search for: cophenetic

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 &l...

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...

...o, drop = FALSE] } identical(canonicalize.dist(d2), canonicalize.dist(d3)) [1] TRUE Bill Dunlap TIBCO Software wdunlap tibco.com On Thu, Apr 21, 2016 at 2:37 AM, Alberto Fern?ndez Sabater < alberto.fernandez at urv.cat> wrote: > 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...

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

...0.00913 0.01506 $tip.label [1] "H" "G" "F" "E" "D" "C" "B" attr(,"class") [1] "phylo" The only problem is i can't access or save the individual trees after importing. What i want to do is calculate the cophenetic distance for each tree and take the correlation between pairs of trees. I keep getting errors like this: x<- anj30[1] > class(x) [1] "list" > as.phylo(x) Error in as.phylo(x) : no applicable method for "as.phylo" > cophenetic.phylo(x) Error in cophenetic.phy...

Hello, I analyse some free-sorting data so I use hierarchical clustering. I want to compare my proximity matrix with the tree representation to evalute the fitting. (stress, cophenetic correlation (pearson's correlation)...) "The cophenetic similarity of two objects a and b is defined as the similarity level at wich objects a and b become members of the same cluster during the course of clustering" Legendre, P and Legendre, L Numeri Ecology, 1998. I've made a...

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

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...

Hi List, I am looking for a variable selection procedure with a forward-backward selection method. Firstly, it is meant to work with the cophenetic correlation coefficient (CPCC) and intended to find the variable combination with the highest cophenetic correlation. Secondly, it is aimed at Gower metric with wards method (though this could be easily extended) aimed at categorical data. What I have so far is a function for backward selection th...

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

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

I know that within sum of squares, DB, sillhouette and cophenetic are indicators of clustering quality, but what indicators I need to observe when I choose attributes for kmeans? -- View this message in context: http://r.789695.n4.nabble.com/Feature-selection-for-kmeans-tp4657830.html Sent from the R help mailing list archive at Nabble.com.

Hello. I'd like to compute the associate vector of distances between leaves in a binary non-rooted tree. The definition of a distance between two leaves in a binary non-rooted tree is the number of edges in the path joining the two leaves. I've tried the ape package but I'm unable to find this vector. For example, using rtree(5,rooted=F) I've obtained the following tree: $edge

...library(cluster) library(mva) daisemol<-daisy(emol,type=list(asymm=c(1:21))) layout(matrix(c(1,1,2,2),2,2,byrow=TRUE)) hclustmol<-hclust(daisemol,method="average") plot(hclustmol,cex=0.6) agnesmol<-agnes(daisemol,method="average") pltree(agnesmol,cex=0.6) coagnes<-cophenetic(agnesmol) cor(coagnes,daisemol) cohclust<-cophenetic(hclustmol) cor(cohclust,daisemol) I'm using R 1.7.1 (2003-06-16) on Windows XP. Library "cluster" version 1.7.4 and library "mva" version 1.7.1. Best wishes, Mikkel Mikkel Grum International Plant Genetic Resource...

...322347 1.289899 1.553109 1.872578 1.452274 1.456126 1.335005 1.184658 1.018210 The problem is that these matrices are the endpoint of an extensive simulation involving phylogenetic trees and the order of the columns and rows shifts around according to how they were ordered in the tree. I used cophenetic.phylo to get the distance matrix and now I need to find a way to reorder or sort the columns and rows such that the two matrices match and cor is taking the correlation of the corresponding column and row and not just the one in the same position. I don't want to sort the values in the col...

...ng the partial mantel method. However, i am having trouble creating compatible matrices. I can create matrices from my numerical data using the 'distance(x, method)' function from ecodist, but the row/column names are out put as numbers. While when i create a phyo-distance matrix using 'cophenetic(x)' from APE, the row/column names are the taxa names. Different data sets incorporate different taxa from the tree, which requires me to prune it for each data set, meaning I cannot just convert the taxa names to corresponding numbers in the data matrix (because the numbers will change for eac...

dear R users, I have troubles performing Moran.I test as suggested on http://www.ats.ucla.edu/stat/r/faq/morans_i.htm my spatial data are longitude and lattitide of communities. The calculation of the inverse distance matrix according to the homepage (using my data) datAL <- read.csv2("C:\\Konvergenz AL.csv", header=T) ALdist <- as.matrix(dist(cbind(datAL$L?nge,

...2) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug The same problem comes up when I try to run an autocorrelative model with some dummy continuous data. (I've tried many different functions, all produce similar error responses): > Moran.I(dummy$dist, cophenetic(sa)) Error: cannot allocate vector of size 1.4 Gb R(539,0xa0810fa0) malloc: *** mmap(size=1488809984) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug R(539,0xa0810fa0) malloc: *** mmap(size=1488809984) failed (error code=12) *** error:...

...`priority'. o termplot() uses factor levels rather than 1,2,3... for x-axis. o Workaround for optimization bugs on gcc 3.1/2 on 32-bit Solaris. o The trace() function has been robustified and a new function tracingState() added to turn tracing temporarily on and off. o New cophenetic() in "mva" as utility for hierarchical clustering. o p.adjust() has two new methods, 'Hommel' and 'FDR', contributed by Gordon Smyth <smyth at wehi.edu.au>. o stars() now has add and plot arguments. DEPRECATED & DEFUNCT o The assignment operator...

...`priority'. o termplot() uses factor levels rather than 1,2,3... for x-axis. o Workaround for optimization bugs on gcc 3.1/2 on 32-bit Solaris. o The trace() function has been robustified and a new function tracingState() added to turn tracing temporarily on and off. o New cophenetic() in "mva" as utility for hierarchical clustering. o p.adjust() has two new methods, 'Hommel' and 'FDR', contributed by Gordon Smyth <smyth at wehi.edu.au>. o stars() now has add and plot arguments. DEPRECATED & DEFUNCT o The assignment operator...