Hi all.
To the original question, you should be able to get these values first
using gls(...,correlation=corBrownian(...)) in nlme & then applying
residuals to the fitted model returned by gls. For instance, for data
frame X with variables x & y, and ultrametric phylogeny tree, you might
compute:
library(ape)
library(nlme)
fit<-gls(y~x,data=X,correlation=corBrownian(1,tree))
residuals(fit)
(phytools also has a function for this, phyl.resid, but it does exactly
the same thing as the code above, and thus there is really no reason to
prefer that function - except perhaps to cross-check your result for
errors.)
With regards to Ted's comment, indeed these are different quantities.
Though the fitted coefficients from a contrasts regression should be the
same as above, the residuals will be different (and there will be one
fewer of them, besides). These residuals, from the contrasts regression,
should be phylogenetically independent; however they are not longer
associated with species, but with 'contrasts' or nodes in the tree. To
obtain these residuals from a contrasts regression you should be able to
do something like:
X<-X[tree$tip.label,] ## precautionary
pic.x<-pic(X[,"x"],tree)
pic.y<-pic(X[,"y"],tree)
fit<-lm(pic.y~pic.x-1)
residuals(fit)
There is no particular reason to prefer one set of quantities over the
other - it just depends on what subsequent analyses are intended. In the
former case, the residuals are associated with species - but these
residuals consequently will be phylogenetically correlated & thus the
tree needs to be taken into consideration in any subsequent analysis.
The latter residuals are phylogenetically independent, but no longer
associated with species. (I hate to cite myself, but this is discussed
in my paper Revell 2009; Evolution.)
I hope this is of some help.
All the best, Liam
Liam J. Revell, Assistant 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 6/24/2015 12:35 PM, Theodore Garland Jr wrote:
Hi All,
I am going to suggest that when people want any sort of "phylogenetic residuals" they do
some checking on their own to try to verify what, exactly, they are getting. Here's one check you
can do. Compute phylogenetically independent contrasts for two traits. Perform a regression
(through the origin, of course) of one trait on the other. Save the residuals. Compare them with
the "phylogenetic residuals" you get from some other program that does a PGLS regression
(not with any transformation of the branch lengths). Let us know what you find!
Cheers,
Ted
Theodore Garland, Jr., Professor
Department of Biology
University of California, Riverside
Riverside, CA 92521
Office Phone: (951) 827-3524
Facsimile: (951) 827-4286 (not confidential)
Email: tgarl...@ucr.edu
http://www.biology.ucr.edu/people/faculty/Garland.html
http://scholar.google.com/citations?hl=en&user=iSSbrhwAAAAJ
Director, UCR Institute for the Development of Educational Applications
Editor in Chief, Physiological and Biochemical Zoology
Fail Lab: Episode One
http://testtube.com/faillab/zoochosis-episode-one-evolution
http://www.youtube.com/watch?v=c0msBWyTzU0
________________________________________
From: R-sig-phylo [r-sig-phylo-boun...@r-project.org] on behalf of Sergio
Ferreira Cardoso [sff.card...@campus.fct.unl.pt]
Sent: Wednesday, June 24, 2015 9:21 AM
To: R phylo mailing list mailing list
Subject: [R-sig-phylo] phyres function R package caper
Dear all,
When I try to get a list os phylogenetic residuals using phyres function
from R package I get this message: Error: could not find function "phyres".
Does anyone know how to solve this problem?
phyres(fit.gls1)
Error: could not find function "phyres"
Best regards,
Sérgio.
--
Com os melhores cumprimentos,
Sérgio Ferreira Cardoso.
--------------------
Best regards,
Sérgio Ferreira Cardoso
MSc. Paleontology candidate
Departamento de Ciências da Terra - FCT /Universidade Nova de Lisboa
Geociências - Universidade de Évora
Lisboa, Portugal
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