Hi Philip.

Do not create very short tips. This will actually lead to very high weight being given to any difference between these two observations! Take the average of the different observations. Using the methods of Felsenstein (2008) or Ives & Garland (2007) it is also possible to take into account within-species sampling error, though this is not precisely what you have here (you do not know how uncertain each measure is, nor how uncertain are your estimates for other species), nor is this implemented in R.


All the best, Liam

Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org

On 1/27/2017 11:45 AM, Philip Shirk wrote:
I know this is a repeat question (
http://www.mail-archive.com/r-sig-phylo@r-project.org/msg04424.html) but I
didn't see any reponses/answers to the first posting, so I thought I'd ask
again:

I have a pre-published tree for my species of interest that includes all
the species in my dataset. However, my dataset contains duplicate data for
a few species (different estimates from different authors). What is the
best way to incorporate all the data into a PGLS analysis? When I try to
run the analysis with gls() I get the error:
"Error in Initialize.corPhyl(X[[i]], ...) : number of observations and
number of tips in the tree are not equal."

I imagine that I could:
1. toss out duplicates
2. average/combine duplicates
3. create very short branches for duplicate species and treat them as very
closely-related but separate species (but I don't know how to actually do
this.)
4. ???

Thanks,
Philip Shirk

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