similar to: dendrogram ultrametrics

Lisa Holman Research Officer, Vegetation Dynamics Policy & Science Division NSW Department of Environment & Conservation PO Box 1967, Hurstville 2220. ph 02 9585 6507 fax 02 9585 6606 email lisa.holman@npws.nsw.gov.au The NPWS is part of the new Department of Environment & Conservation This message is intended for the addressee named and may contain confidential information. If

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

1. My earlier patch to fix a typo in array.h was not good enough. Here's one that not only compiles, but also doesn't crash: --- dovecot-2.0.alpha2/src/lib/array.h 2009-10-08 10:04:35.000000000 -0500 +++ dovecot/src/lib/array.h 2009-10-29 20:47:47.000000000 -0500 @@ -72,8 +72,7 @@ (elem)++) # define array_foreach_modifiable(array, elem) \ for (elem =

I am getting that pesky "Wine launcher is unable to find xmessage". I asked Mandrake Expert and was told that this is included in XFree86 version 4 (which I am running). I have searched for this file and still can't find it. Any ideas what I can do about it? I am running mdk 8.1. Regards, Jim

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

Good morning, I hate to bother everyone again, but I'm having some more trouble. I have a new machine with an MSI RS480M2-IL motherboard (ATI Xpress200 chipset) and a Hammer DVD Writer (shows up as a Matshita DVD-RAM SW-9585). I get the CD to start (in text mode - don't know why I can't do VGA or better), and it asks me What type of media contains the packages to be installed.

Howdy, I hate to bother everyone with something so simple, but I've beat my head bloody on this one. I have a new machine with an MSI RS480M2-IL motherboard (ATI Xpress200 chipset) and a Hammer DVD Writer (shows up as a Matshita DVD-RAM SW-9585). Anyway, I downloaded the CentOS 4.3 iso's and burned them to CD. When I boot the new machine it says: Boot CD: DISK BOOT FAILURE, INSERT

R 2.4.1 on Windows XP. Question: In traditional graphics, is it possible to find out the height of a line of text in units that can be used in arithmetic and then in calls to text()? Context: I have written a function that draws a plot and then, depending on whether some arguments are TRUE or FALSE, draws various lines of text in the plot. The text lines may be turned on or off individually

On 2/5/2015 12:56 AM, Steffen Kaiser wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > On Wed, 4 Feb 2015, George Sexton wrote: > >> I'm seeing two bogus messages appearing my Maildir/cur directory. >> They're dovecot.index.log and dovecot-uidlist. >> >> -rw------- 1 gsexton users 51 Feb 4 09:04 >> Maildir/cur/dovecot-uidlist:2,S

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

I'm seeing two bogus messages appearing my Maildir/cur directory. They're dovecot.index.log and dovecot-uidlist. -rw------- 1 gsexton users 51 Feb 4 09:04 Maildir/cur/dovecot-uidlist:2,S -rw------- 1 gsexton users 244 Feb 4 09:04 Maildir/cur/dovecot.index.log These files are only appearing in the Maildir/cur directory, and not in any other directory that mail is delivered to (e.g.

Hello All, Our samba server rarely shows up follwing message in syslog. When this message appears, CPU average will be pretty high. winbindd[9585]: [2007/11/28 15:55:02, 0] lib/util_str.c:safe_strcpy_fn(659) winbindd[9585]: ERROR: string overflow by 1 (256 - 255) in safe_strcpy [01092-6821 winbindd[9585]: S-1-5] Hardware: Dell PowerEdge 2950 OS: Red Hat Enterprise Linux ES4 Update 4

Hi All. I have many days reading and research about asterisk and vicidial. I thing this issue is about asterisk and doesnt about vicidial. Isn't it? I have a problem with theses application (I already ask for help in vicidial forums), but I can not fix it. I have debian 5 with asterisk 1.2.24 and vicidial 2.0.4. This server has a IAX tunnel with another asterisk server B which connect to

Dear all, i have a little trouble with cutting an understanding the handling of dendrogram and hclust. plotting clusters does work and it delivers a dendrogram. the problem is that the dendrogram shows lots of pretty small clusters and only some larger ones. i know that this has to do with my data. But is there possibility to tell the plot function just to plot the clusters with more than

Hello, I am a new R user and have a question regarding dendrogram coloring. I would like to color each leaf in the dendrogram (dhc) according to a specific criterion. For me this criterion is the gene name. For this, I created a data.frame with 2 variables: The gene name and the corresponding color. Using the following function, adapted from "dendrapply {stats}", I still have the same

Hi I've made a dendogram but I cannot label with text that I have on one of the columns of the data, anyone can help me thanks Ana [[alternative HTML version deleted]]

Hi all: I already made a dendrogram, I want to change the labels; In my data set there is one column with text that I want to set as the labels, any one can tellme how can I do it? Thanks, Ana Marcela [[alternative HTML version deleted]]

Hi, I am a beginner for R. I had use gplots to generate a heatmap as following: >heatmap.2(matrix, col=topo.colors(75), dendrogram="column", Rowv=FALSE, trace="none", key=TRUE, keysize=0.8, density.info="none", cexRow=0.2, cexCol=0.6) It work well. It generate heatmap whith rcolumn clustering dendrogram and I can export a very nice graph. But I don not know how

Dear all, I generated a heatmap with the heatmap() function with the default "complete" linkage method, but when I add the argument Rowv=as.dendrogram(hclust(dist(matrix), method="complete")), The dendrogram generated is different from the dendrogram produced by heatmap() with default settings. Could someone kindly point out where my mistakes are? P.S. When I did

Dear R friends, I have constructed an object of class 'dendrogram' using an own function, and I'm using the R function plot.dendrogram for visualizing it. It works fine, but I could not find out how to change the font size of edge and leaf labels. ?plot.dendrogram has shown me that the coloring of the edge labels can be changed using plot(my.dendrogram,