Thank you both. Best regards, Sérgio. No dia 24 de Jun de 2015 18:30, "Theodore Garland Jr" < [email protected]> escreveu:
> Thank you, Liam! > > Cheers, > Ted > > From: Liam J. Revell [[email protected]] > Sent: Wednesday, June 24, 2015 10:24 AM > To: Theodore Garland Jr; Sergio Ferreira Cardoso; R phylo mailing list > mailing list > Subject: Re: [R-sig-phylo] phyres function R package caper > > 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: [email protected] > 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: [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: 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 > > > > [[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]/ > > _______________________________________________ > > 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]/ > > [[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]/
