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

__ 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. Lecturer and Consultant Statistician School of Biological Sciences The University of Queensland St. Lucia Queensland 4072 Austra

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)], fixed

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

origin, i.e., for lambda=0 the log-like value is higher than for lambda>0, and for lambda>0 the log-like is only increasing with lambda. Thus a third question: why are these two profile log-likelihood curves different? The final question is: in which technique can we believe? I’m

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

bda>0, and for lambda>0 the log-like is only increasing with lambda. Thus a third question: why are these two profile log-likelihood curves different? The final question 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 -

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 stor

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] CI and PI lines for PGLS with Pagel's ML

r === [[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/ -- Simon Blomberg, BSc (Hons), PhD,

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

> simple funciton to do that? > For any 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

Re: [R-sig-phylo] PGLS confidence intervals?

ersion deleted]] > > ___ > R-sig-phylo mailing list -R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive athttp://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Simon Blomberg, BSc (Hons),

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, MAp

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

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

h floor, E end of bldg) UW-Madison Madison, WI 53706 608-262-1519 On Mar 1, 2015, at 10:53 PM, Simon Blomberg 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-vari

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

e https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read 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

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

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. Senior Lecturer and Consultant Statistician School of Biological Sciences The University of Queensland St. Lucia Queensland 4072 Australia

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

very 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

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

map| for painted 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 -

Re: [R-sig-phylo] interpreting pGLS

il-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://www.evolutio

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

-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/ -

[R-sig-phylo] Bug in ape?

i_1.1.5compiler_3.4.0 scales_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 Statis

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 Em

Re: [R-sig-phylo] [R-sig-eco] GEE and AIC

gt; R-sig-ecology mailing list > [EMAIL PROTECTED] > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Simon Blomberg, BSc (Hons), PhD, MAppStat. Lecturer and Consultant Statistician Faculty of Biological and Chemical Sciences The University of Queensland St. Lucia Qu

Re: [R-sig-phylo] GLS questions

ax: +44 (0)191 3346101 > > http://www.dur.ac.uk/isabella.capellini/ > http://www.dur.ac.uk/anthropology/staff/profiles/?id=2366 > > http://www.bu.edu/phylogeny/index.html > > ___ > R-sig-phylo mailing list > R-sig-phylo@r-projec

Re: [R-sig-phylo] [R-sig-eco] GEE and AIC

On Mon, 2008-06-02 at 15:34 +0200, Emmanuel Paradis wrote: [snip] > R> model.matrix(~ x)[, -1] >x2 x3 x4 > 1 0 0 0 > 2 0 0 0 > 3 1 0 0 > 4 1 0 0 > 5 0 1 0 > 6 0 1 0 > 7 0 0 1 > 8 0 0 1 Or even just model.matrix(~ x-1) Simon. --

Re: [R-sig-phylo] [R-sig-eco] GEE and AIC

x3 x4 1.2609972 -1.4974379 0.1920696 0.8274839 > coef(fit3) x2 x3 x4 -1.4974379 0.1920696 0.8274839 Cheers, Simon. On Tue, 2008-06-03 at 05:51 +0200, Emmanuel Paradis wrote: > Le 03.06.2008 03:16, Simon Blomberg a écrit : > > On Mon, 2008-06

Re: [R-sig-phylo] [R-sig-eco] GEE and AIC

t Yesterday was obviously not a good thinking day for my brain. Cheers, Simon. On Tue, 2008-06-03 at 16:01 +1000, Simon Blomberg wrote: > You're right. I was not thinking. If you are going to use independent > contrasts, you want ~ x -1, though, due to the necessity to fit the > m

Re: [R-sig-phylo] GLS with APE questions

.se > > Tel: ++46-18-471-2930 > > Web page: http://www.iee.uu.se/zooekol/default.php?type=personalpage > <http://www.iee.uu.se/zooekol/default.php?type=personalpage&id=146〈=en> > &id=146&lang=en > > > > > [[alternative HTML version de

Re: [R-sig-phylo] PIC in the case of a nonlinear relationship

but may have forgotten) that the paper only > covers cases where a transformation will linearize/normalize/ > standardize the variance of the data appropriately. > >Try compar.gee in APE or phylog.gls.fit in PHYLOGR. > >Ben Bolker > > >

