search for: hierclust

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() function again? and no sample about it. so could anybody please help me as author? thanks in advance xinan yang xinan at molgen.mpg.de

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() function again? and no sample about it. so could anybody please help me as author? thanks in advance xinan yang xinan@molgen.mpg.de

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...

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() but no significant results. Thank you for...

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: https://stat.ethz.ch/pipermail/r-help/attach...

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

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 load table Since I have a snapshot from...

...the distance matrix are being made, and whether I could somehow stop them from being made. Any other suggestions for how I could get around the memory problem would also be appreciated. (I know of clara in the "cluster" package, but would like to use hierarchical methods.) The function hierclust in multiv seems to demand even more memory, even when bign = T. I am running R-1.3.1 on Sun OS 5.6. Thanks for any help. Matthew Wiener Applied Computer Science and Mathematics Department Merck Research Labs Rahway, NJ 07065-0900 732-594-5303 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-....

...Contents: bea Bond Energy Algorithm ca Correspondence Analysis supplc Supplementary Columns in Correspondence Analysis supplr Supplementary Rows in Correspondence Analysis flou Fuzzy Coding (3-Way) hierclust Hierarchical Clustering logique Logical Coding members Cluster Memberships partition Partitioning by Iterative Optimization pca Principal Components Analysis sammon Sammon's Non-Linear Mapping...

...Contents: bea Bond Energy Algorithm ca Correspondence Analysis supplc Supplementary Columns in Correspondence Analysis supplr Supplementary Rows in Correspondence Analysis flou Fuzzy Coding (3-Way) hierclust Hierarchical Clustering logique Logical Coding members Cluster Memberships partition Partitioning by Iterative Optimization pca Principal Components Analysis sammon Sammon's Non-Linear Mapping...

...<- as.dist(dista) etc. ----- Original Message ----- From: Petra Steiner To: r-help at lists.r-project.org Sent: Wednesday, January 09, 2002 11:13 PM Subject: [R] Distance matrix by cosine? 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 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tu...

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

Hello all, I know this may not be the right forum for this. But I'm relatively new to R (and it's been a while since I did any serious statistical research). I need some help in using R for my project. This is what I need to do : 1. Read time series data (of varying time spans) from text files into R arrays 2. Segregating the time series into "sets" of "classes" that