[R-sig-phylo] Cross-validation with independent contrasts
Dear all, I'm wondering if it would be statistically/philosophically correct to use n-fold cross-validation to evaluate a linear regression with independent contrasts. My doubt comes from the fact that when simply dividing the IC dataset in, lets say, 10 folds, some folds will remove the contrasts of internal nodes without necessarily removing an entire clade above that point, producing what can be viewed as two independent clades (a graphical example would be, in Felsenstein's seminal paper, fig. 8, remove the contrast at node 13, while keeping those at nodes 9 and/or 10). Any thoughts? Best wishes, Diego Bilski [[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] Concentrated changes test
Hi everyone, Just a quick question: I was wondering if there is a R implementation of Wayne Maddison's (1990) concentrated changes test ( http://www.jstor.org/stable/2409434). After a little looking around, I can't seem to find it but was hoping someone else might have some ideas. Thanks in advance, Matt [[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] Concentrated changes test
Isn't it in Mesquite? 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 = Dept. office (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 http://idea.ucr.edu/ Inquiry-based Middle School Lesson Plan: Born to Run: Artificial Selection Lab http://www.indiana.edu/~ensiweb/lessons/BornToRun.html Fail Lab: Episode One http://testtube.com/faillab/zoochosis-episode-one-evolution http://www.youtube.com/watch?v=c0msBWyTzU0 From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Matt Pennell [mwpenn...@gmail.com] Sent: Friday, May 16, 2014 9:04 AM To: R-phylo Mailing-list Subject: [R-sig-phylo] Concentrated changes test Hi everyone, Just a quick question: I was wondering if there is a R implementation of Wayne Maddison's (1990) concentrated changes test ( http://www.jstor.org/stable/2409434). After a little looking around, I can't seem to find it but was hoping someone else might have some ideas. Thanks in advance, Matt [[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] plot trees after different branch transformations
It looks like transform.phylo has been deprecated. Use rescale.phylo. 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 5/16/2014 2:20 PM, Agus Camacho wrote: Dear list users, Im trying to show what happens when we apply lambda transformations to a tree. For that, I was following swenson's book explanations: library(geiger) lambda.phylo=transform(tree,1) however, I got the following errors: lambda.phylo=transform(tree,lambda) Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) : cannot coerce class phylo to a data.frame lambda.phylo=geiger::transform(tree,lambda) Error: 'transform' is not an exported object from 'namespace:geiger' Any one would point to a workaround for branch transformation and posterior visualization of the tree? Thanks in advance. Agus ___ 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] plot trees after different branch transformations
Hi Agus - Geiger has changed - now you should use rescale. E.g. library(geiger) geo - get(data(geospiza)) lphy - rescale(geo$phy, lambda, 0.5) # transform tree in one fell swoop plot(lphy) On May 16, 2014, at 11:20 AM, Agus Camacho agus.cama...@gmail.com wrote: Dear list users, Im trying to show what happens when we apply lambda transformations to a tree. For that, I was following swenson's book explanations: library(geiger) lambda.phylo=transform(tree,1) however, I got the following errors: lambda.phylo=transform(tree,lambda) Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) : cannot coerce class phylo to a data.frame lambda.phylo=geiger::transform(tree,lambda) Error: 'transform' is not an exported object from 'namespace:geiger' Any one would point to a workaround for branch transformation and posterior visualization of the tree? Thanks in advance. Agus -- Agustín Camacho Guerrero. Doutor em Zoologia. Laboratório de Herpetologia, Departamento de Zoologia, Instituto de Biociências, USP. Rua do Matão, trav. 14, nº 321, Cidade Universitária, São Paulo - SP, CEP: 05508-090, Brasil. [[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] Cross-validation with independent contrasts
Thank you both, Ted and Joe, My first (or second) option would be doing what Ted suggested, but it will require a bit more coding than just using already existing functions. I will try to do that anyway, and compare the results to those from the cross-validation on the independent contrasts. Best, Diego On Fri, May 16, 2014 at 2:10 PM, Joe Felsenstein j...@gs.washington.eduwrote: Diego Bilski -- I'm wondering if it would be statistically/philosophically correct to use n-fold cross-validation to evaluate a linear regression with independent contrasts. My doubt comes from the fact that when simply dividing the IC dataset in, lets say, 10 folds, some folds will remove the contrasts of internal nodes without necessarily removing an entire clade above that point, producing what can be viewed as two independent clades (a graphical example would be, in Felsenstein's seminal paper, fig. 8, remove the contrast at node 13, while keeping those at nodes 9 and/or 10). and Ted Garland wrote: Couldn't you also just do this back at the level of the original tree and tip data, creating subsets by pruning the tree before you compute contrasts? Under the model of multivariate normality with Brownian Motion change along the phylogeny, the contrasts are i.i.d. so of course one can use them as points for cross-validation. But of course, unless the regression is nonlinear, there is already a parametric framework for distributions of regression coefficients (and other associated phenomena) in that i.i.d. MVN framework. The issue of what entities should be sampled in cross-validation depends on how, at what level, you expect the model to depart from multivariate normality with Brownian Motion. Diego and Ted seem to have some such expectation but I can't see what that alternative model would be. Joe Joe Felsenstein j...@gs.washington.edu Department of Genome Sciences and Department of Biology, University of Washington, Box 355065, Seattle, WA 98195-5065 USA [[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/ [[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] plot trees after different branch transformations
Thank you both, However, geo - get(data(geospiza)) lphy - rescale(geo$phy, lambda, 0.5) # transform tree in one fell swoop Error in colMeans(x, na.rm = TRUE) : 'x' must be numeric I got this error also for simulated and other real trees. 2014-05-16 15:24 GMT-03:00 Liam J. Revell liam.rev...@umb.edu: It looks like transform.phylo has been deprecated. Use rescale.phylo. 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 5/16/2014 2:20 PM, Agus Camacho wrote: Dear list users, Im trying to show what happens when we apply lambda transformations to a tree. For that, I was following swenson's book explanations: library(geiger) lambda.phylo=transform(tree,1) however, I got the following errors: lambda.phylo=transform(tree,lambda) Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) : cannot coerce class phylo to a data.frame lambda.phylo=geiger::transform(tree,lambda) Error: 'transform' is not an exported object from 'namespace:geiger' Any one would point to a workaround for branch transformation and posterior visualization of the tree? Thanks in advance. Agus ___ 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-ph...@r-project.org/ -- Agustín Camacho Guerrero. Doutor em Zoologia. Laboratório de Herpetologia, Departamento de Zoologia, Instituto de Biociências, USP. Rua do Matão, trav. 14, nº 321, Cidade Universitária, São Paulo - SP, CEP: 05508-090, Brasil. [[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/
