Do you have a plot of the likelihoods versus the parameter value?
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=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: Friday, May 08, 2015 3:33 AM
To: r-sig-phylo@r-project.org
Subject: [R-sig-phylo] Weird estimated Lambda values (PGLS)
Dear all,
I performed a PGLS with a tree with divergence times as branch lengths. I
used 1 dependent and 1 independent variable. When I estimate the Lambda (in
Pagel's method) I get the Maximum Likelihood Lambda ~0 and the Restricted
Maximum Likelihood Lambda 0.878054. This is really strange. I was thinking
I might have a tree with incorrect branchlengths but I checked the plot of
absolute value of contrast vs. standard deviation for both variables and
it's ok (according to Garland et al., 1992). With OU transformation I don't
have the same problem. However, the p-value of phylogenetic (both with OU
or with Brownian Motion PGLS) aren't very different from the ordinary
least-squares. Is there any other ordinary procedure/analysis I should make
other than the plots I checked to check my tree? (I understand that there
is a chance that the characters I am using have influence and maybe the
tree doesn't make any difference).
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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