similar to: Clustering and bootstrap

Dear listers, I need to export a distance matrix in the following format : a 0.0 1.0 0.2 1.0 1.0 b 1.0 0.0 1.0 1.0 1.0 c 0.2 1.0 0.0 1.0 1.0 d 1.0 1.0 1.0 0.0 1.0 e 1.0 1.0 1.0 1.0 0.0 I tried write.matrix() from the MASS library, which gives: a b c d e 0.0 1.0 0.2 1.0 1.0 1.0 0.0 1.0 1.0 1.0 0.2 1.0 0.0 1.0 1.0 1.0 1.0 1.0 0.0 1.0 1.0 1.0 1.0 1.0 0.0 Does anyone know of an R trick to change

Hello all, R just ''stopped working'' on my machine (ibook g4, os 10.3.9). between last time I used it and now, I did not do anything but check emails and browse the internet. when I try to start the GUI, it appears and disappears as rapidly. when I tried to run a session from the terminal, I got the following: mkdir: /tmp/Rtmp590-29493: Permission denied mkdir:

Dear Listers, I am trying to match tables that DO NOT have the same length. The tables result from the function "table()" so they look like this: table 1 2 3 4 3 5 7 table 2 1 2 3 6 4 5 I need the following output: (NOTICE THE ZEROS) 1 2 3 4 table1 0 3 5 7 table2 6 4 5 0 Unfortunately, I was not successful using "match()". Previous postings explain how to do

Dear listers, I am trying to assess variance components for a nested, mixed-effects model. I think I got an answer that make sense from R, but I have a warning message and I wanted to check that what I am looking at is actually what I need: my data are organized as transects within stations, stations within habitats, habitats within lagoons. lagoons: random, habitats: fixed the question is:

Dear listers, a central problem in conservation biology is the selection of sites in reserve network design. many algorithms have been published, and I was wondering any have been implemented in R. I did not seen anything on CRAN or R-help, or on the web in general. Best regards, Eric Eric Pante ---------------------------------------------------------------- College of Charleston, Grice

Hello Listers, I am trying to sample a vector to create a new one of sample length, witha sum equal to the sum of the initial vector: initial = 10, 30, 10 (sum=50) sample example = 5, 35, 10 (sum=50) or 25, 15, 10 (sum=50), etc ... My problem is to control the sum, so it stays constant. Any suggestions would be very helpful ! Thank you in advance, Eric

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

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",

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]]

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 all I have undertaken some phylogenetic and non-phylogenetic regressions with gls() in nlme with single preictor variables. A p value is associated with the intercept (upper p value) and another with the predictor variable (lower). Which p value is important? What does it mean if the intercept p value is insignificant but the predictor is still significant? Thanks a lot, and sorry for my

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

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

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

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

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

Dear all, I'm using the "ape" package in R and want to draw a phylogenetic tree with not only the tip labels but also some labels for the edges. e.g. Mark the edge AB as "m" in the tree ABC. Couldn't find a way to do that. Can someone help? Thanks, Hua

Dear List, I am not sure if A) this is possible or B) the correct place to ask. I am looking to find the mean - i have n, and the two-tailed confidence intervals 0.95 & 0.25 with a p-value of 0.05. Can i find the mean from this data ? Thanks Peter

Hello, I'm struggling with understanding the output on the ancestral.pars() command from the phangorn package, I'm new to doing phylogenetic analyses using R. I used it on nucleotide data, and it works fine, I'm just not sure how to read the output. The output is phyDat class, and outputs a matrix for each node/leaf in the tree. I figured out that the matrix columns represent the four

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,