If I understood you correctly, you have this matrix of indicator variables for
occurrences of terms in documents:
A <- matrix(c(1,1,0,0,1,1,1,0,1,1,1,0,0,0,1), nrow=3, byrow=TRUE,
dimnames=list(paste("doc",1:3), paste("term",1:5)))
A
and want to determine co-occurrence counts for pairs of terms, right? (The
formatting of your matrices was messed up, and some of your co-occurrence
counts don't make sense to me.)
The fastest and easiest solution is
t(A) %*% A
Hope this helps,
Stefan
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