Re: [R-sig-phylo] Is correlation of PICs, with tip data and each terminal node split into male and female, a valid method?

Dear Alberto, I think the problem with including both males and females as separate datapoints in the analysis is that you're artificially doubling the sample size, which will make your statistical results difficult to interpret. Why don't you do two separate analyses (or three)? One with male

Re: [R-sig-phylo] multiple traits measured within species

Dear Kaspar, Are your traits the same? Basically, are the seven color patches on the same individual all one trait, or are they seven traits? Do all species have the seven color patches? Or are the number of color patches variable? (this could also be a character). I think before you attempt

Re: [R-sig-phylo] convergence issues with hansen model

Dear Pascal, Carl, and everyone, Thank you Carl for responding! It is also often helpful to increase the relative tolerance (reltol) parameter. By increasing the tolerance (making the value smaller) it sometimes helps with convergence. You can also use subplex rather than the methods available

Re: [R-sig-phylo] Normality requirement for assessment of lambda with phylosig (phytools) and fitContinuous (geiger)

Hi Nina and everyone, One thing to consider is that not all zero data are the same. Zeros under a model of continuous trait evolution with a gaussian process as assumed under Brownian motion and OU processes would occasionally cross zero, maybe go negative, etc. For example if you were modeling

Re: [R-sig-phylo] Best way to test correlation between discrete and continuous variables ?

Dear Julien, There is no problem with applying an ANOVA within a phylogenetic framework. This is essentially phylogenetic GLS, which you can implement easily with APE. You can have a look at Emmanuel's book (which was just recently came out in the second edition Nov. 2011, by the way). http://

Re: [R-sig-phylo] Ouch v.2.8-2 on the same tree gives different results (maybe)

Dear Elena, If I understand you correctly, you are trying to fit a unique regime to each branch of the tree? This is not advisable, as there are more branches than there are more branches than there are terminal taxa (data points). So you are trying to fit many more parameters than you have d

Re: [R-sig-phylo] on evolutionary models

Dear Pas, I am wondering what the general aim of your study is? I agree with Ted, that you should be careful about your assumptions and the tools you are using. Ted's point that K is a descriptive statistic is an important one. K describes the expected divergence among tip traits assuming a m

Re: [R-sig-phylo] obtaining reasonable values from OUCH

Good morning Pascal, We (Cressler, King, and myself) have a paper soon to be submitted that shows that model selection is very robust, but parameter estimates, esp. alpha and sigma are very difficult to estimate, because they have high variance. Although the bias is manageable, it is very har

Re: [R-sig-phylo] NEWBIE - ANOVA and PGLS for categorical data

Hi Anna, You may also want to try ouch. It allows you to fit models of adaptive evolution to continous data based on adaptation to selective regimes specified by the ecological factors. What you describe is exactly the situation that ouch was designed for. Another method OUwie, is along th

Re: [R-sig-phylo] Question on ace ML reconstruction of discrete binary character

Hi Tom, One thing to keep in mind is the information content of the data relative to what you are trying to infer. Basically, you have data only at the tips, but are trying to infer the state of the root deep in the tree. So therefore there is actually very little information being brought to b

Re: [R-sig-phylo] Question on ace ML reconstruction of discrete binary character

Oops. Sorry the citation is Schluter, Price, Mooers, Ludwig 1997. Likelihood of ancestor states in adaptive radiation. Evolution 51:1699-1711. This issue has been known for a long time. On Jul 30, 2013, at 6:51 AM, Marguerite Butler wrote: > Hi Tom, > > One thing to keep in mi

Re: [R-sig-phylo] compar.ou

2013 at 10:21 AM, sandra goutte wrote: >> >>> Thank you Marguerite. Looking at OUwie and OUCH/SLOUCH, i see that alpha is >>> estimated along the other parameters, whereas in Hansen 1997 and other >>> papers it is suggested that this would lead to very large standard e

Re: [R-sig-phylo] Trait simulations

Hi Sam and Jeremy, On May 19, 2009, at 11:34 AM, Sam Brown wrote: > > >> I was just wondering if there is a package or function in R that >> can simulate >> two continuous traits with a user-specified correlation coefficient >> using a >> known tree topology, branch lengths, and a model of Br

Re: [R-sig-phylo] ancestral trait reconstruction and OU model

well so that you end up at the proper "target" -- the data which you are trying to fit). Hope this is not too confusing. Take care, Marguerite Butler On Oct 26, 2009, at 8:53 AM, Andrew Hipp wrote: > Dear Fabio, > > In ouch v2 and up, the root state is not treated as a f

Re: [R-sig-phylo] Identifying nodes in ouch tree

Hi Alejandro, The info you want is given in the example script of the dataset bimac, which is included for ouch. To see the help page: require(ouch) data(bimac) ?bimac Then what you need is: tree <- with(bimac,ouchtree(node,ancestor,time/max(time),species)) plot(tree,node.names=TRUE) The opti

Re: [R-sig-phylo] Dealing with Bounded Trait Measures

Hi David, Liam and everyone, Reflecting traits at boundaries or absorbing them is something that can be done, but I guess I'd like to encourage everyone to think carefully about the interpretation of such simulations. What are you trying to model and what does it mean at the end? Doing these bo

