    ## random intercept
    for ( i in 1:nAnimals )
    {
        d[i] ~ dnorm(0.0, tau.d)
    }
    tau.d ~ dgamma(0.001, 0.001)
}