Agreed!
Similarly, Pagel's lambda ad Grafen's rho were designed from a purely
statistical perspective, whereas OU and ACDC models are motivated by ties to a
possible set of biological processes.
Cheers,
Ted
From: Alejandro Gonzalez Voyer [alejandro.gonza...@iecologia.unam.mx]
Sent: Thursday, May 14, 2015 8:47 AM
To: Theodore Garland Jr
Cc: Sergio Ferreira Cardoso; R phylo mailing list mailing list
Subject: Re: [R-sig-phylo] Non-ultrametric tree PGLS
Hi Sergio,
I would add to Ted’s reply that you are not only considering alternative
statistical models but that the evolutionary assumptions from the models you
are fitting also differ, and you need to keep this in mind when comparing
models. Comparison of AICs or any other estimate of goodness of fit must also
involve careful consideration of the assumptions of the models you are
comparing. In your particular case, the tree with branch lengths set to equal
values (all branch lengths = 1) implies different amount of time to evolve for
each of your species (in other words the expected variances - diagonal terms in
the variance-covariance matrix - differ between the species), and thus you
should consider whether such an assumption makes biological sense in your
system.
Cheers
Alejandro
___
Dr Alejandro Gonzalez Voyer
Laboratorio de Conducta Animal
Instituto de Ecología
Circuito Exterior S/N
Ciudad Universitaria
Universidad Nacional Autónoma de México
México, D.F.
04510
México
Tel: +52 55 5622 9044
E-mail:
alejandro.gonza...@iecologia.unam.mxmailto:alejandro.gonza...@iecologia.unam.mx
El 14/05/2015, a las 10:39, Theodore Garland Jr
theodore.garl...@ucr.edumailto:theodore.garl...@ucr.edu escribió:
Hi Sergio,
I am not quite understanding the situation nor why you see a problem. if I
understand correctly, you are considering these five (5) alternative models for
some sort of simple or multiple regression:
OLS = star phylogeny
PGLS with real-time branch lengths (ultrametric)
Pagel's lambda with real-time branch lengths (ultrametric)
PGLS with all branch legnths equal to 1.0
Pagel's lambda with all branch lengths equal to 1.0
To help decide which model best fits your data, you can look at AIC or for some
comparisons do a likelihood ratio test.
My experience is that any of the transform models (Pagel's lambda, Grafen's
rho, OU in various implementations, ACDC) can sometimes yield really bizarre
results when you start with a non-ultrametric tree. You need to be careful and
check the REML likelihood surface for multiple peaks, etc.
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.edumailto:tgarl...@ucr.edu
http://www.biology.ucr.edu/people/faculty/Garland.html
http://scholar.google.com/citations?hl=enuser=iSSbrhwJ
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: Thursday, May 14, 2015 8:32 AM
To: r-sig-phylo@r-project.org
Subject: [R-sig-phylo] Non-ultrametric tree PGLS
Hello all,
I have an ultrametric phylogenetic tree with divergence times as branch
lengths. To see if there was a big difference between using these branch
lengths and equal (=1) branch lengths I set all lengths to 1 and ran a
PGLS. I ran with Lambda transformations and the estimation is that Lambda
is superior than 1 (both with ML and REML estimation). I suppose this is a
consequence of the tree being non ultrametric. Is there a solution for this
problem or should I, in this case, just ran a GLS (Brownian Motion) to
avoid the over estimation of the phylogenetic signal?
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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