Hi,
You could also be interested in the function phyloSignalBS available in
the package phylosignal.
Best,
François
Le 08/12/2016 à 17:26, Carturan, Bruno a écrit :
Hello R-sig-phylo community,
I am trying to measure the phylogenetic signal of functional traits with the
Blomberg’s K and Pagel’s λ methods. My problem is that I don’t have one
phylogenetic tree but 1000 (the trees were created by first combining different
molecular, morphologic and taxonomic trees, then by conducting a MCMC analysis
and finally by selecting the 1000 trees – work made by Huang and Roy 2015).
Is there a way to proceed to test the significance of the K and λ values for
each trait with these 1000 trees?
An idea I have is to run the test and obtain a p value for each of the 1000
trees, which would give me a distribution of p values, and then consider that
if 80% (for instance) of the p values are significant, the K or λ value is
significant. This is computationally very demanding (I have 735 species) and I
don’t know if this could be considered as a valid procedure.
I am looking forward for you answer.
Bruno Carturan
PhD Candidate
Complex Environmental Systems Lab
University of British Columbia
Okanagan Campus
________________________________________
From: Liam J. Revell [liam.rev...@umb.edu]
Sent: Wednesday, December 07, 2016 6:54 AM
To: Carturan, Bruno
Subject: Re: A question about phylogenetic signal significance with 1000 trees
Bruno.
This is an interesting question. Since this doesn't pertain specifically
to phytools, perhaps you should pose it to the R-sig-phylo email
list-serve. You may get a good answer there.
All the best,
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 12/6/2016 6:16 PM, Carturan, Bruno wrote:
Hello Dr. Revell,
I am a PhD student from the Complex Environmental Systems Lab, from the
University of British Columbia and I would like to ask you question.
I am trying to measure the phylogenetic signal of functional traits with
the Blomberg’s K and Pagel’s λ methods. My problem is that I don’t have
one phylogenetic tree but 1000 (the trees were created by first
combining different molecular, morphologic and taxonomic trees, then by
conducting a MCMC analysis and finally by selecting the 1000 trees –
work made by Huang and Roy 2015).
Is there a way to proceed to test the significance of the K and λ values
for each trait with these 1000 trees?
An idea I have is to run the test and obtain a p value for each of the
1000 trees, which would give me a distribution of p values, and then
consider that if 80% (for instance) of the p values are significant, the
K or λ value is significant. This is computationally very demanding (I
have 735 species) and I don’t know if this could be considered as a
valid procedure.
I am looking forward for you answer.
Best regards,
Bruno Carturan
PhD Candidate
Complex Environmental Systems Lab
University of British Columbia
Okanagan Campus
<http://www.ubc.ca/okanagan/>
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