> Actually, I hadn't realized, but 'permutation_test_score' is named
> 'score', and it does not follow the 'bigger is better rule'. So, in
> addition to there being a documentation problem, there is a consistency
> problem.

unless you see it as a permutation test on a score. It's not a score
function by itself.

> I think that I would favor changing it so that it returns -log(p) (yay,
> another API breakage :$ ).

not really convinced as for permutations you're unlikely have numerical
underflows.

and I prefer - log10(p) for p-values.

> What do people think?

maybe rename the function but keep the behavior.

Alex a bit biased as he wrote this ...

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