how to calculate Euclidean distance between two matrices in R

Question

I have two huge matrices with equal dimensions. I want to calculate Euclidean distance between them. I know this is the function:

euclidean_distance <- fu         


        

Answer 1

This is a job for the base function outer:

outer(mat1,mat2,Vectorize(euclidean_distance))

         x         y         z
x  9220.40  9260.736  8866.034
y 12806.35 12820.086 12121.927
z 11630.86 11665.869 11155.823

Answer 2

You can use the package pdist:

library(pdist)
dists <- pdist(t(mat1), t(mat2))
as.matrix(dists)
         [,1]      [,2]      [,3]
[1,]  9220.40  9260.735  8866.033
[2,] 12806.35 12820.086 12121.927
[3,] 11630.86 11665.869 11155.823

this will give you all Euclidean distances of the pairs: (mat1$x,mat2$x), (mat1$x,mat2$y),..., (mat1$z,mat2$z)