Sorry about the misunderstanding. If you form matrix m as I wrote before, then I think the following will give you the matrix you are interested in: > obj <- c(1,2,3,4,5) > group <- c(1,2,1,1,3) > m <- matrix(rep(0,3*5),nrow=5,ncol=3) > m [,1] [,2] [,3] [1,] 0 0 0 [2,] 0 0 0 [3,] 0 0 0 [4,] 0 0 0 [5,] 0 0 0 > for (i in 1:5) {m[obj[i],group[i]]=1} > m [,1] [,2] [,3] [1,] 1 0 0 [2,] 0 1 0 [3,] 1 0 0 [4,] 1 0 0 [5,] 0 0 1 > c <- crossprod(t(m),t(m)) > c [,1] [,2] [,3] [,4] [,5] [1,] 1 0 1 1 0 [2,] 0 1 0 0 0 [3,] 1 0 1 1 0 [4,] 1 0 1 1 0 [5,] 0 0 0 0 1 Note that crossprod(m,m) will give you counts of objects within groups: > c <- crossprod(m,m) > c [,1] [,2] [,3] [1,] 3 0 0 [2,] 0 1 0 [3,] 0 0 1 Hope this helps. Sean On 11/11/03 6:37 AM, "Alexey Shipunov" <a.shipunov@rbgkew.org.uk> wrote: >> The object indices are in rows, and group indices in columns. > ... but I actually mean that columns and > rows are _both_ represent objects, not groups. Thus, if two objects > (say, 2 and 3) share the same group, the cells [2, 3] and [3, 2] > have value "1". > > Best wishes, > > > ================================= > Dr. Alexey B. Shipunov > Section of Molecular Systematics > Jodrell Laboratory > Royal Botanic Gardens, Kew, > Richmond, Surrey, TW9 3DS, U.K. > e-mail: a.shipunov@rbgkew.org.uk >