Question

I want all pairwise comparisons for all rows in the matrix, obviously double for loop will work but extremely expensive for large dataset.

I looked up implicit loop like apply(), etc. but have no a clue how to avoid the inner loop.

How can it be achieved?

Answer 1

I’m assuming you’re trying do some type of comparison across all row-pairs of a matrix.
You could use outer() to run through all pairs of row-indices, and apply a vectorized
comparison function to each row-pair. E.g. you could calculate the squared Euclidean distance among all row-pairs as follows:

m <- matrix(1:12,4,3)     
> outer(1:4,1:4, FUN = Vectorize( function(i,j) sum((m[i,]-m[j,])^2 )) )
     [,1] [,2] [,3] [,4]
[1,]    0    3   12   27
[2,]    3    0    3   12
[3,]   12    3    0    3
[4,]   27   12    3    0