[SciPy-User] Fisher exact test, anyone?

Ralf Gommers ralf.gommers@googlemail....
Tue Nov 16 07:04:52 CST 2010

On Mon, Nov 15, 2010 at 12:40 AM, Bruce Southey <bsouthey@gmail.com> wrote:

> On Sat, Nov 13, 2010 at 8:50 PM,  <josef.pktd@gmail.com> wrote:
> > http://projects.scipy.org/scipy/ticket/956 and
> > http://pypi.python.org/pypi/fisher/ have Fisher's exact
> > testimplementations.
> >
> > It would be nice to get a version in for 0.9. I spent a few
> > unsuccessful days on it earlier this year. But since there are two new
> > or corrected versions available, it looks like it just needs testing
> > and a performance comparison.
> >
> > I won't have time for this, so if anyone volunteers for this, scipy
> > 0.9 should be able to get Fisher's exact.
> https://github.com/rgommers/scipy/tree/fisher-exact
All tests pass. There's only one usable version (see below) so I didn't do
performance comparison. I'll leave a note on #956 as well, saying we're
discussing on-list.

 I briefly looked at the code at pypi link but I do not think it is
> good enough for scipy. Also, I do not like when people license code as
> 'BSD' and there is a comment in cfisher.pyx  '# some of this code is
> originally from the internet. (thanks)'. Consequently we can not use
> that code.

I agree, that's not usable. The plain Python algorithm is also fast enough
that there's no need to bother with Cython.

> The code with ticket 956 still needs work especially in terms of the
> input types and probably the API (like having a function that allows
> the user to select either 1 or 2 tailed tests).

Can you explain what you mean by work on input types? I used np.asarray and
forced dtype to be int64. For the 1-tailed test, is it necessary? I note
that pearsonr and spearmanr also only do 2-tailed.

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