Hi,

I've been using MCMCglmm to do ordinal regressions with phylogenetic
structure. At the moment I've been using the ginverse argument, and a
sparse inverse matrix created with

> inverseA(phylo.object)$Ainv

after running MCMCglmm, I get the warning that "some combinations in animal
do not exist and missing records have been generated"

I assume this is because internal nodes are part of the inverse matrix and
I only have data for the tips. If I then only use a subset of my data, I
get the same warning; but my parameter estimates seem reasonable. Does the
program skip these rows internally? I tried to create a matrix for tips
only and I would always end up with a matrix too large in size that would
crash the computers. This wouldn't happen when using all nodes.

My question is, should I be pruning my tree to match every subset of data
and then generating an inverse matrix for tips only? Is the default por
inverseA to scale branch lengths?

best regards,

Luis

	[[alternative HTML version deleted]]

