sparse matrix

On Mon, 8 Jan 2001, Prof Brian Ripley wrote:

A matrix in R is a vector plus a dim atttribute.  I presume you mean a
numeric matrix (there are other types).  Then it needs a 8byte space per
entry.

Yes. Numeric matrix.

There are other ways to handle matrices: look at package Matrix, for
example.

One obvious representation is to store the non-zero elements and their
locations.

Just how large is this matrix, and does it have a pattern to its sparsity?

10000 x 10000 elements and 50 000 x 50 000 elements
There is no pattern of sparsity. Values in matrix means some distance
between words (for 10000 and 5 0000 words). 
98% of elements in matrix are the same (with value 7500)

And what do you want to do with it?  Doing things with sparse matrices has
a tendency to make them less sparse.

Hierarchical clustering. Input matrix is distance matrix for hierarchical
clustering with function hclust.