similar to: Model Selection with Phylogenetic Independent Contrasts

Hi, Using Ape, I have constructed an object of class "phylo", using the method 'nj' (lets call the object 'tree_ja'). I also have a given subset of 'tree_ja' in a vector (lets call the vector 'subspecies'). What I want to do, is construct a nj tree - plot(tree_ja) - but have the species in vector 'subspecies' shown as red at the tips of the

I use R 2.15.2 on MacosX 10.8.2 I have a problem checking for a package that I want to submit in CRAN. When I check like that, no problem or warning are detected. system("R CMD check '[path]/phenology'") I create the .tar.gz package with that. The file phenology_3.43.tar.gz is generated. I can install the package and it works. system("R CMD build

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

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

Hi, I try to make my first package? The HelloWorld.R file is: #### HelloWorld.R #### #' showHello est une fonction R permettant d'afficher le message #' "Hello World!" sur la console. #' @title la fonction showHello() showHello <-function(){ cat("Hello World!\n") } I use the following procedure to get the tar: # set the working directory where the file is

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

Hello, I am trying to carry out a phylogenetic autoregression to test whether my data show a phylogenetic signal, but I keep calculating bizzare R-squared values. My script is: > library(ape) > x <-

Hello, I am trying to import a phylogenetic tree from Mesquite into R. When I use the read.nexus command I get the following message: Warning message: In matrix(x, ncol = 2, byrow = TRUE) : data length [589] is not a sub-multiple or multiple of the number of rows [295] A phylo object is created but I am unable to plot it (when I try R freezes) and I can tell by looking at the tip labels that

Dear R-er, For a non-linear optimisation, I used optim() with BFGS method but it stopped regularly before to reach a true mimimum. It was not a problem with limit of iterations, just a local minimum. I was able sometimes to reach better minimum using several rounds of optim(). Then I moved to optimx() to do the different optim rounds automatically using "Nelder-Mead" and

Apologies for the empty email earlier! I have species abundance data sampled at a weekly frequency or sometimes monthly depending on the year. The goal is to identify the dates in an annual cycle in which the cumulative abundance of a species reaches some threshold. Here's an example of the data for 1 species over an annual period: "mc_pheno" is the object created from this data:

Can you recommend an R library that will help me create a diagram of a phylogenetic tree on which specific images are placed at appropriate nodes of the tree? For example, I have specific image files associated with each member of the phylogenetic tree, and I would like to automate the display of the image next to the correct node of the tree. I can provide an image file with an example.

Hello, Is it possible to include information about phylogenetic relatedness among species (when species are replicates for each study within a meta-analysis) in a meta-anlaysis in the metafor package? Alternatively, I wonder if the method f Lajeunesse 2009 American Naturalist has been adopted in R in any fashion? Thanks, Scott Chamberlain [[alternative HTML version deleted]]

Hi I am looking for a package that 1. reads in a phylogenetic tree in NEXUS format 2. given two members/nodes on the tree, can return the distance between the two using the tree. I came across the following packages on CRAN ouch, ape, apTreeShape, phylgr all of which seem to provide extensive range of functions for reading in a Nexus-format tree and performing phylogenetic analyses, tree

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 all, I would like to ask you the following: I have data about different manuscripts, together with data about the presence/absence of copying errors, in the days when manuscript were really manuscripts. I would ideally like to use the data to draw a phylogenetic tree, so that I can infer which ms was copied from which. The error presence/absence is coded in binary format. The plan is to use

Hello, My name is Sivan and I am a master degree student in statistics,my problem is as follows: I have a dataset containing gene sequences and I would like to create a phylogenetic tree from it. The problem that I can't seem to find a function to do this kind of operation. I read the ape package manual and I haven't found a command that takes raw data and turns it into a tree. does anyone

Hello R users, Can any one please help me to find a way to build phylogenetic tree by R program from any distance matrix. Suppose I have a data like : MATRIX [1] '1' 0.0 [2] '2' 0.071 0.0 [3] '3' 0.036 0.286 0.0 [4] '4' 0.429 0.75 0.714 0.0 [5] '5' 0.679 0.179 0.214 0.536 0.0 [6] '6' 0.893 0.929 0.964 0.464 0.357 0.0 [7]

Let's say I would like to look inside the function corBrownian in library (ape). When I type in the function name I get the following, which is not nearly the detail that goes into this function. I am wondering how to begin cracking this function open (and others) so I can learn more about it and perhaps code my own corClass one day. Thanks. > corBrownian function (value = 1, phy, form

Hi all, I want to calculate distances between phylogenetic trees. I found functions for symmetric difference (e.g. in ape and in some other packages). In addition to this I also want to calculate quartets and nearest neighbor interchange distances; are there any functions for this? My apologies if they exist and I overlooked. best regards