Jim,
The next step for understanding what happens is to subset a complicated
expression
and see what its sub-pieces are doing.
Since
apply(a[!is.na(a)],2,sum)
doesn't work, start by looking at each of the arguments to apply.
You already verified that
!is.na(a)
gives what you want. Now take the next step and see that
a[!is.na(a)]
doesn't give what you want.
Looking at nested sets of sub-expressions is the key to learning R.
Rich
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