similar to: Problem with cluster analysis

I try to use the routine cutree to cut a tree (created by hclust) into several groups by specifiing the hight of the cut. a<-1:10 cutree(tree, h=a*100) The Matrix with group meberships returned is ok for most of the hights, but in some cases (as for example h=800 and h=900) the results don't make sense (group membership=0 or 58965231, it looks like the range of data allowed by the data

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

Hello all, I am using libraries (mva,cluster) to produce dendrograms. With 1000 examples the dendrogram gets too crowded, and i am wondering whether there is an option (which i cannot find) to set the number of leaf nodes, like in matlab, and return the plot and the assignment map examples -> leaf nodes. Any suggestion is appreciated. Thanks Edo

howdy R friends, I've searched CRAN but to no avail... I'm trying to use mva's hclust and print out for say 10 clusters in batch. How do I do this? It's unclear if I can use cutree. thanks, John Strumila -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send

I'm using the hclust method from the package mva (pre-compiled-version on Win NT) and would like to cut the tree in pieces. Have someone implemented the function cutree (as in S-PLUS) in R? Many thanks Markus Huerzeler -- Dr. Markus Huerzeler Phone: +41 / 61 / 686 98 83 AICOS Technologies AG Fax: +41 / 61 / 686 98 88 Efringerstrasse 32 mailto:mhuerzeler at

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")

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 <-

Dear R users, I am mailing you about the graphical output of silhouette (cluster package) From the example of silhouette in help(silhouette): > ar <- agnes(ruspini) > si3 <- silhouette(cutree(ar, k = 5), # k = 4 gave the same as pam() above + daisy(ruspini)) > plot(si3, nmax = 80, cex.names = 0.5) from which one may conclude that group 1 is composed by

Hello, I have used the functions agnes and cutree to cluster my data (4977 objects x 22 variables) into 8 clusters. I would like to refine the solution using a k-means or similar algorithm, setting the initial cluster centres as the group means from agnes. However my data matrix has NA's in it and the function kmeans does not appear to accept this? > dim(centres) [1] 8 22 > dim(data)

Hello all, A question/suggestion: I was wondering if there is a chance of changing stats::cutree to be S3 and use cutree.hclust? For example: cutree <- function(tree, k = NULL, h = NULL,...) { UseMethod("cutree") } cutree.hclust <- stats::cutree # This will obviously need the actual content of stats::cutree This would be nicer for people like me to add new methods to

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

Full_Name: Anja von Heydebreck Version: 1.3.0 OS: Alpha Unix Submission from: (NULL) (141.14.19.61) Hi, I repeatedly obtained meaningless results from the function 'cutree' in the 'mva' package, when the argument 'h' was greater or equal to the maximum height occuring: > library('mva') > y [,1] [,2] [,3] [,4] [1,] 0 1 -1 1 [2,] 0 -1

I have Windows XP Professional Version 2002 and the R-Version 2.1.1. I did cluster analysis with the cluster package and the agnes (method = ?ward?). The results are satisfactory. But the dendrogram of agnes is confused to work with the results. Is there a tool, I can get a clear arrangement of the results for the cluster analysis. For example a matrix with different numbers for each group.

Ladies and Gentlemen, As Johan Lindberg points out, the documentation for handling dendrograms is sparse....Does anyone know who is responsible for or working on development of tree methods and objects? I've written a couple of scripts for my own use to translate between parenthetical (A(B(CD))) or binary A00 B10 C11 D11 tree formats and cluster objects in R, but as an inexperienced

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

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

Hello! Those of you, who use Sweave a lot, will probably find my shell script usable. You can get it at: http://www.bfro.uni-lj.si/MR/ggorjan/programs/shell/Sweave.sh No warranty, however don't hesitate to contact me if you find an error or have a patch! -- Lep pozdrav / With regards, Gregor GORJANC --------------------------------------------------------------- University of

Hi - a tiny bug report: the list of mirror sites given at www.r-project.org/ mentions http://cran.mirror.aarnet.edu.au/ This domain does not exist (well, from Western Australia netscape says the domain doesn't exist) but I found the mirror at http://mirror.aarnet.edu.au/pub/CRAN/ regards Adrian Baddeley -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-

Hi - a tiny bug report: the list of mirror sites given at www.r-project.org/ mentions http://cran.mirror.aarnet.edu.au/ This domain does not exist (well, from Western Australia netscape says the domain doesn't exist) but I found the mirror at http://mirror.aarnet.edu.au/pub/CRAN/ regards Adrian Baddeley -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-