similar to: intermediate linkage clustering

Hi! Its not an R specific question but had no idea where to ask elsewhere. Does anyone know the orginal reference to the CAMBERA DISTANCE? Eryk. Ps.: I knew that its an out of topic question (sorry). Can anyone reccomend a mailing list where such questions are in topic?

Hi there, is there any R-function for k-nearest neighbour agglomerative hierarchical clustering? By this I mean standard agglomerative hierarchical clustering as in hclust or agnes, but with the k-nearest neighbour distance between clusters used on the higher levels where there are at least k>1 distances between two clusters (single linkage is 1-nearest neighbour clustering)? Best regards,

Hi All, I need to evaluate a series expansion using Legendre polynomials. Using the 'orthopolinom' package I can get a list of the first n Legendre polynomials as character strings. > library(orthopolynom) > l<-legendre.polynomials(4) > l [[1]] 1 [[2]] x [[3]] -0.5 + 1.5*x^2 [[4]] -1.5*x + 2.5*x^3 [[5]] 0.375 - 3.75*x^2 + 4.375*x^4 But I can't figure out how to

Hello All, Does anyone know of a package that performs constraint-based clusters? Ideally the package could perform "Time-Ordered Clustering", a technique applied in a recent journal article by Runger, Nelson, Harnish (using MS Excel). Quote, "in our specific implementation of constrained clustering, the clustering algorithm remains agglomerative and hierarchical, but observations

Hello All,I am Nirmal Singhania from NIIT University,India. I am interested in Clustering of search results Topic. I have been in field of practical machine learning and information retrieval from quite some time. I took various courses/MOOC on Information retrieval and Text Mining and have been working on real life datasets(KDD99,AWID,Movielens). Because the problems you face in real life ML/IR

I haven't read the book, but could anyone explain more about this parameter? help(agnes) says that ac measures the amount of clustering structure found. From the definition given in help(agnes.object), however, it seems that as long as the dissimilarity of the merger in the final step of the algorithm is large enough, the ac value will be close to 1. So what does ac really mean? Thank

Dear R-Help Does "The R Package for Multivariate and Spatial Analysis Version 4.0 (Casgrain and Legendre, 2001)" exist on CRAN and under what name? It supposedly has a chronological clustering program ,CHRONO, that I would like to use. Alternatively, I would ask if there is a R based program that performs chronological clustering? Thanks Alex Alex Hanke Department of Fisheries and

Hi, I would like to solve a double integral of the form \int_0^1 \int_0^1 x*y dx dy using Gauss Quadrature. I know that I can use R's integrate function to calculate it: integrate(function(y) { sapply(y, function(y) { integrate(function(x) x*y, 0, 1)$value }) }, 0, 1) but I would like to use Gauss Quadrature to do it. I have written the following code (using R's statmod package)

Hello everyone, I would like to find out if there are already implemented function for legendre polynomials. I tried google but returns nothing. How do you suggest me to search for that? Regards Alex [[alternative HTML version deleted]]

It is a trivial problem, but in the book I couln`t figure out how to put different colours at different regression lines plot(bif,abund,type="n", xlab= "number_bifurcations", ylab="abundances") sbif<-split(bif,stage) sabund<-split(abund,stage) points(sabund[[2]],sbif[[2]],pch=16, col="red") for(i in 1:2) abline(lm(sabund[[i]]~sbif[[i]])) Thanks in

I''ve been tasked at my workplace to upgrade our puppet installation to a more modern version. Currently all the environments run a RubyGem version of puppet 0.25.4 on mostly RHEL/Centos 5.3 - 5.5 (there are, like most environments, a few laggards running RHEL4 or new machines running CentOS 6). The plan is to upgrade these to the most stable version of Puppet, which at the time of

Pierre Legendre has developed a beta version of a new redundancy analysis package called RdaTest that is available on his web page at the Universit® de Montréal. The test example that is included with the package is based on the example provided in his book (Numerical Ecology, Chapter 11 (Legendre & Legendre 1998)) I have downloaded the package and am attempting to run it so that I might

Hello List, I am trying to implement a hierarchical cluster using the hclust method agglomerative single linkage method with a small wrinkle. I would like to cluster a set of numbers on a number line only if they are within a distance of 500. I would then like to print out the members of this list. So far I can put a vector: > x<-c(2,10,200,300,600,700) into a distance matrix: >

Hello, In the documentation for agnes in the package 'cluster', it says that NAs are allowed, and sure enough it works for a small example like : > m <- matrix(c( 1, 1, 1, 2, 1, NA, 1, 1, 1, 2, 2, 2), nrow = 3, byrow = TRUE) > agnes(m) Call: agnes(x = m) Agglomerative coefficient: 0.1614168 Order of objects: [1] 1 2 3 Height (summary): Min. 1st Qu. Median Mean 3rd

Hello, I had a question regarding clustering using the agnes() function from the 'cluster' package. I was wondering if anyone knew how I can identify cluster points after running the agnes function. For example, I created a dataset with points randomly scattered around (0,0), (0,1) and (1,0). After clustering, the dendrogram shows all the clustered points and I get the ordering and

On Wed, May 27, 2015 at 05:08:25PM -0400, Daniel Kahn Gillmor wrote: > On Tue 2015-05-26 15:39:49 -0400, Mark D. Baushke wrote: > > Hi Folks, > > > > The generator value of 5 does not lead to a q-ordered subgroup which > > is needed to pass tests in > > > > http://csrc.nist.gov/publications/nistpubs/800-56A/SP800-56A_Revision1_Mar08-2007.pdf > > I

Hi, I'm trying to find out what threshold of indicator value in labadsv should be used to accept a specie as an indicator one? So far I assumed that indval=0.5 is high enough to avoid any mistakes but it was based only in my intuition. I'd be greatful for any advise best regards Agnieszka

I stumbled across this link and was wondering if this has any relation to the R project. http://www.fas.umontreal.ca/BIOL/Casgrain/en/labo/R/index.html -jennifer ----------------------------------- J. Steinbachs, Ph.D. Computational Biologist http://compbiology.org ----------------------------------- -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing

Hi, I'm clustering objects defined by categorical variables with a hierarchical algorithm - average linkage. My distance matrix (general dissimilarity coefficient) includes several distances with exactly the same values. As I see, a standard agglomerative procedure ignores this problems, simply selecting, above equal distances, the one that comes first. For this reason the analysis in output

Dear all, Has anyone written R code for partial Mantel Tests- as described for instance in Legtendre & Legendre (1998) ? In other words, in a community ecology analysis, I would like to calculate the correlation between two dissimilarity matrices, controlling for a third distance matrix representing geographical distances between sites. Thanks! Christophe Bouget Biodiversité et gestion des