Distance Matrix
Computes the Euclidean distance between rows of two matrices.
distmat(X, Y) pdist(X) pdist2(X, Y)
X |
matrix of some size |
Y |
matrix of some size |
Computes Euclidean distance between two vectors A and B as:
||A-B|| = sqrt ( ||A||^2 + ||B||^2 - 2*A.B )
and vectorizes to rows of two matrices (or vectors).
pdist2 is an alias for distmat, while pdist(X) is the
same as distmat(X, X).
matrix of size m x n if x is of size m x k and
y is of size n x k.
If a is m x r and b is n x r then
apply(outer(a,t(b),"-"),c(1,4),function(x)sqrt(sum(diag(x*x))))
is the m x n matrix of distances between the m rows
of a and n rows of b.
This can be modified as necessary, if one wants to apply distances other than the euclidean.
BUT: The code shown here is 10-100 times faster, utilizing the similarity between Euclidean distance and matrix operations.
Copyright (c) 1999 Roland Bunschoten for a Matlab version on MatlabCentral
under the name distance.m. Translated to R by Hans W Borchers.
A <- c(0.0, 0.0)
B <- matrix(c(
0,0, 1,0, 0,1, 1,1), nrow=4, ncol = 2, byrow = TRUE)
distmat(A, B) #=> 0 1 1 sqrt(2)
X <- matrix(rep(0.5, 5), nrow=1, ncol=5)
Y <- matrix(runif(50), nrow=10, ncol=5)
distmat(X, Y)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.