I think this will do what you want, though there may be ways of speeding it
up further.

theta.dist <- function(x)
as.dist(acos(crossprod(t(x))/sqrt(crossprod(t(rowSums(x*x)))))/pi*180)





***********************************
Simon Gatehouse                                  
CSIRO Exploration and Mining,
Newbigin Close off Julius Ave
North Ryde, NSW
 
Mail:      PO Box 136, North Ryde
           NSW 1670, Australia
Phone:     61 (2) 9490 8677
Fax:       61 (2) 9490 8921
Mobile:    61  0407 130 635 
E-mail:    simon.gatehouse@csiro.au
Web Page:  http://www.csiro.au/ <http://www.csiro.au/> 


-----Original Message-----
From: Xiao-Jun Ma [mailto:xma@arcturusag.com <mailto:xma@arcturusag.com> ] 
Sent: Friday, November 28, 2003 10:02 AM
To: 'r-help@stat.math.ethz.ch '
Subject: [R] Getting rid of loops?


I wrote a function to calculate cosine distances between rows of a matrix.
It uses two loops and is slow. Any suggestions to speed this up? Thanks in
advance.


theta.dist <- function(x){

  res <- matrix(NA, nrow(x), nrow(x))

  for (i in 1:nrow(x)){
    for(j in 1:nrow(x)){
      if (i > j)
        res[i, j] <- res[j, i]
      else {
        v1 <- x[i,]
        v2 <- x[j,]
        good <- !is.na(v1) & !is.na(v2)
        v1 <- v1[good]
        v2 <- v2[good]
        theta <- acos(v1%*%v2 / sqrt(v1%*%v1 * v2%*%v2 )) / pi * 180
        res[i,j] <- theta
      }
    }
  }
  as.dist(res)
}

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