[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 - 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/
Re: [R-sig-phylo] phyres function R package caper
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: 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: 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 - 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/
Re: [R-sig-phylo] phyres function R package caper
Thank you, Liam! Cheers, Ted From: Liam J. Revell [liam.rev...@umb.edu] 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: liam.rev...@umb.edu 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: 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: 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 - 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
Re: [R-sig-phylo] phyres function R package caper
Thank you both. Best regards, Sérgio. No dia 24 de Jun de 2015 18:30, Theodore Garland Jr theodore.garl...@ucr.edu escreveu: Thank you, Liam! Cheers, Ted From: Liam J. Revell [liam.rev...@umb.edu] 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: liam.rev...@umb.edu 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: 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: 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 - 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
