similar to: cophenetic matrix

Hello, I have been using the "cophenetic" function for objects of class "dendrogram" and I have realised that it gives different results when it is used with objects of class "hclust". For instance, running the first example in the help file of the "cophenetic" function, d1 <- dist(USArrests) hc <- hclust(d1, "ave") d2 <-

Note that cophenetic.default (which works on the output of hclust(dist(X))) uses the row names of X as labels. as.dendrogram.hclust does not retain those row names so cophenetic.dendrogram cannot use them (so it orders them based on the topology of the dendrogram). Bill Dunlap TIBCO Software wdunlap tibco.com On Thu, Apr 21, 2016 at 7:59 AM, William Dunlap <wdunlap at tibco.com> wrote:

I am trying to write a wrapper for the last example in help(cv.glm) that deals with leave-one-out-cross-validation (LOOCV) for a logistic model. This wrapper will be used as part of a bigger program. Here is my wrapper funtion : logistic.LOOCV.err <- function( formu=NULL, data=NULL ){ cost.fn <- function(cl, pred) mean( abs(cl-pred) > 0.5 ) glmfit <- glm(

Sir, I found your description of the dataset about nodal involvement in prostate cancer. It comes from the book biostatistics casebook. I like to use the dataset for doing logistics regression. Can you tell me where I can find the dataset. Thanks and greetings Wim van Baarle wvbaarle@wxs.nl [[alternative HTML version deleted]]

Hello, My PDC is working but I have some errors on my log, I'm searching since some days but I cannot find why. In log.smbd I have [2006/08/22 16:30:22, 0] lib/util_sock.c:get_peer_addr(1229) getpeername failed. Error was Noeud final de transport n'est pas connect?? And In log.MachineName I have [2006/08/22 19:17:33, 0] auth/auth_util.c:create_local_nt_token(899)

Hello, I want to split a string including a "+" but it seems there is no effect because of this special character. Just to explain, I convert frequencies to midi notes (external program) but I don't want to keep information about quater-tone! > s <- c("Fd4+1/4") (i't a note!) > strsplit(s,"+") [[1]] [1] "F" "d" "4"

I think the results differ only in the order of the labels. The following function puts the labels in a standard order and then the results are the same: canonicalize.dist <- function (distObject) { o <- order(labels(distObject)) as.matrix(distObject)[o, o, drop = FALSE] } identical(canonicalize.dist(d2), canonicalize.dist(d3)) [1] TRUE Bill Dunlap TIBCO Software

Hello, I've been trying to figure out how to access the individual elements from an object of class phylo. I am reading in 201 trees created by paup as below. > read.nexus("A_30knj_200t.txt", tree.names= NULL) -> anj30 > anj30[1] $tree1 $edge [,1] [,2] [1,] "-1" "-2" [2,] "-2" "-3" [3,] "-3" "1"

Hello all, I wish to compare two dendrograms (representing Hierarchical Clusterings). My problems are several: 1) how do I manually create a dendrogram object ? That is, how can I reconstruct it as an "hclust" object that creates such a dendrogram, when all I have is the dendrogram image (but don't have the underlaying distance matrix that produced it) ? I see that there is a

Hello, I run a samba (v3.0.10) PDC and openLdap server on the same machine. They work fine, except sometimes the smb server cannot contact the ldap server. From a windows client, it looks like the server gets stuck, and it takes a few minutes before the shares are available again. In the /var/log/messages file, i get these error messages :

Is there a function available in R that implements Mojena's Upper Tail Rule or that draws a Mojena plot? I would also like to find a function that implements Duda and Hart's stopping rule. Finally with function cophenet how can I achieve a straightforward Cophenet correlation coefficient (i.e. one number for example 0.876) that gives the agreement between the structure of the

Dear R users, I would like to write a script to launch R commands from a Unix prompt but I do not have any idea how to do it. Can someone bring me help please? Thanks in advance Denis Choquet -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or

Hello, I've some problems to concatenate elements of a list: > s1 [1] 1 2 3 4 > s2 [1] 6 7 > l <- list(s1,s2) > l [[1]] [1] 1 2 3 4 [[2]] [1] 6 7 but now I want to get this: > l [[1]] [1] 1 2 3 4 [[2]] [1] 6 7 [[3]] [1] 1 2 3 4 6 7 ## l[1] with l[2] Someone can help me? Thanks Olivier Houix -- Olivier Houix <houix at ircam.fr> tel: 01 44 78 15 51

Hi, I have a problem of Access denied to samba server from win7 64bit behind a VPN. the samba server is 3.2.5-4 release on a debian lenny (I will upgrade it soon), member of a win2K AD domain. the win7 PCs are on the same AD domain, they can access to an other samba server witch is very similar (same release, same smb.conf, same VPN config). If I do on a win7 PC: net view \\srvlinux I see:

Dear All, I wrote a function for cluster analysis to compute cophenetic correlations between dissimilarity matrices (using the VEGAN library) and cluster analyses of every possible clustering algorithm (SEE ATTACHED) http://old.nabble.com/file/p26288610/cor.coef.R cor.coef.R . As it is now, it is extremely long, and for the future I was hoping to find a more efficient way of doing this sort of

I'd like to get a measure of goodness of fit for a heirarchical clustering result from hclust. Something that would indicate the extent to which the dendrogram accurately represents the original dissimilarity matrix. Is there an easy way to do this? Or, does anyone have code for computing distances between nodes given an hclust structure? So far, my searches have come up dry. -- David

Hi, I'm new to R and I wonder if it's possible to have grid lines on a graph? Thanks. Yves Gauvreau -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To:

Hi, Here is my log, does someone know what it means ? Jan 6 11:20:38 SAMBA1 smbd[3053]: write_socket: Error writing 4 bytes to s ocket 22: ERRNO = Connexion r??-initialis??e par le correspondant Jan 6 11:20:38 SAMBA1 smbd[3053]: [2006/01/06 11:20:38, 0] lib/util_sock.c:s end_smb(647) Jan 6 11:20:38 SAMBA1 smbd[3053]: Error writing 4 bytes to client. -1. (Co nnexion r??-initialis??e par le

Dear all, I have a question with regard to the use of hclust. I would like to be able to specify my own distance matrix instead of asking R to compute the distance matrix for me. It is computationally easier for me this way. My question is: How can I get hclust to accept this? Thanks, Ranjan -- *************************************************************************** Ranjan

Hello, how can I get the similarity value (i.e., the inner cluster similarity) that was used to cut a hierarchical tree at a specific height? I would appreciate your help! Best regards, Madeleine