Thanks very much for your detailed response! Yes, I am building the file containing the data myself, so I don't need to store the lower triangle of NAs, as you have pointed out. This will be input to a program (not written by me), so I am not entirely sure how the items will be accessed- I will check with the author, and see if I can order the matrix in a way that the program can read speedily! Thanks again for your helpful advice.