Re: [R-sig-phylo] Dealing with Bounded Trait Measures

ot; traits, absorbing boundaries don't seem like a good model to me. I have never been able to think up a good biological mechanism for a reflecting boundary. Sorry for the extra email from the incomplete thought. M On Mar 5, 2011, at 8:50 PM, Marguerite Butler wrote: > Hi David,

Re: [R-sig-phylo] Dealing with Bounded Trait Measures

at measurements of > signal might be prone to odd results with the kludge, because the data > structure would still be quite different from BM expectation. Perhaps, > the threshold model might be of a lot of use here; I'm going to have > to look into that much more. > > T

Re: [R-sig-phylo] multi-state categorical predictor variables in PGLS

Hi Andrew, >> >> Does this sidestep the degrees of >> freedom problem discussed by Garland et al.? Can anybody point me to >> references discussing the mechanics of this process and why this is an >> appropriate thing to do? > Others on this list will disagree with me, but it's not a "degree

Re: [R-sig-phylo] How to detect phylogenetic signal (lambda) in one unscaled trait?

Hi Alberto and Ted, and others, Maybe this is too late to jump into the discussion, but I wanted to add a few comments regarding analysis of the evolution of size and shape. I agree with Ted that there are a number of important considerations: (1) size and its meaning, (2) how you remove it,

Re: [R-sig-phylo] How to detect phylogenetic signal (lambda) in one unscaled trait?

erite On Apr 1, 2011, at 7:57 AM, Marguerite Butler wrote: > Hi Alberto and Ted, and others, > > Maybe this is too late to jump into the discussion, but I wanted to add a few > comments regarding analysis of the evolution of size and shape. I agree with > Ted that there are a

Re: [R-sig-phylo] Interpretation of standard errors of parameter estimates in OUwie models

, Paleobiology > > Department of Geological Sciences > > Stanford School of Earth, Energy & Environmental Sciences > > williamgearty.com <http://williamgearty.com/> > > > > [[alternative HTML version deleted]] > > > >

Re: [R-sig-phylo] estimate ancestral state with OUwie models

FAX: 808-956-4745 http://butlerlab.org http://manoa.hawaii.edu/biology/people/marguerite-butler http://www2.hawaii.edu/~mbutler > On Jun 11, 2018, at 7:33 PM, Simone Blomberg wrote: > > This sounded wrong to me, as the OU process should be agnostic to the > dataset: There are no

Re: [R-sig-phylo] OU for non-ultrametric trees

.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > -- Marguerite A. Butler Professor Department of Biology 2538 McCarthy Mall, Edmondson Hall 216 Ho

Re: [R-sig-phylo] model averaging for discrete character evolution

.revell%40umb.edu%7Ce85015cb8c314c684bdc08d71b4c8fee%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637007887976657803&sdata=ogCaep2DN92bk6%2FZwOOcpmHaCPQwX7BzNgKo2UMcWtw%3D&reserved=0 > > > >> > > > [[alternative HTML version deleted]] > > __

Re: [R-sig-phylo] units of sigsq

r Department of Biology 2538 McCarthy Mall, Edmondson Hall 216 Honolulu, HI 96822 Office: 808-956-4713 Dept: 808-956-8617 Lab: 808-956-5867 FAX: 808-956-4745 http://butlerlab.org http://manoa.hawaii.edu/biology/people/marguerite-butler http://www2.hawaii.edu/~mbutler [[alternative HTML ve

Re: [R-sig-phylo] units of sigsq

nt of Biology 2538 McCarthy Mall, Edmondson Hall 216 Honolulu, HI 96822 Office: 808-956-4713 Dept: 808-956-8617 Lab: 808-956-5867 FAX: 808-956-4745 http://butlerlab.org http://manoa.hawaii.edu/biology/people/marguerite-butler http://www2.hawaii.edu/~mbutler [[alternative HTML version delete

Re: [R-sig-phylo] How to sort trait data according to tree

earchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > -- ____ Marguerite A. Butler Professor Department of Biology 2538 McCarthy Mall, Edmondson Hall 216 Honolulu, HI 96822 Office: 808-956-4713 Dept: 808-956-8617

Re: [R-sig-phylo] How to sort trait data according to tree

p)# calculate correlation separately gls(Y ~ X, dat, correlation = cbm) ## works! Thanks, Marguerite On Fri, May 14, 2021 at 10:21 PM Marguerite Butler wrote: > Aloha Oliver, > > From the cor.Brownian help page, the explanation for the form argument is > this: > > a

Re: [R-sig-phylo] How to sort trait data according to tree

is called. > > So you make it work by removing "dat$" in the call to corBrownian(): > > cbm <- corBrownian(1, tree, form = ~Species) > > Best, > > Emmanuel > > - Le 17 Mai 21, à 6:22, Marguerite Butler mbutler...@gmail.com a > écrit : > > &g

Re: [R-sig-phylo] How to sort trait data according to tree

. Thanks again for your kind replies, Marguerite On Sun, May 16, 2021 at 8:58 PM Emmanuel Paradis wrote: > - Le 17 Mai 21, à 13:41, Marguerite Butler a > écrit : > > Thank you very much for the reply Emmanuel! > > OK, yes I just tried and Iʻm surprised that this

Re: [R-sig-phylo] If my trait X cannot be regressed by body size, how can I rescue residuals corrected by the phylogeny and SE?

; 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 ar

Re: [R-sig-phylo] issue with reading matrix in R package DispRity

> 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/ > -- Marguerite