[R] pairwise difference operator

[Gabor Grothendieck]

Gabor Grothendieck <ggrothendieck <at> myway.com> writes:

: 
: Adaikalavan Ramasamy <ramasamy <at> cancer.org.uk> writes:
: 
: : 
: : Thank you to Marc Schwartz and Gabor Grothendieck for their responses.
: : Both solutions are useful.
: : 
: : It would be nice to generalise this problem to situations where other
: : operations besides difference. Maybe a new member of apply family -
: : pwapply for pairwise apply ? 
: : 
: : Of course the output would be different if the results of an operation
: : on two columns produce a vector (like pairwise difference here) or a
: : single value (like in correlation or pairwise t-test) and one need to
: : somehow account for this.
: 
: Since the general case would involve columns or array slices between
: two not necessarily identical arrays I think the general case is really
: just a sort of generalized inner product.
: 
: In the case that the generalized difference is a scalar its usually called 
: a product and the Euclidean inner product is the most common and takes 
: the form of matrix multiplication which can be done in the one of 
: the following ways:
: 
: 	res1 <- t(mat) %*% mat
: 	res2 <- crossprod(mat, mat)
: 	res3 <- crossprod(mat)
: 
: A generalized inner product, f, replacing the Euclidean one can be
: obtained using a double apply like this:
: 
: 	res4 <- apply(mat, 2, function(a) apply(mat, 2, function(b) sum(a*b)))
: 
: where sum(a*b) can be replaced by f(a,b) for a general inner product
: function.  This actually works even if f returns a vector or other
: array; however, you may need to reshape the result in that case.
: 
: In  the above cases the two matrices were the same but, as mentioned,
: they need not be and you can't count on symmetry between f(a,b) and
: f(b,a).   If your two matrices are the saame and  you can count on
: symmetry then you may want only the lower triangular part and in
: that case you can use lower.tri like this:
: 
: 	res4[lower.tri(res4)]

In rereading what I had written it occurred to me that you
also may be interested in ?dist and the references therein
for a number of special cases and for converting matrices to 
dist objects.  Also see ?var