[SciPy-User] Fisher exact test, anyone?

Bruce Southey bsouthey@gmail....
Sun Nov 14 10:40:28 CST 2010


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.

I also do not have time for this month.

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.

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).

Bruce

>
> As an aside:
> There is a related ticket for numerical precision problems in the sf
> calculations of discrete distributions,
> http://projects.scipy.org/scipy/ticket/1218 . However, this requires a
> rewrite of the current generic cdf calculation and adding a matching
> sf version. The current implementation only works under special
> assumptions which luckily are satisfied by all current discrete
> distributions. I think, I will find time for this before 0.9.
>
> Josef
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