millions of comparisons, speed wanted

Dear Andy,

Just some untested idea:
If the data are all 0/1, you could use dist(input, method="manhattan"), and
then check which entry equals 1.  This should be much faster than creating
all pairs of rows and check position-by-position.

Thanks for the idea, I played a little with it. At the beginning yes, the data 
are all 0/1, but during the minimizing iterations there are also "x" values; 
for example comparing:
0 1 0 1 1
0 0 0 1 1
should return
0 "x" 0 1 1

whereas
0 "x" 0 1 1
0 0 0 1 1
shouldn't even be compared (they have different number of figures).

Replacing "x" with NA in dist is not yielding results either, as with
NA 0 0 1 1
0 0 0 1 1
dist returns 0.

I even wanted to see if I could tweak the dist code, but it calls a C program 
and I gave up.

Nice idea anyhow, maybe I'll find a way to use it further.
Best,
Adrian

Adrian DUSA
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