similar to: dist function in R is very slow

> By the way, since the tcrossprod function in the Matrix package is so fast, the Euclidean distance can be computed very fast: Indeed. > euc_dist <- function(m) {mtm <- Matrix::tcrossprod(m); sq <- rowSums(m*m); sqrt(outer(sq,sq,"+") - 2*mtm)} There are two reasons why I didn't use this optimization in "wordspace": 1) It can be inaccurate for small

Dear R developers, I am visualising high dimensional genomic data and for this purpose I need to compute pairwise distances between many points in a high-dimensional space (say I have a matrix of 5,000 rows and 20,000 columns, so the result is a 5,000x5,000 matrix or it's upper diagonal).Computing such thing in R takes many hours (I am doing this on a Linux server with more than 100 GB of RAM,

Hi, Samba team! I am trying to install samba4 on FreeBSD 9.2 as a domain DC to join an existing samba4 domain controller on FreeBSD 9.2. I followed the instruction of: Samba4/HOWTO/Join a domain as a DC Everything is OK until I run the following command: root at mtm:/var/named/etc/namedb # samba-tool drs showrepl Default-First-Site-Name\MTM DSA Options: 0x00000001 DSA object GUID:

Hi all, I just failed in loading a saved wordspace (13MB of size), and received these errors: Warning: stack imbalance in 'missing', 52 then 51 Warning: stack imbalance in 'if', 50 then 53 Warning: stack imbalance in 'as.environment', 57 then 59 Warning: stack imbalance in 'ls', 54 then 53 Warning: stack imbalance in '.Internal', 54 then 53 Warning: stack

Dear Users,I have two matrices A=15*365 and B=1*365. i want to calculate "Euclidean Distance" between these matrices in such a way that i should have euclidean distance of matrix B against all the columns of matrix A. More precisely, first i want euclidean dist. of column 1 of A against B, then column 2 against B, 3rd column of A against B and so on.is there a way in r to do it?your help

Hello, I have a problem with asterisk when dial out to a SIP provider. Asterisk send a INVITE with no credentials, the provider reply with a 401 Unauthorized. However, Asterisk DOES NOT resend the invite again with credentials. But it hangs there (maybe waiting for a ok) It is this a bug in asterisk or the provider is supposed to send something else rather than a 401 as answer for a INVITE ?

Hello, I am working with a matrix of multilocus genotypes for ~180 individual snail samples, with substantial missing data. I am trying to calculate the pairwise genetic distance between individuals using the stats package 'dist' function, using euclidean distance. I took a subset of this dataset (3 samples x 3 loci) to test how euclidean distance is calculated: 3x3 subset used

the first line of dist() says if (!is.na(pmatch(method, "euclidian"))) shouldn't that be "euclidean" ? --------------------- R version 2.5.1 (2007-06-27) i486-pc-linux-gnu locale:

I work with Windows and use R version 2.4.1. I am JUST starting to learn this program... I get this warning message 'NAs introduced by coercion' while trying to build a distance matrix (to be analyzed with NMDS later) from a 336 x 100 data matrix. The original matrix has lots of zeros and no missing values, but I don't think this should matter. I searched this forum and people have

Hello, everybody, I hope somebody could help me with a dist() function. I have a data frame of size 2*4087 (col*row), where col corresponds to the treatment and rows are species, values are Hellinger distances, I should reconstruct a distance matrix with a dist() function. I know that "euclidean" method should be used. When I type: dist(dframe,"euclidean") it gives me a

Hello, I am trying to do a multi-dimensional scaling of the World Bank's quality of governance indicators for the Balkan region. I am having trouble labelling my plot. Could some kind person help me out. How do I set the attribute Label by a variable (say, "Code")? At present I get this: >qog.dist<-dist(Balkans.data, method = "euclidean", diag = FALSE, upper =

Vince Carey found this (thank you!). Since the fix to the problem is not entirely obvious, I post this to R-devel as RFC: help(dist) says: >> Missing values are allowed, and are excluded from all computations >> involving the rows within which they occur. If some columns are >> excluded in calculating a Euclidean, Manhattan or Canberra >> distance, the sum is

What are the plans for the CentOS repos with respect to authentication and https everywhere? At the moment it is a trivial exercise to perform a MTM attack during a yum update over http. -- *** e-Mail is NOT a SECURE channel *** Do NOT transmit sensitive data via e-Mail James B. Byrne mailto:ByrneJB at Harte-Lyne.ca Harte & Lyne Limited

> 3x3 subset used > Locus1 Locus2 Locus3 > Samp1 GG <NA> GG > Samp2 AG CA GA > Samp3 AG CA GG > > The euclidean distance function is defined as: sqrt(sum((x_i - y_i)^2)) My > assumption was that the difference between

Hi guys, I've been using the kmeans and hclust functions for some time now and was wondering if I could specify a custom metric when passing my data frame into hclust as a distance matrix. Actually, kmeans doesn't even take a distance matrix; it takes the data frame directly. I was wondering if there's a way or if there's a package that lets you create distance matrices from

Hi All, I'm working on analyzing a large data set, lets asume that dim(Data)=c(1000,8700). I want to calculate the canberra distance between the columns of this matrix, and using a toy example ('test' is a matrix filled with random numbers 0-1): > system.time(d<-as.matrix(dist(t(test), method = "canberra", diag = FALSE, upper = FALSE, p = 2))) user system

Hi all, I have a matrix of about 100.000?x 4?that I need?to classify using euclidean metric. For that I am using dist?or daisy functions, but I am afraid that the message: Error in vector("double", length) : vector size specified is too large, means too much lines. Can anyone suggest me how should I analyse this matrix? Thanks in advance, Diogo Andr? Alagador MNCN,CSIC, Madrid, Spain

Dear all: I want to ask question about "binary" distance measure. As far as I know, there are many binary distance measures,eg, binary Jarcad distance, binary euclidean distance, and binary Bray-Curtis distance,etc. It is even more confusing because many have more than one name. So , I wan to know what the definite name of the binary distance measure of the "dist" function

hi, i have just begun using R, so please bear with me. i am trying to use cmdscale and display the result. i read the data using read.table(), calculate the proximity matrix using dist() and the display the result using the cmdscale(). this is very fine. in addition, i want the display to distinguish between two classes of records in my data. i have my data records marked as "1" or

This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. ---559023410-162216788-916833047=:29339 Content-Type: TEXT/PLAIN; charset=US-ASCII On my R installation (0.62.4) there is no dist() function, so I attach one possibility. It provides