similar to: pvclust distance matrix

Hi, I am new to clustering and was wondering why pvclust using "maximum" as distance measure nearly always results in p-values above 95%. I wrote an example programme which demonstrates this effect. I uploaded a PDF showing the results Here is the code which produces the PDF file: ------------------------------------------------------------------------------------- s <-

hello, i'd be happy if someone could provide help with the following problem: i have a dist.matrix that comes from vegdist() function of the vegan package. the used method = "horn" is not accepted as argument in hvcluster(...,dist.method="..."). is there a way to incorporate the method "horn" in hvcluster()? thanks in advance! yours, kay -- View this

Good morning, I am analyzing a dataset composed by 364 subjects and 13 binary variables (0,1 = absence,presence). I am testing possible association (co-presence) of my variables. To do this, I was trying with cluster analysis. My main interest is to check for the significance of the obtained clusters. First, I tried with the pvclust() function, by using method.hclust="ward" and

Hi all, I'm new to R and I'm struggling to decipher an error message. Briefly, I am trying to use the pvclust package to do hierarchical clustering of some CGH data. The data is from the Progenetix CGH database. It is arranged as a table where each column is a single case and each row is a single chromosome band. The value in each cell is either 0, 1, 2, or -1. Corresponding to no change,

Dear All I'm using PVClust to perform hierarchical clustering, for the output plot I can control most of the graphical I need, however the plot is large and I would like to split it vertically into two panels one above the other. Is there a way to plot only part of a PVClust plot, I tried to convert it to a dendrogram with result2 = as.dendrogram(result) however I get the error message

Is there a way to assign color to nodes as with hclust/as.dendrogram/dendrapply when using pvclust? The problem is that as.dendrogram isn't working on the pvclust objects. library(pvclust) pvc <- pvclust(matrix, nboot=1000) plot(pvc) -- View this message in context: http://www.nabble.com/Node-colors-in-pvclust-tp24405329p24405329.html Sent from the R help mailing list archive at

You should reply to the list, not just me, and even more because I cannot really help you!! My guess (but I don't know this package, and even less this function) is that pvclust() is expecting a matrix as the first argument. However, "cluster" is no data, it is a function. Why, I don't know. Take a closer look at ?pvclust, especially the "usage",

Hello, I am relatively new to R and I am working through the code that is provided in the book Numerical Ecology with R and I have run across an error message that I can't seem to figure out. I am using the vegan, ade4, gclus and cluster packages. The code is as follows: # Ordered community table # Species are ordered by their weighted averages on site scores or <- vegemite(spe,

I realize questions about packages should go to the package maintainer, but perhaps I have an old email address (suzuki3 at is.titech.ac.jp) Also I have both a general, and a specific, question. 1) General question: i've used pvclust before to assess significance of clusters and got reasonable results. However, on a new data set (see below) the results seem odd. I wonder if pvclust is a

Hi all I am writing to you with a question regarding the pvclust package. And yes, before the usual people produce their usual contact-the-package-maintainers line, ye, I tried that but the emails one can find on the web either bounce or are not responded to. Also, yes, this error has already been reported as a bug but been shot down as not reproducible

Hi, if you look at the first image (Image1) you see that there are 2 main clusters 7 and 8 I wanted to use pvclust to calculate a p-value whether these clusters are due to chance or statistically significant. Unfortunately pvclust does not provide a p-value for the first brunch (7 and 8). So I added a row to my matrix which is very different to the rest of the data to create an additional

Hello all, I posted a question to this list last week and received no response. I am unsure if this means no-one knows the answer or if I posed the question badly. I'm going to assume I posed the question badly and try again. I am new to R so it is quite likely it's a very naive question, however if there is something blindingly obvious that I am missing or if there is another resource I

Hi all I am trying to perform the follwing: fit<-pvclust(wq, method.hclust="ward", method.dist="euclidean") but get a strange error message that I just cant figure out. Has anyone come across this? Any help would be most appricieated Error in hclust(distance, method = method.hclust) : NA/NaN/Inf in foreign function call (arg 11) In addition: Warning message: NAs

Hello there, Here's a question regarding p-values on clusters produced by hierarchical cluster analysis. A web search led me to the program pvclust to tackle this problem. But when I run the problem I get strange results. The 'AU' (approximately unbiased) p-values are very different from the 'BP' values (ordinary boot-strap) p-values. The AUs commonly are in the 80-100

Dear ecology fellows, I tried to implement Morisita-Horn distance (instead of Bray that is in the current version) in the code for the Simper analysis in vegan. I would be very grateful if someone can check if the code is right. function (comm, group, ...) { if (any(rowSums(comm, na.rm = TRUE) == 0)) warning("you have empty rows: results may be meaningless")

I am trying to reproduce an analysis done in SAS from which Type III Sums of squares are used. How can you get Type III sums of squares in an aov similar to what SAS provides? With best wishes and kind regards I am Sincerely, Corey A. Moffet Instructor Department of Range, Wildlife, and Fisheries Management Mail Stop 2125 Texas Tech University Lubbock, Texas 79409-2125 (806) 742-2843 Voice

Dear All, I would like to use the simprof function (clustsig package) but the available distances do not include Jaccard distance, which is the most appropriate for pres/abs community data. Here is the core of the function: > simprof function (data, num.expected = 1000, num.simulated = 999, method.cluster = "average", method.distance = "euclidean", method.transform =

Hi I have just (finally) started to poke around in R and wanted to analyse a stream fish dataset with 28 sites and 18 species. When trying to follow the Vegan manual to run nmds from distance measures calculated by the vegdist function it turns out that I have two sites (streams) with the exactly the same four species (I have used pres-abs data in this case). When I try to run isoMDS I get an

Dear all, in package Hmisc `rcorr' computes a matrix of Spearman's `rho' rank correlation coefficients for all possible pairs of columns of a matrix. What if I want a matrix of rank correlation coefficients for pair of columns of two different matrices? I have the same question about distance metrics in package Vegan. The function 'vegdist' computes distance indexes for all

If you submit these lines, you end up with variable "vare.dis". I want to export vare.dis to csv. Stuck I am. library(vegan,logical.return = TRUE) #return=true verifies package is available library(MASS,logical.return=TRUE) #return=true verifies package is available data(varespec) #varespec is an example data file in the vegan package vare.dis <- vegdist(varespec)