Hi Jarrod,

I am using the new family="threshold" in MCMCglmm version 2.18 with a
5-variate ordered response. I would like to obtain the predicted responses
for on the original ordinal scale, but I am not sure how to do so for
either "ordinal" or the "threshold" family.

 1. For family="threshold" the posterior predicted probabilities are :

                post.pred[, keep] <- pnorm(post.pred[, keep], 0,
sqrt(postvar[, keep]))

How can I classify these probabilities into the original ordinal scale?


2. I can see that for family="ordinal", cut points (CP) are used in
predict.MCMCglmm():

  for (i in 2:(dim(CP)[2] - 1)) {
                  q <- q + (pnorm(CP[, i + 1] - post.pred[, keep],  0,
sqrt(postvar[, keep] + 1)) - pnorm(CP[, i] - post.pred[, keep], 0,
sqrt(postvar[, keep] + 1))) * (i - 1)
                                        }
Are the thresholds and the posterior predictive values (using type =
"terms") on the linear (latent variable) scale?

What would be the interpretation of the predicted values obtained from
using type= "response" with family = "ordinal"? (All 5 ordinal responses
are coded 1-3, and the predicted values from predict.MCMCglmm are real
numbers between 0-6.)

Regards,
Shamil.

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