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...ns are one off. That is accounted for in the code.) In reality the data will be much bigger, containing 10000 rows and a variable number of columns (inds) between 10 and 500. The correct result is: > cmat tru_rr tru_rv tru_vv call_rr 2 2 0 call_rv 0 4 0 call_vv 0 0 4 I am not sure what the best way to do this is. I implemented it once using two for loops. Then I tried to use lapply and came up with a nested lapply solution, but it was slower than the simple loops. I still think that there is a better way and I was hoping for some advic...