[R-sig-ME] trouble getting data scale predictions from a binomial MCMCglmm model

Kari Ruohonen kari.ruohonen at utu.fi
Wed Mar 23 13:19:29 CET 2011

I have fitted a binomial model (logit link) with MCMCglmm by fixing the
unit variance to 1 as discussed in the CourseNotes of MCMCglmm.

Now, I would like to get predictions on the data scale. I know there is
a predict function that does this but I need to be able to predict
outside R. With the usual X%*%b where X is the model matrix and b the
vector of coefficients I get predictions on the link scale. The
predictions I get match those from the predict.MCMCglmm method with the
type="terms" option. However, I cannot figure out how to get the
predictions on the data scale. CourseNotes discuss and give an example
of scaling the coefficients suitably with c2 <- (16*sqrt(3)/(15*pi))^2
and then dividing with (sqrt(1+c2*residual var)) to obtain estimates
under residual variance =0 but I cannot figure out how to apply this to
the case of predictions.

Here is a small example based on one in the CourseNotes:


# the next predictions correspond to those from predict.MCMCglmm with "
# type="terms"

# but these do not correspond those with type="response"

I am obviously missing something and would be grateful to someone
helping me out.

Many thanks, Kari

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