Re: [R-sig-phylo] Count the number of character/state changes in a tree

Hi Luiz, didn’t try that out, but here is some code I wrote for some of the megaphylogenies I produced where you don’t want to search in a pdf or so where the transitions are… It’s two months ago so don’t know if it was totally save I think you should make sure the order of the tree and tip.sta

Re: [R-sig-phylo] Array of all branch lengths

Hi Rémi, those are stored in your phylo object: phy <- read.tree(“yourtree.tre”) phy$edge.length You find the components of the phylo object if you type ?phylo. Best, Franz > On 04 Mar 2015, at 15:24, Rémi Tournebize wrote: > > Hello everyone, > > I am new to ape and I beg your pardon if my

Re: [R-sig-phylo] Ancestral state problem (length of phylogenetic and phenotypic data don't match)

Hi Hannah, if you provide MCTree then I guess the first column is the species and the second column is the character vector. Try providing only the state vector. I think in this case “length” does count the length of your MCTree data.frame which would be 2 and not the length of your character v

[R-sig-phylo] corDISC binary coding problems

Hello, I have used the Pagels 94’ extended version in corDISC with 3 binary traits and 1300 species. To be able to use it, I had to code two binary character out of a continuous. My continuous variable is substrate proportion data. So 100% is gymnosperm exclusivity, 0% is gymnosperm exclusivity

[R-sig-phylo] convergence problem using phyloglm and IG10

Hello, after a discussion with Brian (see [R-sig-phylo] corDISC binary coding problems, 04/15) I used the method from Ives and Garland (2010), which is implemented in the R package phylolm. The problem is, that the likelihood estimator does not converge. Here is my code: fit <- phyloglm(rot.fi

Re: [R-sig-phylo] testing for variation in rates of evolution among traits

Hi, don’t know if this is what you search, but have a look at following publication: Mayrose & Otto 2011, A likelihood method for detecting trait-dependent shifts in the rate of molecular evolution. and function “traitrate” in package “ips” Best, Franz BSc. Franz Krah Mobile: 0170 5221189 Eco

[R-sig-phylo] test random drift only?

Dear everyone, I want to test if a trait evolved by random drift only without selection. My hypothesis regarding a specific trait - I don’t want to tell which if it turns out to be a good idea ;-) - is, that there is no selection acting on it and it is evolving by random mutations only. Thus u

[R-sig-phylo] REML version of Lynch1991?

Hi all, is there a REML implementation of the Lynch 1991 method in R? I found the implementation with the EM method in APE, however, my data size is big (>2000 terminals) and calculations really slow, considering that you have to start stuff several times… If its not there, can anyone implement

Re: [R-sig-phylo] Error in PGLS

Hi Nicolas, can u please do class(DIV) `DIV` does not sound like a phylogeny though… > On 11 May 2017, at 12:26, Nicolas Brualla > wrote: > > Hi, i'm asking you because, when i try to run my script on R with this > command : > > pglsModelLambdaD <- gls(lnBRW ~ lnBW, correlation = corPa

Re: [R-sig-phylo] Add terminal branches to tree

Hi Sergio, try ‘bind.tip' and just make a loop to add more. Or ‘bind.tree’ if you want to add a clade. Cheers, Franz > On 19 Jun 2017, at 13:58, Sergio Ferreira Cardoso > wrote: > > Hello all, > > I'm using the package 'phytools' to try to add terminal branches to a tree > (attached). I

[R-sig-phylo] phylogenetic circular linear regression

Hi all, it there something like a phylogenetic circular linear regression or such? I want to test if the hue (circular 360°) of species differs between two lifestyles? Hope someone can help? If this is not there please also let me know. Cheers, Franz