okay, that makes sense. i will revert that and change the tests it
affected.


On Thu, Dec 5, 2013 at 11:06 AM, Jai Ram Rideout
<notifications@github.com>wrote:

> In qiime/pycogent_backports/test.py:
>
> > @@ -645,32 +766,25 @@ def mc_t_two_sample(x_items, y_items, tails=None, permutations=999,
> >              better = (array(perm_t_stats) <= obs_t).sum()
> >          elif tails == 'high':
> >              better = (array(perm_t_stats) >= obs_t).sum()
> > -        nonparam_p_val = (better + 1) / (permutations + 1)
> > -
> > +        nonparam_p_val = better/permutations
>
> The +1 is for counting the original unpermuted data. This also ensures
> that the p-value never drops below 1 / (num_perms + 1) . This is how
> nonparametric p-values are computed in R and elsewhere in our stats code.
> I've also read papers / online sources that describe this method of
> computing monte carlo p-values (can dig those up if you want).
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/qiime/qiime/pull/1091/files#r8138114>
> .
>