Re: [R-sig-phylo] PGLS transformations

Hi Sergio. Yesterday you asked if it would be reasonable to use the tree with branch lengths simulated assuming a Yule process if the topology is known in phylogenetic regression. I wondered what would happen if, for a given tree topology, we simulated a set of trees with branches as if the

Re: [R-sig-phylo] PGLS transformations

Thank you Liam. I'll check it now. Best regards, Sérgio. 2015-04-14 18:27 GMT+01:00 Liam J. Revell liam.rev...@umb.edu: Hi Sergio. Yesterday you asked if it would be reasonable to use the tree with branch lengths simulated assuming a Yule process if the topology is known in phylogenetic

Re: [R-sig-phylo] PGLS transformations

Than you all. Best regards, Sérgio. ᐧ 2015-04-13 22:02 GMT+01:00 Emmanuel Paradis emmanuel.para...@ird.fr: Le 13/04/2015 19:13, Sergio Ferreira Cardoso a écrit : Hello, Thank you both for the help. Emmanuel, so is there a way to see contrasts in R? Yes! The function pic() has been in

Re: [R-sig-phylo] PGLS transformations

Ferreira Cardoso [sff.card...@campus.fct.unl.pt] Sent: Monday, April 13, 2015 10:13 AM To: Emmanuel Paradis Cc: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] PGLS transformations Hello, Thank you both for the help. Emmanuel, so is there a way to see contrasts in R? Reading this paper - Garland

Re: [R-sig-phylo] PGLS transformations

Hello, So what you're suggesting is that I do that and then fit-gls(X~Y,corr=corBrownian(1,t.pb),data=df,method=ML, right? Thanks. Best regards, Sérgio. ᐧ 2015-04-13 18:42 GMT+01:00 Liam J. Revell liam.rev...@umb.edu: Hi all. I just wanted to add that it should be straightforward to sample

Re: [R-sig-phylo] PGLS transformations

Hi all. I just wanted to add that it should be straightforward to sample edge lengths as if they arose under a specific process. For instance, here on my blog I show how to sample branching times edge lengths as if they arose under a pure-birth (i.e., 'Yule') process, given a particular

Re: [R-sig-phylo] PGLS transformations

Le 13/04/2015 19:13, Sergio Ferreira Cardoso a écrit : Hello, Thank you both for the help. Emmanuel, so is there a way to see contrasts in R? Yes! The function pic() has been in ape since its first release (ver. 0.1 in Aug 2002), and there is an option to output the contrasts scaled or not.

Re: [R-sig-phylo] PGLS transformations

Hi Sérgio, There is indeed generally a relationship between branch length transformations and correlation structures. You may check that with the function vcv2phylo, e.g.: tr - rcoal(20) co - corGrafen(1, phy = tr) ts - vcv2phylo(vcv(co)) all.equal(tr, ts) [1] FALSE

Re: [R-sig-phylo] PGLS transformations

, April 12, 2015 12:47 PM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] PGLS transformations Hi everyone, I'm relatively new in phylogenetic comparative methods. I'm a little confused about branch length transformations. I'm using a tree with divergence time (My) as branch lengths. When I use

[R-sig-phylo] PGLS transformations

Hi everyone, I'm relatively new in phylogenetic comparative methods. I'm a little confused about branch length transformations. I'm using a tree with divergence time (My) as branch lengths. When I use corPagel, corGrafen or corMartins in R, the branch lengths, are the branch lengths automatically