Re: [R-sig-phylo] writing list of trees to file

) newlist - lapply(phylist, function(z) { z$tip.label - c(G,H,I,J,K) class(z) - phylo z }) class(newlist) - multiPhylo write.tree(newlist,file=newlist) On Mon, 2008-09-01 at 10:55 +1000, Simon Blomberg wrote: Try class(newlist) - multiPhylo Then use write.tree. Cheers

Re: [R-sig-phylo] writing list of trees to file

-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Simon Blomberg, BSc (Hons), PhD, MAppStat. Lecturer and Consultant Statistician Faculty of Biological and Chemical Sciences The University of Queensland St. Lucia Queensland 4072 Australia

Re: [R-sig-phylo] Correcting for body size using PGLS

question, but it was honestly over my head. Thanks in advance! Cheers, Eli Swanson ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Simon Blomberg, BSc (Hons), PhD, MAppStat

Re: [R-sig-phylo] r-squared for PGLS regression

A good general reference for r^2 is: @ARTICLE{generalized.r^-1, author = {Nagelkerke, N. J. D.}, title = {A Note on a General Definition of the Coefficient of Determination}, journal = {Biometrika}, year = {1991}, volume = {78}, pages = {691-692}, number = {3} } Simon. Simon

Re: [R-sig-phylo] PIC vs. PGLS

help. - Liam Liam J. Revell NESCent, Duke University web: http://anolis.oeb.harvard.edu/~liam/ NEW email: lrev...@nescent.org ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Simon Blomberg

Re: [R-sig-phylo] ape-package/ possibility to get the transformed residuals (phylogentic corrected residuals)?

___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat Lecturer and Consultant Statistician School of Biological Sciences The University of Queensland St. Lucia Queensland 4072 Australia T: +61 7 3365

Re: [R-sig-phylo] Model-Selection vs. Finding Models that Fit Well

___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat Lecturer and Consultant Statistician School of Biological Sciences The University of Queensland St. Lucia Queensland 4072

Re: [R-sig-phylo] phylogenetically-informed Reduced Major Axis regression in R?

...@gs.washington.edu Dept. of Genome Sciences, Univ. of Washington Box 355065, Seattle, WA 98195-5065 USA ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Simon Blomberg, BSc (Hons), PhD, MAppStat

Re: [R-sig-phylo] comparative analysis using multiple regression of contrasts?

/mailman/listinfo/r-sig-phylo -- Simon Blomberg, BSc (Hons), PhD, MAppStat. Lecturer and Consultant Statistician School of Biological Sciences The University of Queensland St. Lucia Queensland 4072 Australia T: +61 7 3365 2506 email: S.Blomberg1_at_uq.edu.au http://www.uq.edu.au/~uqsblomb/ Policies: 1

Re: [R-sig-phylo] query: how to use an existing covariance matrix directly in a gls procedure in R?

I used to do this before ape existed. Here is some example code. library(ape) data(bird.orders) # some made up data dat - data.frame(y=rnorm(23), x=rnorm(23)) rownames(dat) - bird.orders$tip.label mat - vcv(bird.orders, cor=TRUE) fit - gls(y~x, correlation=corSymm(mat[lower.tri(mat)],

Re: [R-sig-phylo] possible issue when incorporating a phylogenetic correlation structure (corPagel) in a linear mixed effect model (lme)

using the version 2.14.1 of R, 3.1-96 of nlme, and 3.0-1 of ape. Best, Rudolf -- Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat. Lecturer and Consultant Statistician School of Biological Sciences The University of Queensland St. Lucia Queensland 4072 Australia T: +61 7 3365 2506 email

Re: [R-sig-phylo] possible issue when incorporating a phylogenetic correlation structure (corPagel) in a linear mixed effect model (lme)

is: in which technique can we believe? I’m using the version 2.14.1 of R, 3.1-96 of nlme, and 3.0-1 of ape. Best, Rudolf -- Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat. Lecturer and Consultant Statistician School of Biological Sciences The University of Queensland St. Lucia Queensland 4072

