Re: [R-sig-phylo] Phylogenetic Signal in Internal Node Data

Hi Matt, You can think about a randomization procedure: rTraitDisc(), rTraitCont(), and rTraitMult() all have the option 'ancestor' to output the values of a trait simulated along a phylogeny for all terminal and internal nodes. HTH Best, Emmanuel - Le 27 Jan 21, à 0:42, Matthew Helmus m

Re: [R-sig-phylo] Phylogenetic Signal in Internal Node Data

I can think of a kludge approach for a single trait. Use Felsenstein's phylogenetically independent contrasts. Work down from the tips, calculating the internal nodes as specified by the algebra of the method. Stop when you get to a set of nodes of interest. Use the methods in Blomberg et al. (2003

[R-sig-phylo] Phylogenetic Signal in Internal Node Data

Hello, Is there a method that can test for phylogenetic signal in data associated with the internal nodes of a tree rather than data associated with tree tips? Thank you! Matt -- Matthew R. Helmus, Ph.D. Integrative Ecology Lab Ce

Re: [R-sig-phylo] phylogenetic signal with sample sizes but no standard errors

There is also an implementation of this method in two functions in ape, see: ?pic.ortho ?varCompPhylip There are examples with simulated data in both help pages. The second function requires PHYLIP (similarly to Rphylip) . Best, Emmanuel Le 04/08/2017 à 14:36, Joe Felsenstein a écrit : The

Re: [R-sig-phylo] phylogenetic signal with sample sizes but no standard errors

There is also my C program Contrast, which implements a method from a 2008 paper I wrote: Felsenstein, J. 2008. Comparative methods with sampling error and within-species variation: contrasts revisited and revised. American Naturalist 171: 713-725. This estimates the within-species covariances

Re: [R-sig-phylo] phylogenetic signal with sample sizes but no standard errors

The original paper is here, with Matlab code. Others can tell you where this is in R. Ives, A. R., P. E. Midford, and T. Garland, Jr. 2007. Within-species variation and measurement error in phylogenetic comparative methods. Systematic Biology 56:252–270. Cheers, Ted On Wed, Aug 2, 2017 at 7:50

[R-sig-phylo] phylogenetic signal with sample sizes but no standard errors

Dear list users, I'm interested in testing for phylogenetic signal in a trait of parasites: the number of host species a parasite infects. I have a phylogeny for the parasites and I have tabulated the number of host species each parasite infects from the literature. However, some parasites are wel

Re: [R-sig-phylo] phylogenetic signal different from BM and random

here is an answer that is clear, simple, and wrong.' (Henry Louis Mencken) -- *Von:* Theodore Garland <mailto:theodore.garl...@ucr.edu> *Gesendet:* Mittwoch, 30. November 2016 18:38 *An:* Menzel, Dr. Florian *Cc:* r-sig-phylo@r-project.org<mailto:r-sig-

Re: [R-sig-phylo] phylogenetic signal different from BM and random

gt; > -- > *Von:* Theodore Garland > <mailto:theodore.garl...@ucr.edu> > *Gesendet:* Mittwoch, 30. November 2016 18:38 > *An:* Menzel, Dr. Florian > *Cc:* r-sig-phylo@r-project.org<mailto:r-sig-phylo@r-project.org> > *Betreff:* Re: [

Re: [R-sig-phylo] phylogenetic signal different from BM and random

G_HTML.php > > Gemeinsam einen Unterschied machen! > www.synagieren.de > > 'For every complex problem there is an answer that is clear, simple, and > wrong.' (Henry Louis Mencken) > > > -- > *Von:* Theodore Garland > *Gese

Re: [R-sig-phylo] phylogenetic signal different from BM and random

nd Gesendet: Mittwoch, 30. November 2016 18:38 An: Menzel, Dr. Florian Cc: r-sig-phylo@r-project.org Betreff: Re: [R-sig-phylo] phylogenetic signal different from BM and random Dear Florian, What do you mean, exactly? Do you mean the K statistics is, say, about 0.5, and that the randomizaton te

Re: [R-sig-phylo] phylogenetic signal different from BM and random

Gesendet: Mittwoch, 30. November 2016 18:38 An: Menzel, Dr. Florian Cc: r-sig-phylo@r-project.org Betreff: Re: [R-sig-phylo] phylogenetic signal different from BM and random Dear Florian, What do you mean, exactly? Do you mean the K statistics is, say, about 0.5, and that the randomizaton test

Re: [R-sig-phylo] phylogenetic signal different from BM and random

Dear Florian, What do you mean, exactly? Do you mean the K statistics is, say, about 0.5, and that the randomizaton test for phylogenetic signal (Blomberg et al. 2003), which is based on the MSE not K, is significant, indicating that you do have some degree of signal (more than zero)? Cheers, Te

[R-sig-phylo] phylogenetic signal different from BM and random

Dear all, I am analysing phylogenetic signal using Blomberg's K. For several of my traits (univariate, continuous), the signal strongly deviates both from random and from the Brownian Motion. I am unsure how to interpret this. Can you give me some advice what this could mean? Thanks a lot!

