Lawrence,

Though you mentioned that you checked them, what you described frequently 
occurs when names are not the same in the data matrix and phylogeny. Since you 
did not specify how they were checked, I would use the ‘match’ function. If any 
NAs appear, you have a name mismatch.

If that is not it, I would need some more information from you to help diagnose 
the problem.

Dean

Dr. Dean C. Adams
Director of Graduate Education, EEB Program
Professor
Department of Ecology, Evolution, and Organismal Biology
Iowa State University
www.public.iastate.edu/~dcadams/<http://www.public.iastate.edu/~dcadams/>
phone: 515-294-3834

From: Lawrence Fatica <lawrence.m.fat...@gmail.com>
Sent: Friday, May 25, 2018 8:36 PM
To: MORPHMET <morphmet@morphometrics.org>
Subject: [MORPHMET] procD.pgls

Hi all,
I'm trying to perform a multivariate phylogenetic generalized least squares on 
PC scores in geomorph, and I keep getting the same error message:

Error in Cov[id, id] : subscript out of bounds

I get the same error whether I use procD.pgls or procD.lm with a VCV matrix 
from vcv.phylo. I've double checked the numbers--my tree and matrices all have 
the same number of taxa and matching names--and made sure I'm using the current 
versions of morpho and R.

Has anyone else encountered this problem or have any ideas what I might be 
doing wrong?

Many thanks,
Lawrence
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