Super, I will do just that. Thanks!! Andrea ~~ Andrea Berardi, PhD Postdoctoral Researcher, Smith Lab EBIO, University of Colorado-Boulder andrea.bera...@colorado.edu
On Mar 2, 2015, at 5:52 PM, Theodore Garland Jr <theodore.garl...@ucr.edu> wrote: > Andrea, remember that you can and should also do the "OLS" models (i.e., > assuming a star phylogeny) with measurement error considered. That's in the > programs that accompany Ives, Midford, and Garland (2007, Syst. Biol. > 56:252–270), and were in the batch I just sent you. > > 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 Andrea > Berardi [andrea.bera...@colorado.edu] > Sent: Monday, March 02, 2015 3:57 PM > To: r-sig-phylo@r-project.org > Cc: Anthony R Ives; Peter Smits > Subject: Re: [R-sig-phylo] phytools - evaluating significance of pgls.Ives > > Thank you all very much for the comments! They are so helpful. > > Yes, I do only have 8 species, and 3 replicates each. It is not ideal, but > it's what we have and we have a phylogeny, so I'd like to try some tests > incorporating phylogeny. > > I probably should have added that I plan on running OLS to test each > regression without the tree. This should give me an idea of the general > relationship. > > Regarding Liam's comment in pgls.Ives: Is the "lower=c(1e-8,1e-8)" call of > the pgls.Ives call the part where it constrains the slope to (almost)zero? > > I'll definitely give the MERegPHYSIGv2.m method a try as well, with Tony's > diagnostic suggestions. > > I will also go the LRT route with the data. > > Thanks very much again for your help! > Andrea > > ~~ > Andrea Berardi, PhD > Postdoctoral Researcher, Smith Lab > EBIO, University of Colorado-Boulder > andrea.bera...@colorado.edu > > > > On Mar 1, 2015, at 8:42 PM, Liam J. Revell <liam.rev...@umb.edu> wrote: > >> Hi Andrea. >> >> This is not presently implemented, but since this is a likelihood method it >> would be straightforward to constrain to a slope of zero and then do a LR >> test. This would be probably be the easiest way to test a hypothesis about >> the regression. >> >> That being said, as noted in the function documentation, some problems have >> been reported with the optimization algorithm for this model, which is >> simple and thus may fail to find the ML solution. Consequently, I would >> encourage you to look for other implementations of the method so that you >> can be confident in your result. I'm not aware of one in R at this time. >> >> 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 3/1/2015 10:31 PM, Andrea Berardi wrote: >>> Hi all, >>> >>> I'm just learning how to do PGLS analyses, and I'm looking for advice on >>> how to evaluate the significance of the regression fit using pgls.Ives in >>> the phytools package. I'm using this function because it incorporates >>> sampling error of species means, and my data has about 3 individuals per >>> species, with 8 species. My goal is to test whether a flower trait predicts >>> the leaf trait, while controlling for shared ancestry. Here is the output >>> from pgls.Ives: >>> >>>> fit <- pgls.Ives(Tree, Flower_trait, Leaf_trait) >>>> fit >>> $beta >>> [1] 96.3963098 0.1292656 >>> >>> $sig2x >>> [1] 22218901073 >>> >>> $sig2y >>> [1] 23027587 >>> >>> $a >>> [1] -10063.150 -1204.422 >>> >>> $logL >>> [1] -158.2337 >>> >>> $convergence >>> [1] 0 >>> >>> $message >>> [1] "CONVERGENCE: REL_REDUCTION_OF_F <= FACTR*EPSMCH" >>> >>> I am also running pgls on species averages for the traits using the gls >>> function in nlme and the corBrownian and corMartins functions in ape. But, >>> we are interested in incorporating the within-species variation in our >>> small dataset. >>> >>> Any suggestions would be welcome! >>> >>> Thanks for your help, >>> Andrea >>> >>> ~~ >>> Andrea Berardi, PhD >>> Postdoctoral Researcher, Smith Lab >>> EBIO, University of Colorado-Boulder >>> >>> _______________________________________________ >>> R-sig-phylo mailing list - R-sig-phylo@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >>> Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ >>> > > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