[R-sig-phylo] phylogenetic signal test for discrete trait

Dear all, I would like to test for phylogenetic signal in a discrete trait with 3 states (trait “str”) and another discrete trait with 7 states (trait “hab") using Pagel’s lambda. I have tried to apply the function “fitDiscrete” in geiger to my data, but not sure whether this is correct or not

Re: [R-sig-phylo] phylogenetic signal-Blomberg's K

Regarding question (1) here is a solution that I posted earlier: http://blog.phytools.org/2014/12/testing-hypothesis-that-phylogenetic.html. All the best, Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.

[R-sig-phylo] phylogenetic signal-Blomberg's K

Dear r-sig-phylo community, I am analysing phylogenetic signal in univariate quantitative traits in insects. I use Blomberg's K (command phylosignal, library picante). Here I have two questions: - how can I test whether K differs from the Brownian Motion Model? - is it safe to assume phylogene

[R-sig-phylo] Phylogenetic signal

Dear all, I was trying to find the pylogenetic signal for a trait and I used phylosig(): phylosig(tree, trait, method="lambda", test=TRUE, nsim=999) If I use, for instance, a lambda correlation in a gls, am I expected to obtain the same value? gls(trait~var1+var2, corPagel(value=1,phy=tree,fixe

[R-sig-phylo] phylogenetic signal in binary traits

Dear all, I have calculated phylogenetic signal on a binary trait (using the phylo.d function from the caper package), and, given that I found significant phylogenetic signal, I would now like to know which clades are responsible of this signal. Does anyone know if it is possible to estimate this?

Re: [R-sig-phylo] Phylogenetic signal in MCMCglmm

Hi Shinichi, Thanks so much for the prompt and detailed response. I should've reread some of that literature before writing to the list-serv. So, what I am gathering from your answer is that it is unnecessary to co-estimate lambda and transform the tree's branch lengths by it, since lambda is

Re: [R-sig-phylo] Phylogenetic signal in MCMCglmm

Hi, Daniel lamda and H^2 are equivalent as we say in Hadfield and Nakagawa (2010) or said also in Housworth et al (2004) Housworth E, Martins E, Lynch M (2004) The phylogenetic mixed model. Am Nat 163(1):84–96. lamda = var(phylo)/(var(phylo)+var(residuals)) A mathematical proof of this is in

Re: [R-sig-phylo] Phylogenetic signal in MCMCglmm

Dear R-sig-phylo list, I'm following up on a, seemingly unaddressed question from August 2013 about whether or not MCMCglmm co-estimates Pagel's lambda within a phylogenetic regression. Seraina's original message is copied at bottom. From what I can tell MCMCglmm doesn't co-estimate lambda,

Re: [R-sig-phylo] 'phylogenetic signal' of a tree independently from a character

Hi Mattia, The saturation plot is a classic exercise with ape: see ?dist.dna. This function allows you to count the numbers of Ts or Tv, or any kind of distances. Then using standard plot commands in R, you can make your own satutation plots easily. See ?delta.plot in ape for another method.

[R-sig-phylo] 'phylogenetic signal' of a tree independently from a character

Hi all, I know there's plenty of methods (many already available in R) to evaluate phylogenetic signal of a tree with respect to a character. But I have found the term 'phylogenetic signal' also in the context of a sole alignment/tree without the presence of associated characters. For instance, a w

Re: [R-sig-phylo] Phylogenetic signal, variation in rates and sample size

"I tried Brownian rate parameter estimation by tranforming the branch lengths according to the lambda values of trait in each group. It gives me lower varaince for the group that has higher lambda value and that is confusing. In fact with the same trait values, if I transform the branch length

Re: [R-sig-phylo] Phylogenetic signal, variation in rates and sample size

Dear All,Thank you very much for your suggestions. It is really helpful. I will go through all these and hopefully understand it. Best regards,Imran Khaliq From: omeara.br...@gmail.com Date: Mon, 5 May 2014 13:26:16 -0400 Subject: Re: [R-sig-phylo] Phylogenetic signal, variation in rates and

