similar to: question about hierclust {multiv}

my major is bioinformatics, and i'm trying to cluster ( agglomerate the closest pari of observations ) in R. i have already got my own similarities metric, but do not know how to clust it based on similarities instead of dissimilarities. since the help document of hierclust mentions the parameter "sim", which seems good to me, but it doesn't appear in the code of hierclust()

I use hierclust (hierarchical clustering) in multiv package. In the documentation it is said that plclust (plotting a dendrogram) is available in S-plus. Can I find it anywhere (I have searched through http://lib.stat.cmu.edu/S and found only quotations of plclust in multiv) or is it only part of the S package (which I don't have)? Thanks --------------- Charles RAUX, Laboratoire

Hallo Friedrich, I have read your announcement, downloaded and installed it in R-0.61.3. But now I have problems :) > hc <- hierclust(dist(t(pollen)), method=3) Error in pmatch(x, table) : argument is not of mode character > hc <- hclust(dist(t(pollen))) > members(hc) Error in .Fortran("assgn", n = as.integer(n), nplus1 = as.integer(nplus1), : C/Fortran function not in

Dear R-help list members i would like to use R to produce clustering or partitioning of a dataset. I am trying to use the functions: - hierclust() of the package multiv -pam(), agnes() and fanny() of the package cluster But I cannot get any result because of lack of memory. Would you know any clustering function not to greedy in memory? I have tried to expand my memory limit with memory.limit()

I've ported F. Murtagh's statlib package "multiv" to R, it can be found in the usual place on CRAN. Contents: bea Bond Energy Algorithm ca Correspondence Analysis supplc Supplementary Columns in Correspondence Analysis supplr Supplementary Rows in Correspondence Analysis flou

I've ported F. Murtagh's statlib package "multiv" to R, it can be found in the usual place on CRAN. Contents: bea Bond Energy Algorithm ca Correspondence Analysis supplc Supplementary Columns in Correspondence Analysis supplr Supplementary Rows in Correspondence Analysis flou

Hi, all. I'm trying to cluster 12,500 objects using hclust from package mva. The distance matrix takes up nearly 600 MB. The distance matrix also needs to be copied when being passed to the fortran routine that actually does the clustering (it's modified during the clustering), so that's 1200 MB. I'm actually on a machine with 2.5 GB of memory (and nothing else running), so I

Hello, a. is there a possibility to obtain a distance matrix with the cosine between vectors?? hclust, hierclust, dist will not work and seem to be hard to extend. b. if there is not: Is the cosine between vectors implemented somewhere? Thanks for all hints and advice! Petra Steiner -------------- next part -------------- An HTML attachment was scrubbed... URL:

What happened to multiv package? I have installed R 2.0.0 in my Mac and I could not find this package. I see other things have been reorganized. I have read "What's New" and I have used the search facility in the RHelp panel to no avail. Oscar A. Moreno oscar.moreno at att.net

> Hello, > > I want to install the package "multiv" which is not maintained any > more (found in the archive: multiv_1.1-6.tar.gz from 16 July 2003). I > have installed an older version of R 1.4.1 on my Windows Vista in > order to match the older package. > > As no binary is distributed, is it necessary to compile the package? > If so, how? > >

When I try to run the "sammon" function of the multiv package, I always get this error message: Error in as.vector(dist(a)) : couldn't find function "dist" It happens even with example(sammon). I am running R 1.5.0 on Win98 and I have still installed R 1.4.1 but it doesn't work on the old R version with the older multiv package either. Is there a problem with the

Hi, Li, Thanks for reply. It is strange that I used RBGL_1.6.0 successfully on the same linux system with R 2.3.1 before! After trying to install R 2.5.1, the RBGL_1.12.0 failed to be installed. Then, I uninstalled R. Delete the directory R/lib/. Installed R.2.3.1 again. And run getBioC1.8.5 for R 2.3.1 to download the three packages graph_1.10.6, RBGL_1.12.0 and Ruuid_1.10.0. But still

Hello, Can someone point me to documentation or ideas on how to calculate the centroids of clusters identified with hclust ? I would like to be able to chose the number of clusters (in the style of cutree) and then get the centroids of these clusters. This seems like a quite obvious task to me, but I haven't been able to put my hands on a relevant command. Thank you, Moritz

Hi, I have an nxp data set of time series. For my final year project, I would like to partition this data set into a smaller number of units ( < n). Where each of the units contains time series that move closely together (i.e. in unison), and the "simmilarity" (in terms of occurence & amplitudes of peaks and troughs) between the segregated units is "low". I know

Hi everyone, I’m looking for a clever bit of code to replace NA’s with a specific score depending on an indicator variable. I can see how to do it using lots of if statements but I’m sure there most be a neater, better way of doing it. Any ideas at all will be much appreciated, I’m dreading coding up all those if statements!!!!! My problem is as follows: I have a data set with

Dear Wizards - Thank you so much for your help. That was exactly what I was looking for. Now, I have been working on conditional selection of columns in a data frame. My goal is to calculate the total revenue per sales representative per status in a table. I have come to a complete stop: Let's say, we have a data.frame called df with several columns and a number of rows: df <-

Hi, Li and all lists, More, I have searched the web, and found one solution as described in: https://stat.ethz.ch/pipermail/bioc-devel/2007-June/001168.html But, My condition is some how different: 1) my g++ version is: g++ (GCC) 3.2.2 20030222 (Red Hat Linux 3.2.2-5) 2) the SHLIB file is the same, but some difference in /usr/local/lib/R/etc/Makeconf: SHELL = /bin/sh SHLIB_CFLAGS =

Dear all, I meet error when installing the newest Bioconductor packages 2.0 for R 2.5.1. the enviroments are as bellow: > sessionInfo() R version 2.5.1 (2007-06-27) i686-pc-linux-gnu locale:

Dear all, I am reading the book "statistic analysis of gene expression microarray data" by Terry Speed . On page16-17, there is an example that I can not repeat. The content can be found using below linkage:

Dear all, below you find enclosed my message from January 9th and my program (attention: beginner). Thanks for both answers! a. However, as far as I know the cosine is not the same as the Pearson correlation (only in special cases). b. Reid Huntsinger's hint was very useful, however I had to transpose the matrix first, for I want to calculate the distance of the _rows_. Regards, Petra