Re: [R-sig-phylo] PIC in the case of a nonlinear relationship

forcing me to be more explicit on this. Cheers, Simon. On Thu, 2008-06-12 at 09:46 +1000, Simon Blomberg wrote: > That paper really annoyed me. Of course you can fit polynomial models, > or splines etc. or even nonlinear regression models to independent > contrasts. You do it the same

Re: [R-sig-phylo] Beta coefficients in R

ank you! > > > > Best wishes, > > > > Alejandro > > _______ > 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] writing list of trees to file

mes<-c("G","H","I","J","K") newlist <- lapply(phylist, function(z) { z$tip.label <- c("G","H","I","J","K") class(z) <- "phylo" z }) class(newlist) &

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

uot;) > +z > +}) > > write.tree(newlist,file="newlist") > Error in write.tree(newlist, file = "newlist") : > object "phy" is not of class "phylo" > > (and yes, write.tree did work on the multiphylo object before I d

Re: [R-sig-phylo] GLS slopes for study on allometry

864365 0.01356346 # phylogenetic effect is 99% of the residual variance. Simon. -- 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 Room 320 Goddard Build

Re: [R-sig-phylo] GLS slopes for study on allometry

945 Random effects: ~1 | species Variance list: mat2 species resid Standard Dev: 0.8626083 0.10114964 % Variance: 0.9864365 0.01356346 # phylogenetic effect is 99% of the total variance. Simon. -- Simon Blomberg, BSc (Hons), PhD, MAppStat. Lecturer and Consult

[R-sig-phylo] read.nexus in package ape

nexus gives us the following error: > tr2 <- read.nexus("tree6.txt") Error in trees[[i]] : subscript out of bounds Has anyone else come across this problem? Simon. -- Simon Blomberg, BSc (Hons), PhD, MAppStat. Lecturer and Consultant Statistician School of Biological Sciences Th

Re: [R-sig-phylo] read.nexus in package ape

> Reading NEXUS file aborted at tree no.1 > > > > > > I can fix that error by removing the extra pair of parentheses in your > > tree, e.g. > > > > tree Bioperl_1 = [&R] (c,(a, b)[]); > > > > which read.nexus() reads successfully for me. > >

Re: [R-sig-phylo] Confidence intervals on slope for RMA regression through origin?

-- Brian Sidlauskas > > * These are allometric slopes, and so we're interested in testing for > deviations from slope = 1. Ordinary least-squares regression tends to > underestimate the slopes pretty drastically. > > -- Simon Blomberg, BSc (Hons), PhD, MAppStat. Lecturer a

Re: [R-sig-phylo] multiple observations per species tip?

pecies, would be to make an > N-way polytomy at each tip - but this would be prohibitively slow when > sample sizes per species get larger, and it seems like there should be > a faster way. Is there an better way to incorporate multiple observations > per tip into a phylogenetic analysis? > &

Re: [R-sig-phylo] Kcal issue, related to CorSymm

[1,] 0.1138656 > > What is wrong (singular) with this tree that Initialize.corSymm (or the > associated gls call) doe snot handle ???!!! > > Any help or insight appreciated > Cheers > SebL > > > ___ > R-sig-phylo mailing

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

gt; > 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. Lecturer and Consultant Statistician School of

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] Newbie - PGLS with categorical data

No you do not have to use dummy variable coding if using gls or lme from the nlme packages. These functions use standard R methods to construct the design matrix themselves. So dummy coding IS used, but it is all behind the scenes. You can change the type of coding using the contrasts argument to t

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

d at the following URL: http://dx.doi.org/10./j.2041-210X.2010.00044.x or on my website (URL below). I hope this is of some help. - Liam Liam J. Revell NESCent, Duke University web: http://anolis.oeb.harvard.edu/~liam/ NEW email: lrev...@nescent.org ___

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

iling list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ___ 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 Statisticia

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

t.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 2506 email: S.Blomberg1_at_uq.edu.au

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

z.ch/mailman/listinfo/r-sig-phylo Luke Harmon Assistant Professor Biological Sciences University of Idaho 208-885-0346 lu...@uidaho.edu ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Si

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

Joe Felsenstein, j...@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 Bl