Re: [R-sig-phylo] Phylogenetic signal, variation in rates and sample size

> -Dan Gates > PhD candidate > Smith/Pilson Lab University of Colorado/Nebraska > http://ec2-54-186-114-109.us-west-2.compute.amazonaws.com:8080/DanielJGates > > From: r-sig-phylo-boun...@r-project.org > on behalf of imran khaliq > Se

Re: [R-sig-phylo] Phylogenetic signal, variation in rates and sample size

mith/Pilson Lab University of Colorado/Nebraska http://ec2-54-186-114-109.us-west-2.compute.amazonaws.com:8080/DanielJGates From: r-sig-phylo-boun...@r-project.org on behalf of imran khaliq Sent: Monday, May 5, 2014 5:15 AM To: r-sig-phylo@r-project.org Subjec

[R-sig-phylo] Phylogenetic signal, variation in rates and sample size

Dear All, I am trying to understand the effects of incomplete phylogenies on the phylogenetic signal. I am using different trees and I have at least 100 species in each tree but still these are only 2 % of total species. So how can I be sure that results are generalize enough to apply on the who

[R-sig-phylo] Phylogenetic signal in MCMCglmm

Dear MCMCglmm users,   I am running a simple model corrrecting for phylogenetic relationships using MCMCglmm. Now I am interested in the phylogenetic signal, the analogue to Pagels lambda.   Now I have two questions: 1.) According to Hadfield and Nakagawa (2010) the analogue to lambda (Pagel)

Re: [R-sig-phylo] Phylogenetic signal and PGLS

Hi, ASReml is another option, which uses REML. It takes 1/10th of a second on a 1000 tip phylogeny and is considerably more flexible. fit<-asreml(y~x,random=~giv(species),data=dat,ginverse=list(species=sm2asreml(Ainv))) # with the data set up as: ntips<-1000 tree<-rcoal(ntips) # si

Re: [R-sig-phylo] Phylogenetic signal and PGLS

Thanks to everyone for your suggestions, the input has been very useful! Antigoni On 11/28/2012 08:36 PM, Liam J. Revell wrote: Hi Antigoni. The other responders are correct, but just to be a little more concrete: # using ape & nlme library(ape); library(nlme) # assuming your data are contain

Re: [R-sig-phylo] Phylogenetic signal and PGLS

Hi Antigoni. The other responders are correct, but just to be a little more concrete: # using ape & nlme library(ape); library(nlme) # assuming your data are contained in named vectors x & y y<-y[names(x)] fit<-gls(y~x,data.frame(x,y),correlation=corPagel(1,tree,fixed=FALSE),method="ML") # assum

Re: [R-sig-phylo] Phylogenetic signal and PGLS

Hi Antigoni, I would also suggest looking at the caper package by Orme et al. (http://cran.r-project.org/web/packages/caper/index.html) it has PGLS with lambda transforms and it allows you to look at the likelihood surface for the lambda estimate as well. Sam ---

Re: [R-sig-phylo] Phylogenetic signal and PGLS

o Gonzalez Voyer [alejandro.gonza...@ebd.csic.es] Inviato: mercoledì 28 novembre 2012 18.16 A: Antigoni Kaliontzopoulou Cc: Oggetto: Re: [R-sig-phylo] Phylogenetic signal and PGLS Hi Antigoni You can try ape (and nlme) with the functions gls and corPagel (the latter to define the covariance structu

Re: [R-sig-phylo] Phylogenetic signal and PGLS

Hi Antigoni You can try ape (and nlme) with the functions gls and corPagel (the latter to define the covariance structure, ie the evolutionary model) and also caper (I don't know the exact function there). Cheers Alejandro _ Dr. Alejandro Gonzalez Voyer E

[R-sig-phylo] Phylogenetic signal and PGLS

Hello everyone, I am trying to implement Liam Revell's suggestion on the evaluation of Pagel's lambda simultaneous to fitting PGLS to minimize the effects of wrong model selection (OLS vs. PGLS) on species data (i.e. Revell 2010, Methods in Ecology and Evolution 1: 319-329). Does anyone know

[R-sig-phylo] phylogenetic signal in parasite-host associations

Dear all, I am comparing parasite (insect herbivores) and host (plant) phylogenetic trees. These insects are specialised and mostly monophagous, but some colonize up to seven different (related) plant species. One plant species can be colonized by up to 3 different parasite species. So it is a

[R-sig-phylo] phylogenetic signal on multistate discrete traits

Hi all, I am new to this forum and also new to phylogenetic analysis. I am trying to study phylogenetic signal on traits from plant communities following an environmental gradient. Part of my traits are continuous and for them I have used Blomberg's K. However for the multistate discrete traits I