distance between two matrices

Sounds like knn classification.  See function knn1 in package class.

knn(A, B, 1:nrow(A))

gives the same answers as your loop code, and is just a carefully tuned C 
equivalent.

There are faster ways to do this by preprocessing set A discussed e.g. in 
my PRNN book but your numbers took only 11s on my PC.

On Tue, 27 Jan 2004, Sundar Dorai-Raj wrote:

Hi all,
  Say I have a matrix A with dimension m x 2 and matrix B with 
dimension n x 2. I would like to find the row in A that is closest to 
the each row in B. Here's an example (using a loop):

set.seed(1)
A <- matrix(runif(12), 6, 2) # 6 x 2
B <- matrix(runif(6), 3, 2)  # 3 x 2
m <- vector("numeric", nrow(B))
for(j in 1:nrow(B)) {
  d <- (A[, 1] - B[j, 1])^2 + (A[, 2] - B[j, 2])^2
  m[j] <- which.min(d)
}

All I need is m[]. I would like to accomplish this without using the 
loop if possible, since for my real data n > 140K and m > 1K. I hope 
this makes sense.

Thanks,
Sundar