Re: [R-sig-phylo] tips to root brach length

try diag(vcv.phylo(your.tree)) Cheers, Simon. On 03/09/12 19:17, boyang zhe wrote: Hi, everyone I am new to ape and R programming. I have an unrooted tree. I use root() function to reroot the tree by one outgroup. and then I try to extract root to tip distance. the tree$edge.length only

Re: [R-sig-phylo] PGLS on a sample of trees

://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat. Lecturer and Consultant Statistician School of Biological Sciences The University of Queensland St. Lucia Queensland 4072

Re: [R-sig-phylo] MCMC converged or not im MCMCglmm

help I am very grateful. Best, Sereina -- Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat. Senior Lecturer and Consultant Statistician School of Biological Sciences The University of Queensland St. Lucia Queensland 4072 Australia T: +61 7 3365 2506 email: S.Blomberg1_at_uq.edu.au http

Re: [R-sig-phylo] [R] APE

the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat. Senior Lecturer and Consultant Statistician School of Biological Sciences The University of Queensland St. Lucia Queensland

Re: [R-sig-phylo] The Value of Responding on R-sig-phylo, was: phytools - evaluating significance of pgls.Ives

, at 10:53 PM, Simon Blomberg s.blombe...@uq.edu.au wrote: Hi Ben, Yes, you would have to assume constant variance across species to use N=24. I think that is the only option. But given that biological data often has a positive mean-variance relationship, again I'm dubious about the exercise. YMMV

Re: [R-sig-phylo] phytools - evaluating significance of pgls.Ives

Am I missing something? The OP only has 8 species in the data set. I wouldn't put much store in fancy PCM modelling based on such a small data set. And 3 individuals per species is not enough for a good estimate of the within-species variance. Simon. Simon Blomberg, BSc (Hons), PhD, MAppStat

Re: [R-sig-phylo] phytools - evaluating significance of pgls.Ives

Hi Ben, Yes, you would have to assume constant variance across species to use N=24. I think that is the only option. But given that biological data often has a positive mean-variance relationship, again I'm dubious about the exercise. YMMV, however! Cheers, Simon. Simon Blomberg, BSc (Hons

Re: [R-sig-phylo] Non Parametric PGLS

://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat. Senior Lecturer and Consultant Statistician School of Biological Sciences The University of Queensland St. Lucia Queensland 4072 Australia T: +61 7 3365 2506 email: S.Blomberg1_at_uq.edu.au http

Re: [R-sig-phylo] How to embed a function within a matrix

much in advance, Alexandre -- Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat. Senior Lecturer and Consultant Statistician School of Biological Sciences The University of Queensland St. Lucia Queensland 4072 Australia T: +61 7 3365 2506 email: S.Blomberg1_at_uq.edu.au http

Re: [R-sig-phylo] plot trees distribution

d trees. > > PhD @ Biomathematics Research Centre > Room 523 - Erskine Building > University of Canterbury > Christchurch - New Zealand > > phone: +64 3 364 2987 ext 4869 > > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-p

Re: [R-sig-phylo] interpreting pGLS

chive.com/r-sig-phylo@r-project.org/ -- Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat. Senior Lecturer and Consultant Statistician School of Biological Sciences The University of Queensland St. Lucia Queensland 4072 Australia T: +61 7 3365 2506 email: S.Blomberg1_at_uq.edu.au http://www.evolutionarys

Re: [R-sig-phylo] summary stats for comparative methods p-values

ig-phylo@r-project.org/ -- Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat. Senior Lecturer and Consultant Statistician School of Biological Sciences The University of Queensland St. Lucia Queensland 4072 Australia T: +61 7 3365 2506 email: S.Blomberg1_at_uq.edu.au http://www.evolutionarystatistic

[R-sig-phylo] Bug in ape?

ales_0.4.1 I am not getting the error on two other machines with the same OS and (as far as I can tell) the same setup. Any help would be greatly appreciated! Cheers, Simon. -- Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat. Senior Lecturer and Consultant Statistician School of Biological Sc

Re: [R-sig-phylo] Bug in ape?

False alarm. I cleared my workspace and re-started R and the problem has gone away. I'm curious to know how it occurred but I'm happy that it has been resolved. We now return you to your scheduled R programming... Cheers, Simon. On 27/04/17 12:44, Simon Blomberg wrote: Hi Emmanuel