From: Charles C. Berry <cberry_at_tajo.ucsd.edu>

Date: Tue 23 Jan 2007 - 23:20:53 GMT

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Wed Jan 24 10:25:37 2007

Date: Tue 23 Jan 2007 - 23:20:53 GMT

I am rusty on 'Matrix', but I see there are crossprod methods for those classes.

gives your result up to scale factors of sqrt(res[i,i]*res[j,j]), so something like

diagnl <- Diagonal( ncol(x), sqrt( diag( res ) )

final.res <- diagnl %*% res %*% diagnl

should do it.

On Tue, 23 Jan 2007, Jose Quesada wrote:

> (Extremely sorry, disregard previous email as I hit send before pasting the latest version of the example; this one is smaller too)

*> Dear R users,
**>
**> I want to apply a function that takes two vectors as input to all pairs
**> (combinations (nrow(X), 2))of matrix rows in a matrix.
**> I know that ideally, one should avoid loops in R, but after reading the docs for
**> do.call, apply, etc, I still don't know how to write the nested loop in a
**> vectorized way.
**>
**> Example data:
**> x = matrix(rnorm(100), 10, 10)
**> # this is actually a very large sparse matrix, but it doesn't matter for the
**> # example
**> library(Matrix)
**> x = as(x,"CsparseMatrix")
**>
**> # cosine function
**> cosine = function (x, y){
**> if (is.vector(x) && is.vector(y)) {
**> return(crossprod(x, y)/sqrt(crossprod(x) * crossprod(y)))
**> } else {stop("cosine: argument mismatch. Two vectors needed as input.")}
**> }
**>
**> # The loop-based solution I have is:
**> if (is(x, "Matrix") ) {
**> cos = array(NA, c(ncol(x), ncol(x)))
**> for (i in 2:ncol(x)) {
**> for (j in 1:(i - 1)) {
**> cos[i, j] = cosine(x[, i], x[, j])
**> }
**> }
**> }
**>
**> This solution seems inneficient. Is there an easy way of achieving this with a
**> clever do.call + apply combination?
**>
**> Also, I have noticed that getting a row from a Matrix object produces a normal
**> array (i.e., it does not inherit Matrix class). However, selecting >1 rows, does
**> produce a same-class matrix. If I convert with as() the output of selecting one
**> row, am I losing performance? Is there any way to make the resulting vector be a
**> 1-D Matrix object?
**> This solution seems inneficient. Is there an easy way of achieving this with a
**> clever do.call + apply combination?
**> --
**> Thanks in advance,
**> -Jose
**>
**> --
**> Jose Quesada, PhD
**> Research fellow, Psychology Dept.
**> Sussex University, Brighton, UK
**> http://www.andrew.cmu.edu/~jquesada
**>
**> ______________________________________________
**> R-help@stat.math.ethz.ch mailing list
**> https://stat.ethz.ch/mailman/listinfo/r-help
**> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
**> and provide commented, minimal, self-contained, reproducible code.
**>
*

Charles C. Berry (858) 534-2098 Dept of Family/Preventive Medicine E mailto:cberry@tajo.ucsd.edu UC San Diego http://biostat.ucsd.edu/~cberry/ La Jolla, San Diego 92093-0901 ______________________________________________R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Wed Jan 24 10:25:37 2007

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