"Most likely reason is that the number of unique values in the rows of
habs is not the same."

Yes, I think that is the problem, thank you.
How would I write the code to include 0s in the matrix, 
ie, I want to have a record of when 1, 2, or 3 does not get sampled, 
to come up with a frequency of each value for each nn (which in this case is
5)

I tried 'factor' but what ends up happening is that the matrix gets reduced
to zero 
after a couple of iterations.

habs=t(apply(habs, 1, function(x) table(factor(x, levels = 1:3))))

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