Yes, I believe these are the ones (attached). It's really weird. Even when I use a normal GLS the p-value between phylogenetic and non-phylogenetic least-squares doesn't differ much. Thanks for answering.
Best regards, Sérgio. 2015-05-08 16:36 GMT+01:00 Theodore Garland Jr <[email protected]>: > 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: [email protected] > 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 [[email protected]] on behalf of Sergio > Ferreira Cardoso [[email protected]] > Sent: Friday, May 08, 2015 3:33 AM > To: [email protected] > 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 > ᐧ > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/[email protected]/ > -- 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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