Seeds: Random effect logistic
regression
This example is taken from Table 3 of Crowder (1978), and concerns the proportion of seeds that germinated on each of 21 plates arranged according to a 2 by 2 factorial layout by seed and type of root extract. The data are shown below, where r i and n i are the number of germinated and the total number of seeds on the i th plate, i =1,...,N. These data are also analysed by, for example, Breslow: and Clayton (1993).

The model is essentially a random effects logistic, allowing for over-dispersion. If p i is the probability of germination on the i th plate, we assume
r i ~ Binomial(p i , n i )
logit(p i ) = a 0 + a 1 x 1i + a 2 x 2i + a 12 x 1i x 2i + b i
b i ~ Normal(0, t )
where x 1i , x 2i are the seed type and root extract of the i th plate, and an interaction term a 12 x 1i x 2i is included. a 0 , a 1 , a 2 , a 12 , t are given independent "noninformative" priors.
Graphical model for seeds example
BUGS language for seeds example
model
{
for( i in 1 : N ) {
r[i] ~ dbin(p[i],n[i])
b[i] ~ dnorm(0.0,tau)
logit(p[i]) <- alpha0 + alpha1 * x1[i] + alpha2 * x2[i] +
alpha12 * x1[i] * x2[i] + b[i]
}
alpha0 ~ dnorm(0.0,1.0E-6)
alpha1 ~ dnorm(0.0,1.0E-6)
alpha2 ~ dnorm(0.0,1.0E-6)
alpha12 ~ dnorm(0.0,1.0E-6)
tau ~ dgamma(0.001,0.001)
sigma <- 1 / sqrt(tau)
}
Data ( click to open )
Inits ( click to open )
Results
A burn in of 1000 updates followed by a further 10000 updates gave the following parameter estimates:
We may compare simple logistic, maximum likelihood (from EGRET), penalized quasi-likelihood (PQL) Breslow and Clayton (1993) with the BUGS results
Heirarchical centering is an interesting reformulation of random effects models. Introduce the variables
m i = a 0 + a 1 x 1i + a 2 x 2i + a 12 x 1i x 2i
b i = m i + b i
the model then becomes
r i ~ Binomial(p i , n i )
logit(p i ) = b i
b i ~ Normal( m i , t )
The graphical model is shown below
This formulation of the model has two advantages: the squence of random numbers generated by the Gibbs sampler has better correlation properties and the time per update is reduced because the updating for the a parameters is now conjugate.