similar to: Heirarchical tree data structure

Dear R users, I'm interested in measuring the stability of a heirarchical clustering, of the overall clustering and finding sub clusters (from cutting the heirarchical clustering at different levels) which demonstrate stability. I saw some postings on the R help from a while back about bootstrapping for clustering (using sample and generating a consesus tree with a web based tool CONSENSE)

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 have a distance matrix which is computed by user defined method. I would like to plot the dendrogram. I would like to use different color and want the leaves laying down bottom. The script like this. I am not familiar with R. I followed the example shown in http://stat.ethz.ch/R-manual/R-devel/library/stats/html/dendrogram.html dist.obj <- as.dist(matrix.distance) hc.obj <-

Dear useRs, I am working on a project involving the clustering of a large dataset. I need to extract specific sub-clusters from the parent dendrogram for further analysis. The data is too large for the use of convenient tools such as identify.clust (it selects the specific group of interest on a graph), so alternatively I have saved the plot as a large image file so that it can be printed or

I have been using a nlme model and wish to specify the correlation structure. My data is grouped (bas), but I have no time component or adequate spatial description beyond the grouping variable. So I chose the simplest structure and updated my original nlme model by: update(model, corr=corCompSymm(~1|bas)) This is not significant. One of my variables measures area upstream of the sample. Area

Hi, How to plot the dendrogram or tree for kmeans, like we do for hclust ? [[alternative HTML version deleted]]

Dear useRs,Is there a command or package in R to do heirarchical clustering by "modified ward method"??regardseliza [[alternative HTML version deleted]]

Hi Guys I have been taking a close look at some networking opportunities which are being frustrated by the limits which are imposed by NAT. In particular the constraints impose by the embargo on double NATing have an impact for a project I am working on. Has anyone ever seen anything which I would conceptually describe as a reverse NAT proxy? What I want to be able to do is to be able to create

Hi, I've been trying to make use of the dendrogram class to plot a tree. However, my attempts have failed so far because I'm not sure how to build up the nested list. (where do I have to store the nodes?). The tree I want to be drawn is like this: in the form (node, left child,right child) (root,(n1,1,(n2,2,3)),4) If it is not easily possible to draw a tree with the help of the

Hello, I'm trying to assess the similarity of two lines that are represented as points (output of differential equation solvers). Is there a function or a package that deals with things like this? Thanks, John. ==================================================== Johannus (John) Janmaat Assistant Professor of Economics Barber School of Arts and Sciences University of British Columbia -

Dear all What I would like to know is if there is a way to know which specific samples fall within a terminal branch created by tree? The classification summarizes data, but I want to know which specific samples fall within each classification (branch in the dendrogram). Data contains site codes and multiple fields describing the characters of a single specimen of grass growing there.

Hi When I give the command: > heatmap.2(as.matrix(d),Rowv=as.dendrogram(hc.gene),Colv=FALSE,scale="row ",trace="none",col=greenred.colors(79)) The resulting heatmap has re-ordered my columns! This is time-course data, and I don't want my columns re-ordered! Note from the help: Rowv: determines if and how the _row_ dendrogram should be reordered.

Hi, I'm trying to build dendrograms to pass to heatmap(). The dendrograms I build plot properly, but when I pass them to heatmap() I get the error message "row dendrogram ordering gave index of wrong length" (see output log below). I looked in the code of heatmap() and saw that the error was due to a NULL return value from order.dendrogram(), which in turn got a NULL return value

hello i am trying to decipher a dendrogram i have from performing a 'tree'. (attached file) my response variable is factored - low, medium and high threat and the 8 explanatory variables are numeric values. i could do with some help to understand what the values <0.25, <0.5 and <0.75 are on the tree branches? how does one interpret this??? cheers, mann Manju Sharma

Hi, hres <- hclust(smatr,method="single") hresd<-as.dendrogram(hres) as.dendrogram(hres) `dendrogram' with 2 branches and 380 members total, at height 2514.513 plot(hresd,leaflab="none") #<-error here. #the plotted dendrogram is incomplete. The x axis is not drawn. #The interested reader can download the save(hresd,file="hres.rda") #from the

Hi When I use plot(hclust(dist..)...)...) etc to create a dendrogram of a hierarchial cluster analysis, I end up with a vertical tree. What do I need to do to get a horizontal tree? Also, my users are used to seeing trees who's leaves all "end" at the same place (eg. Like in minitab). Is this possible in R? Thanks Mick Michael Watson Head of Informatics Institute for Animal

Hi all, ok, i know i can cut a dendrogram, which i did. all i get is three objects that a dendrograms itself. for example: myd$upper, myd$lower[[1]], myd$lower[[2]] and so on. of course i can plot them seperately now. but the lower parts still have hundreds of branches. i?ll need a 30 " widescreen to watch the whole picture. what i?d like to is group the lower branches , so that i get a

I am having trouble displaying a dendrogram of evolutionary relationships (a phylogram imported from the ape package) as the vertical component of a heatmap, but keeping the hierarchical clustering of the horizontal component. The relationships of the vertical component in the generated heatmap are not that of the dendrogram, although the ordering is. In more detail, I am attempting to generate

Hello, I've been clustering my data using hclust and cutting the resulting tree with cutree. Separately, I visualize the clusterings with heatmap. Is it possible to have the dendrogram on the heatmap reflect the cutree results? That is, instead of having one large dendrogram, it would have 4 or 25 in the example below. Any guidance on if that's possible or not, and what kinds of

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