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

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
4. ???

Philip Shirk

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