Hi,
I think you need quotation around I like the following:
> status
2010 2011 2012
1 A A A
2 A I I
3 A A A
4 U U U
5 A A A
6 I I I
7 U I I
8 A U A
9 I A U
10 I I I
> apply(start,2,function(x) {sum(x=="I",na.rm=TRUE)})
X2010 X2011 X2012
3 4 4
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