similar to: Plotting two distance matrices

Hi all, I've been having trouble reading in distance matrices (values in lower triangle only) that have been created by other programs. They load with NA values in the upper triangle. Is there an option to read the matrices properly? Thanks, Muri ____________________________________________________________________________________ that gives answers, not web links.

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, Using Vegan package I was wondering if there's a way to use a distance matrix as an input for adonis (or any of the other similar hypothesis testing functions) instead of the usual species by sample table. Working in the field of microbial ecology, what I'm trying to do is to overcome the problem of having to use discrete units such as species or OTUs, which are problematic in

Hi, Is there a way to make the filled.contour() function produce a plot similar to the image() function? i.e. not have smooth contours but rather distinct "squares" corresponding to the different cells of the matrix. The reason I ask is because since image doesn't have an option to display colour bars it is a lot less useful. Cheers Muri Soares Department of Maths and Applied

Hello, I would like to place shaded boxes on different areas of a phylogenetic tree plot. Since I can not determine how to find axes on the phylogenetic tree plot I am not able to place the box over certain areas. Below is example code for the shaded box that I have tried to use, and the first four values specify the position. rect(110, 400, 135, 450, col="grey",

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.

Dear moderator, If possible I would like to send in the following question for R-help: I am analyzing a small data set using PGLS with phylogenetic uncertainty taken into account and thereby including 100 potential phylogenetic tree scenarios. I've managed to run models on all of the different trees and performed model averaging to get parameter estimates for the intercept and most of the

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]

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

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]]

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 & bioconductor Sorry for cross-posting, this concerns R-programming stuff applied on Bioconductor context. Also sorry for this long message, I try to be complete in my request. I am trying to write a subset method for a specific class (ExpressionSet from Bioconductor) allowing selection more flexible than "[" method . The schema I am thinking for is the following:

friends, I need some tool to visualize the results of hierarchical clustering. Specifically, I want to plot it as a radial plot as a phylogenetic tree. In addition, I want to specify the color to each leaf node. I search all phylogenetic tree plotting routines here, they all cannot show the leaf nodes and their colors. Since i will have a lot of leaf nodes, the color needs to be specified and

Hi everyone, I have a matrix that contains 1000 replicates of a sample of a list of values. I want to group each row (row=replicate) into my defined bin ranges and then calculate the mean and stdev for each of the bin ranges (so I will have 1000 rows but ncol=number of bin ranges). I don't know how to group rows in a matrix matrix according to another vector (which is what I think I need to

Hello R Forum users, I was hoping someone could help me with the following problem. Consider the following "toy" dataset: Accession SNP_CRY2 SNP_FLC Phenotype 1 NA A 0.783143079 2 BQ A 0.881714811 3 BQ A 0.886619488 4 AQ B 0.416893034 5 AQ B 0.621392903 6 AS B 0.031719125 7 AS NA 0.652375037 "Accession"

In this years biostat teaching I will include Rcommander (it indeed simplifies syntax problems that makes students frequently miss the core statistical problems). But I could not find how to make a simple chisquare comparison between observed frequencies and expected frequencies (eg in genetics where you expect phenotypic frequencies corresponding to 3:1 in standard dominant/recessif

Dear all, I don't understand the following behaviour: Running compar.gee (in library ape ) with and without the option 'data', it give me different results Example: .... Start R .... > load("eiber.RData") > ls() [1] "gee.na" "mydata" "mytree" > library(ape) > # runnig with the option data= mydata > compar.gee(alt ~ R,

Dear coleges, How to use the genotype from microsatelite markers from many different populations to construct a tridimensional phylogenetic tree with R? Any suggestions? Thank you very much! Baron, Erica Dra. Erica Baron Universidade dos A?ores - Departamento de Ci?ncias Agr?rias Grupo de Biotecnologia - Campus de Angra Terra-Ch? 9701-851 A?ores - Portugal Tel. +351 295 402 235 Fax. +351 295

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

Hi everyone, I have a problem with running a glm using a subset of my data. Whenever I choose a subset, in the summary the factors arent shown (as if the variable was a continuous variable). If I dont use subsets then all the factors are shown. I have copied the output from summary for both cases. Thanks for the help, Muri > model<-glm(log(cpue)~year,family=gaussian) Call: glm(formula =