similar to: Minimum Spanning Trees

Hi all, I'm very new to R and read a few tutorials, however I'm having difficulty trying to figure out how to plot a minimum spanning tree. I have a csv file that contains an n-by-n matrix of distances between strains of bacteria called matrix.csv. Looks like: id,strain1, strain2,strain3 strain1,0,.2,.8 strain2,.3,0,.7 strain3,.4,.6,0 I've been messing around with some information

I would like to apply network measures (such as betweenness centrality, upper boundedness, etc.) to a weighted graph with non-integer weights, defined by a euclidean distance matrix. The package sna provides the measures that I want to use, but seems only to operate on binary graphs. I have read work by Mark Newman (http://aps.arxiv.org/abs/cond-mat/0407503/), who suggests that a weighted graph

Dear all, I have an ontology which I would like to load in R to then compute the minimum distance between elements. Since this ontology is not only DAG, the problem is non trivial and therefore decided to use R with the powerful e1071 library (allShortestPaths) to do that. That method requires to provide a distance matrix between the various objects. My ontology contains 32768 objects and

hi I am struck with a problem in igraph package of R. My problem is as follows I want to plot a power law fit for my data (in .net format --- pajek format) syntax for that in R is g <- read.graph("filename.net", "pajek") d <- degree (g, mode="in") power.law.fit (d+1, 2) it gives me desired out put if my if input a single file but I want to use a variable

Hello, I am working with graph and adjacency matrix, the package 'graph' seems to be appropriate for this. An example in the package > mat <- rbind(c(0, 0, 1, 1), + c(0, 0, 1, 1), + c(1, 1, 0, 1), + c(1, 1, 1, 0)) > rownames(mat) <- colnames(mat) <- letters[1:4] > graph1 <- new("graphAM", adjMat=mat) > graph1 A

My understanding is that single linkage clustering is equivalent to finding the minimum spanning tree. Hclust works very nicely for finding the clusters but I am unable to find enough information in its output to construct the minimum spanning tree. In particular, I want to find a minimum spanning tree path between two items in the tree. Is this possible with hclust or is there another

Hi, I wanted to make a graph with the following table (2 rows, 3 columns): a b c x 1 3 5 y 5 8 6 The first column represents the start cordinate, and the second column contains the end cordinate for the x-axis. The third column contains the y-axis co-ordinate. For example, the first row in the matrix above represents the points (1,5),(2,5), (3,5). How would I go about making a discontinuous graph

Thanks Mike. My data has longitude and latitude coords and I used distAB {clim.pact} then mst {ape} to calculate my minimum spanning tree. The nodes are telecoms sites from all over Australia. My goal is to determine the minimum cost of linking them via cabling, and I'm starting by calculating the distance "as the crow flies", but will probably eventually need to calculate the

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Let's say I had a matrix like this: library(Ryacas) x<-Sym("x") m<-matrix(c(cos (x), sin(x), -sin(x), cos(x)), ncol=2) How can I use R to obtain the eigenvalues and eigenvectors? Thanks, John [[alternative HTML version deleted]]

Hi, I am new to R and I want to know how to use C code which contains two functions one called inside another.I know that how to use C code in R if it has only one function but dont know how to do it in above case. I want to use the same in R .My C code is as follows. //#include <R.h> void sayHello(); void g(); void sayhello() { Rprintf("Hello world %d\n",global); } void

Hi, If I used drop1 in a weighted lm fit, it seems to ignore the weights in the AIC calculation of the dropped terms, see the example below. Can this be right? Yan -------------------- library(car) > unweighted.model <- lm(trSex ~ (river+length +depth)^2- length:depth, dno2) > Anova(unweighted.model) Anova Table (Type II tests) Response: trSex Sum Sq Df F value

Dear R-experts: I am using survreg() to estimate the parameters of a Weibull density having right-censored observations. Some observations are weighted. To do that I regress the weighed observations against a column of ones. When I enter the data as 37 weighted observations, the parameter estimates are exactly the same as when I enter the data as the corresponding 70 unweighted observations.

Dear R Users, I have a network of 25000 total nodes and a list of 500 node which is a subset of all nodes. Now I want to calculate the APSP (all pair shortest path) matrix only for these 500 nodes. I would appreciate any help. Thanks in advance Dinesh -- Dinesh Kumar Barupal Research Associate Metabolomics Fiehn Lab UCD Genome Center 451 East Health Science Drive GBSF Builidng University of

Hi,    I have a file containing gene expressions written using the tillingArray package. I used load() and attach() to get the data into R. Both of them works fine. Now I want to see the contents of the file. How can I see the contents of the file? Thankyou for your time. Regards, Ambuj The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. [[alternative HTML version

Hi, Could you please tell me whether SVM can do multiple regression or not? Cheers, Amy _________________________________________________________________ Browse profiles for FREE! Meet local singles online. [[alternative HTML version deleted]]

Dear All, I have data in HDF file format and would like to read it into R. I have tried the package hdf5 without success. Any ideas and suggestions?? Kind regards, Katrin -- Katrin Fleischer Vrije Universiteit Amsterdam Faculty of Earth and Life Sciences Subdepartment Hydrolgy and Geo-Environmental Sciences Room E-360 De Boelelaan 1085 1081 HV AMSTERDAM Tel: +31 20 59 87391

Hello, just a couple of short questions that would be much appreciated. Is there a way of putting a vectors inputs in size order from low to high? And if I had a random list or TRUE and FALSE, is there a way of finding the 100th TRUE? Thank you very much, Elliot Welch elliot.welch at virgin.net Sent from my BlackBerry? smartphone

Hi, > history() gives Error in savehistory(file) : no history available to save although I can scroll throu history with C^uparrow an C^downarrow. How can I make history() work and/or show the current history in a file, so that I can choose from previous commands? The web did not throw up anything useful. TIA --Christian -- Christian W. Hoffmann, CH - 8915 Hausen am Albis,

foreach (or virtually anything you might use for concurrent programming) only really makes sense if the work the "clients" are doing is substantial enough to overwhelm the communication overhead. And there are many ways to accomplish the same task more or less efficiently (for example, doing blocks of tasks in chunks rather than passing each one as an individual job). But more to the