Re: [R] vectorize an expression

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From: Prof Brian Ripley (ripley@stats.ox.ac.uk)
Date: Tue 25 May 2004 - 23:14:57 EST


Message-id: <Pine.LNX.4.44.0405251406310.2515-100000@gannet.stats>

Suggestion 1: Use the R function `dist'.

Suggestion 2: Don't mask an R system function name.

Suggestion 3: Time this. I don't think it is worth vectorizing.

Suggestion 4: The bit which is actually nonvectorized is your function
dist. If you had a vectorized distance function, you could do

for(i in 1:5) array[i,] <- dist(a[i,,drop=FALSE] , a)

but that would need

dist <- function(x1,x2) sqrt(rowSums(x1-x2)^2)

I could tell you how to fully vectorize it, but I doubt if it would have
any benefit.

(None of this is tested, because of 1 and 3.)

On Tue, 25 May 2004, Robin Hankin wrote:

> Hi guys. Another thing I cannot vectorize:
>
> I have an array "a", of size 5-by-2, for example, of 5 2D vectors. I
> also have a distance function that computes the distance between two
> vectors (usual Euclidean distance is a good example but I have other metrics I
> want to use as well). I want a 5-by-5 array with the [i,j]th element being
> the distance from a[i,] to a[j,]
>
> To Wit:
>
> a <- matrix(1:10,5,2)
> array <- matrix(NA, 5, 5)
> dist <- function(x1,x2){sqrt(sum(x1-x2)^2)}
>
> #NONVECTORIZED BIT FOLLOWS
> for(i in 1:5) {
> for(j in 1:5) {
> array[i,j] <- dist(a[i,] , a[j,])
> }
> }
>
> (note that array[i,i]=0 for i=1:5 as expected).
>
> How to vectorize this?
>
>
>

-- 
Brian D. Ripley,                  ripley@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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