search for: ultrametrics

Dear R-help listers, Is anyone aware of a function that outputs dendrogram ultrametrics? Cheers, Lisa. PS please reply to me personally as well as to the list because the website wasn't letting me subscribe for some reason. thanks... Lisa Holman Research Officer, Vegetation Dynamics Policy & Science Division NSW Department of Environment & Conservation PO Box 1967, Hur...

I am beginning to work with the 'ape' package in R, and have run into some trouble. I generated a UPGMA tree based on DNA sequence distance in Paup* and read it into R, where it became an object of class "phylo". However, I need it to be classified as a "dendrogram" for my purposes (to use it to order the layout of a heatmap). I get an error using as.hclust.phylo

Hi, I'm trying to build a mixed-effects model in which I'd like to include either a distance matrix or a phylogenetic tree as a random effect. The troubles I've had are that: 1. Function lmer() in package lme4 only accepts a data frame column as a random factor and not a distance matrix. 2. Function MCMCglmm() in package MCMCglmm only accepts a rooted and ultrametric phylogenetic

Using Mathematica, I've performed a hierarchical clustering of 3,107 U. S. counties based on 1995-2000 intercounty migration, using an algorithm of my own devising (see http://arxiv.org/abs/0807.1550). I can also generate the associated 3,107 x 3,107 matrix of ultrametric distances. Unfortunately, as far as I have been able to determine, the Mathematica hierarchical clustering package only

Dear all, The version 1.0 of ape (analysis of phylogenetics and evolution) is now on CRAN. The jump from version 0.2-1 to 1.0 is explained by the fact that the initial objectives of the project have been completed. The relevant part of the Changes file is shown below. All comments, suggestions, or bug reports are welcome. Emmanuel Paradis CHANGES IN APE VERSION 1.0 NEW FEATURES

Take a look at lmekin() in the coxme package. The motivating data set for my development of coxme was the Minnesota Family Breast Cancer project: 24050 subjects in 462 families. The random effect is an intercept per subject with sigma^2 K as its variance where K is the kinship matrix (1 for self-self, .5 for parent-child or sib-sib, .25 for uncle-neice, etc). lmekin is a linear models front

Dear R-helpers, Christoph (author of phyloclim) and Luke (author of tkrplot), I would like to get your helps on installing of phyloclim in Ubuntu linux. It seems a package named 'tkrplot' could not be installed at firstly, then packages depends on it could not be installed latter. As I have tested, installation of phyloclim works smoothly in Mac. I attempted to install these packages in

Dear all, I'm trying to use phylo.pca function from phytools for the first time. I'm using an ultrametric tree with 167 tips and all branch lengths transformed to 1. I lunched the pPCA like this: pPCA<-phyl.pca(tree,data,method = "lambda") For some reason it takes for ever and never reaches the end of the process. I tried with method="BM" and the process runs

Hi, I have reconstructed ancestral character states on a phylogeny using MuSSE in the diversitree package and plotted the character state probabilities as pie charts on the nodes. I would, however, like to colour the character states of my extant species, i.e. the tip labels, the same colours as my pie charts, such that all species in state 1 are e.g. blue, species in state 2 red and species in

I've been comparing variables among objects (taxa) related by known trees, using phylogentically independent contrasts in the ape package, and want to move on to more complex models e.g. by using gls with appropriate correlation terms. My trees contain lots of (hard) polytomies and information about ancestors, which I've been including- creating fully dichotomous trees by using zero branch

Dear all, I wanted to let you know about four phylogenetic comparative methods (PCM) packages that have become available on (3 on CRAN and 1 on GitHub) recently that hopefully will be interesting to somebody. Three of them go significantly beyond the Brownian motion (BM) and Ornstein-Uhlenbeck (OU) processes. 1) There is a new version of mvSLOUCH available. The most important change is that the

Dear all, I wanted to let you know about four phylogenetic comparative methods (PCM) packages that have become available on (3 on CRAN and 1 on GitHub) recently that hopefully will be interesting to somebody. Three of them go significantly beyond the Brownian motion (BM) and Ornstein-Uhlenbeck (OU) processes. 1) There is a new version of mvSLOUCH available. The most important change is that the