similar to: Justification of dendrogram labels

Hi all, I recently (today) updated the Matrix package and installed the latticeExtra package, but then when I tried to load the lme4 package, I got the following error message:- > library(lme4) Loading required package: Matrix Loading required package: latticeExtra Error in importIntoEnv(impenv, impnames, ns, impvars) : object(s) '.__C__lmeRep' are not exported by

Hi all, Wouldn't it be nice (??!!) if R automatically issued a warning message when the R console buffer was about to fill so that you could save all your output into a text file? (I know about sink(), but I think it would be good to have an easier mechanism to save a complete record of messages and function output). And on a similar vein, wouldn't it also be nice if R automatically

Hi list, I am doing cluster analysis using the cluster package. I created a dendrogram using the function plot(agnes(myData)). When I try to change the sise of labels, it does not work. I tried cex = 1.5, etc. Nothing worked. Can anyone give me a hint on how to change the sise of the labels, as well as the sise of axes labels. Thanks Mahdi -- ----------------------------------- Mahdi Osman

Hi all, I've ecountered a problem in the last few days with my .Rhistory file not being able to be updated when I quit an R session because its file attributes under Windows have been set as "Hidden". Recently, I put the following line in my global Rprofile file:- history(max.show=Inf) so that I automatically open the entire history file for a project when I begin a session, but I

Hi all, Just to follow up Don Driscoll's earlier post, can anyone please explain why "se.contrast" fails here?? > shp<-factor(rep(c("reserve","strip"),each=96)) > > > site<-factor(rep(c("1g","1p","1t","2g","2p","2t","3g","3p","3t","4g","4p

Hi all, Would someone like to comment on the relation between the "buffer bytes" and "lines" settings in the console settings? Are they interdependent? If so, how? And why allow both to be tweaked? If not, what is the effect of changing "lines", but leaving "buffer bytes" the same? I wanted to be able to see more of some large outputs in my console, as I

Hi all, Regular and avid readers of this column will know that Don Driscoll and I have recently posted two messages requesting assistance concerning an apparent failure of "se.contrast" to produce an se for a contrast. So far, an ominous silence rings in our ears, but read on Gentle Reader, and see if even the machinations of "debug" doesn't stimulate you to respond with a

I'm clustering rather large data sets and would like to cut the dendrograms to get a better view of specific components. I calculate the dissimilarity matrix using daisy() because I have a mixture of variable types: factors, ordered factors and numerical variables. If I want one dendrogram, I use agnes() for the agglomerative nesting and pltree() to draw the dendrogram. That way, I get the

Hello, I have recently noticed that in one of my work areas, a number of packages are automatically loaded without my explicitly requesting them to be loaded (see below). This only happens in one particular workspace (located in a folder). I suspect (without any real evidence) that this may be related to my creating plots using the ggplot2 package earlier in this workspace. I am running R 2.7.0

Well, you don't give much of an example.... I'm replying CC to the R mailing list. Please ask questions there, rather than adressing individuals for basic help. Here is one; does it answer your question ? data(agriculture) ag.ag <- agnes(agriculture) class(ag.ag) pltree(ag.ag) # the dendrogram, if you want to see it ## cut the dendrogram -> get cluster assignments: (ck3 <-

Hi all, I have a bit of a newbie question here that I hope y'all can help with. I've run a cluster analysis using hclust on about 500 objects (using R1.3 under Win 2000). The problem is that the tips of the dendrogram are so close together on the plot that the labels overlap and are unreadable. I've used "cex" to reduce the label sizes but this isn't sufficient with so

Hi, I am clustering objects using the agnes() function and the UPGMA clustering method (function = "average"). Everything works well, but apparently something is wrong with the dendrogram. For example: x<-c(102,102.1,112.5,113,100.3,108.2,101.1,104,105.5,106.3) y<-c(110,111,110.2,112.1,119.5,122.1,102,112,112.5,115) xy<-cbind(x,y) library(cluster) UPGMA.orig<-agnes(x)

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, Hurstville 2220.

Hi R helpers... I am having troubles because of the discrepancy between the dendrogram plotted from hclust and what is wrote in the hc2Newick file. I've got a matrix C: > hc <- hclust(dist(C)) > plot(hc) with the: > write(hc2Newick(hc),file='test.newick') both things draw completely different "trees"... I have also tried with the raw distance matrix D and

Hi, this is rather a (presumed) bug report than a question because I can solve my personal statistical problem by working with hclust instead of agnes. I have done a complete linkage clustering on a dist object dm with 30 objects with agnes (R 1.8.0 on RedHat) and I want to obtain the partition that results from a cut at height=0.4. I run > cl1a <- agnes(dm, method="complete")

Hi, this is rather a (presumed) bug report than a question because I can solve my personal statistical problem by working with hclust instead of agnes. I have done a complete linkage clustering on a dist object dm with 30 objects with agnes (R 1.8.0 on RedHat) and I want to obtain the partition that results from a cut at height=0.4. I run > cl1a <- agnes(dm, method="complete")

Dear list, is there a way how to add information to internal nodes (branching points) in dendrogram created via plot.agnes function (package cluster)? I wish to place colored circles on the nodes, but I don't know how to proceed... I'll be grateful for any suggestion Ond?ej -- Ond?ej Mikula Institute of Animal Physiology and Genetics Academy of Sciences of the Czech Republic Veveri 97,

Thanks a lot, Michael! I cc to R-help, where this question really belongs {as the 'Subject' suggests itself...} -- please drop 'bioconductor' from CC'ing further replies. >>>>> "michael" == michael watson (IAH-C) <michael.watson at bbsrc.ac.uk> >>>>> on Thu, 17 Jun 2004 09:16:59 +0100 writes: michael> OK, admittedly it

If there is a helpfile open (f.e ?glm) and it is the top window, then an exception error occurs (closing RGUI) when I hit the open file button. If the helpfile is not the top window (of the RGUI) I am able to open a new script without any error. The RGUI is not closing complete there is a blank screen left which I have to close with the X Button or Taskmanager Windows XP Home - German Version

Doing the normal build process [1] for a first time with a R 2.0.0 snapshot -- the Sep 21 version I uploaded to Debian's 'experimental' section two days ago, ended in failure. The package in question is cluster 1.9.6 which should be 2.0.0-ready. The (partial) log follows: ----------------------------------------------------------------------------- [...] g77 -mieee-fp -fPIC -g -O2