[R-sig-phylo] Flat likelihood and linear transformation of traits in fitContinuous

alpha OU100$Trait1$alpha # here the difference is impressive Thanks in advance for any feedback, Florian Boucher Laboratoire d'Ecologie Alpine, Grenoble, France trait Description: Binary data tree Description: Binary data ___ R-sig-phylo mailing lis

Re: [R-sig-phylo] Flat likelihood and linear transformation of traits in fitContinuous

em, though. > > Best wishes, > > Daniel > > On 20/11/2012 10:30, "Florian Boucher" wrote: > > Dear list, > > I came across a problem that could be interesting for some of you. > > While fitting various macro-evolutionary models to data, I noticed

Re: [R-sig-phylo] Flat likelihood and linear transformation of traits in fitContinuous

> A suggestion might be to also try fitting the models in OUwie. It uses > exactly the same parameter and likelihood estimators as geiger's > fitContinuous, but it will provide some additional results that may be > helpful for evaluating model fitting (i.e. SEs for the estimate

Re: [R-sig-phylo] how to modify tip label of a phylogenetic tree

Elaine, you can read the tree using the 'ape' package in R: library(ape) tree<-read.nexus('path_to_your_tree.nex') then, you will find the tip labels in the following vector: tree$tip.label you can change the names by selecting one element in the vector and modifying it, for example: tree$tip.la

Re: [R-sig-phylo] Lineages Through Time Plot with Confidence / HPD Interval

Hi Simon, one solution is to extract a vector of branching times and sort this vector for each tree (using branching.times in ape). >From that you can create a matrix with the branching events (ordered in time) as columns and the corresponding time in each tree as rows. Using the quantile function

Re: [R-sig-phylo] Distance matrix from phylogeny

Hi Eugen, to compute a distance matrix from a phylogeny, you can use the cophenetic.phylo function in {ape}. You then have to rescale all distances in you matrix (which are expressed in million years) by the total depth of the tree: dist=cophenetic.phylo(tree) dist2=dist/max(dist) Best, Florian

Re: [R-sig-phylo] phylogenetic tree manipulation

Dear Sereina, the transform.phylo function in the {geiger} package will help you do what you want: for (2) you may transform your original tree using the 'white' model or the 'lamba' model with a parameter of 0 for (3) a 'delta' model with a high value of delta (>1) will do what you want for (4)

Re: [R-sig-phylo] fitting multiple OU optima

chable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > -- Florian Boucher Postdoctoral researcher, Institute of Systematic Botany, Zürich [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-ph

Re: [R-sig-phylo] Prune very large tree

[[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@

Re: [R-sig-phylo] Fitting Brownian evolution with bounds

INDIA > > Ph: +91 80 2366 6504 > Mobile: +918050001886 > Email: saurabh...@gmail.com > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at

Re: [R-sig-phylo] multiple regression with binomial distribution

gt; 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/ -- Florian Boucher Postdoctoral researcher, Institute of Systematic Botany, Zürich

Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position

Hi Branchlizard and list, in order to do this you would first need to rename one of the foo's in each clade (I would always rename the first one) as '6 foo's', '4 foo's', etc. Then you can apply drop.tip on all the foos, as you did before. I hope this helps. Cheers, Florian 2016-09-14 21:32 GMT

Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position

plot(tree2) Let's hope this works as you wished. Cheers, Florian 2016-09-14 22:04 GMT+02:00 branchlizard . : > Florian and list, > > What is your preferred method to go about this? phy$tip.label? If so, how > would one label a tip label from each clade of foo's without having

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

uld be the "baseline model" Ted evoked in his post. I hope it helps... Florian Boucher PhD student, Laboratoire d'Ecologie Alpine, Grenoble, France 2011/1/28 David Bapst > Hello all, > > Apologies for leaving the replies to get cold for a week, but now I > finall

Re: [R-sig-phylo] phylogenetic circular linear regression

Hi Franz, I don't know about anything like what you propose but maybe you could sine-transform your trait and then use phylogenetic linear or logistic regression? Florian 2017-07-27 13:06 GMT+02:00 f.k...@mailbox.org : > Hi all, > > it there something like a phylogenetic circular linear regress

Re: [R-sig-phylo] phylogenetic circular linear regression

Hi again Frank, I just realized that a sine or cosine transformation would leave you with opposite colors on the hue having the same value... probably not so handy. Sorry, that was a poor suggestion... Florian 2017-07-27 14:09 GMT+02:00 Florian Boucher : > Hi Franz, > > I don

Re: [R-sig-phylo] Bounded Brownian model

Hi Roi, you can fit the BBM model using the 'BBMV' package. You will first need to create a likelihood function as follows: BBM <- lnL_BBMV(tree,trait,Npts=100,bounds=c(min(trait),max(trait)),a=0,b=0,c=0) And then you need to find the maximum of the likelihood function: fit_BBM <- find.mle_FPK(

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

Hi Karla, you're almost right, but since sigsq is the variance of the random walk per unit time its unit is actually [unit of the trait]^2/[unit of time] Cheers, Florian Le ven. 19 mars 2021 à 19:12, Karla Shikev a écrit : > Dear all, > > Please indulge me in a simple (newbie) question. > > If