[R] Proportion of equal entries in dist()?

Henrik Bengtsson hb at biostat.ucsf.edu
Wed Jan 21 05:18:52 CET 2015

On Mon, Jan 19, 2015 at 5:38 AM, Jorge I Velez <jorgeivanvelez at gmail.com> wrote:
> Dear all,
> Given vectors "x" and "y", I would like to compute the proportion of
> entries that are equal, that is, mean(x == y).
> Now, suppose I have the following matrix:
> n <- 1e2
> m <- 1e4
> X <- matrix(sample(0:2, m*n, replace = TRUE), ncol = m)
> I am interested in calculating the above proportion for every pairwise
> combination of rows.  I came up with the following:
> myd <- function(X, p = NROW(X)){
> D <- matrix(NA, p, p)
> for(i in 1:p) for(j in 1:p) if(i > j) D[i, j] <- mean(X[i, ] == X[j,])
> D
> }
> system.time(d <- myd(X))

An obvious speed up is to only subset X[i,] onces and not j times.
Also, mean() is a generic function meaning it dispatches on class in
each call, which has some overhead; it's a bit faster to use sum().
Also, beware of the classical matrix(NA, ...) mistake, which does
*not* allocate a numeric matrix and will just results in an extra copy
and coercion, cf.

myd2 <- function(X, p = NROW(X)) {
  D <- matrix(NA_real_, nrow=p, ncol=p)
  for (i in 2:p) {
    Xi <- X[i, ]
    for (j in 1:(i-1)) D[i, j] <- sum(Xi == X[j,])
  D / ncol(X)

That's > 1.5 times faster.  But as others already mentioned, this is
something you'll do best in C/C++, because you can avoid lots of
overhead from subsetting/copying and garbage collection.


> However, in my application n and m are much more larger than in this
> example and the computational time might be an issue.  I would very much
> appreciate any suggestions on how to speed the "myd" function.
> Note:  I have done some experiments with the dist() function and despite
> being much, much, much faster than "myd", none of the default distances
> fits my needs.  I would also appreciate any suggestions on how to include
> "my own" distance function in dist().
> Thank you very much for your time.
> Best regards,
> Jorge Velez.-
>         [[alternative HTML version deleted]]
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