[SciPy-User] fisherexact.py returns None

Pete Shepard peter.shepard@gmail....
Sun Dec 20 15:44:57 CST 2009


I think the indent issue was due to copying and pasting also, attached is
the code.

On Sun, Dec 20, 2009 at 1:05 PM, <josef.pktd@gmail.com> wrote:

> On Sun, Dec 20, 2009 at 3:50 PM, Pete Shepard <peter.shepard@gmail.com>
> wrote:
> > Thanks for the reply Josef,
> >
> > Numpy version =1:1.3.0-3
> > SciPy version=0.7.0-2
> >
> >
> > Here is the code I am using, interstingly line 99 chokes in the
> > testFisherExact() : example, don't know if these problems are related
> >
> >
> > # -*- coding: utf-8 -*-
> >
> > #!/usr/bin/python
> >
> >
> > import re
> > import sys, os
> > from scipy.stats import *
> > #from scipy import array,searchsorted, histogram
> > import re
> > import operator
> > import matplotlib
> > matplotlib.use('PDF')
> > import pylab
> > "
> >
> > def fisherExact(c) :
> >             """Performs a Fisher exact test on a 2x2 contingency table in
> > list of lists
> >                format.  Returns a tuple of (odds ratio, two-tailed
> P-value).
> >
> >                Examples:
> >                >>> fisherExact([[100, 2], [1000, 5]])
> >                (0.25, 0.13007593634330314)
> >                """
> >             oddsRatio = c[0][0] * c[1][1] / float(c[1][0] * c[0][1])
> >             n1 = c[0][0] + c[0][1]
> >             n2 = c[1][0] + c[1][1]
> >             n  = c[0][0] + c[1][0]
> >
> >             mode = int(float((n + 1) * (n1 + 1)) / (n1 + n2 + 2))
> >             pExact = hypergeom.pmf(c[0][0], n1 + n2, n1, n)
> >             pMode = hypergeom.pmf(c[0][0], n1 + n2, n1, n)
> >
> >             if c[0][0] == mode :
> >                     return oddsRatio, 1.0
> >             elif c[0][0] < mode :
> >                     pLower = hypergeom.cdf(c[0][0], n1 + n2, n1, n)
> >
> >                     # Binary search for where to begin upper half.
> >                     min = mode
> >                     max = n
> >                     guess = -1
> >                     while min != max :
> >                             guess = max if (max == min + 1 and guess ==
> min)
> > else \
> >                                             (max + min) / 2
> >
> >                             pGuess = hypergeom.pmf(guess, n1 + n2, n1, n)
> >                             if pGuess <= pExact and hypergeom.pmf(guess -
> 1,
> > n1 + n2, n1, n) > pExact :
> >                                     break
> >                             elif pGuess < pExact :
> >                                     max = guess
> >                             else :
> >                                     min = guess
> >
> >                     if guess == -1 and min == max :
> >                             guess = min
> >
> >                     return oddsRatio, pLower + hypergeom.sf(guess - 1, n1
> +
> > n2, n1, n)
> >             else :
> >                     pUpper = hypergeom.sf(c[0][0] - 1, n1 + n2, n1, n);
> >
> >                     # Special case to prevent binary search from getting
> > stuck.
> >                     if hypergeom.pmf(0, n1 + n2, n1, n) > pExact :
> >                             return oddsRatio, pUpper
> >
> >                     # Binary search for where to begin lower half.
> >                     min = 0
> >                     max = mode
> >                     guess = -1
> >                     while min != max :
> >                             guess = max if (max == min + 1 and guess ==
> min)
> > else \
> >                                             (max + min) / 2
> >                             pGuess = hypergeom.pmf(guess, n1 + n2, n1,
> n);
> >
> >                             if pGuess <= pExact and hypergeom.pmf(guess +
> 1,
> > n1 + n2, n1, n) > pExact :
> >                                     break;
> >                             elif pGuess <= pExact  :
> >                                     min = guess
> >                             else :
> >                                     max = guess
> >
> >                     if guess == -1 and min == max :
> >                             guess = min
> >                         return oddsRatio, pUpper + hypergeom.cdf(guess,
> n1 +
> > n2, n1, n)
>
> this return line has the wrong indent, it should be at the same column
> as the   if guess == -1 and min == max :
>
> Note: I had to reformat the indent to 4 spaces because IDLE
> complained. In these cases, it would be better to also attach the
> file, then I would be sure I have the same file than with copy and
> paste from the mail reader.
>
> Tell me if that solves the problem, I would think it's unlikely that
> your versions of scipy is to old for this.
>
> Josef
>
> >
> > def testFisherExact() :
> >     """Just some tests to show that fisherExact() works correctly."""
> >     def approxEqual(n1, n2) :
> >         return abs(n1 - n2) < 0.01
> >
> >     res = fisherExact([[100, 2], [1000, 5]])
> >     assert(approxEqual(res[1], 0.1301))
> >     assert(approxEqual(res[0], 0.25))
> >     res = fisherExact([[2, 7], [8, 2]])
> >     assert(approxEqual(res[1], 0.0230141))
> >     assert(approxEqual(res[0], 4.0 / 56))
> >     res = fisherExact([[100, 2], [1000, 5]])
> >     #assert(approxEqual(res[1],  0.1973244))
> >         res = fisherExact([[5, 15], [20, 20]])
> >     assert(approxEqual(res[1], 0.0958044))
> >     res = fisherExact([[5, 16], [20, 25]])
> >     assert(approxEqual(res[1], 0.1725862))
> >     res = fisherExact([[10, 5], [10, 1]])
> >     assert(approxEqual(res[1], 0.1973244))
> >
> > D=[[6, 1], [1, 6]]
> > testFisherExact()
> > p=fisherExact(D)
> > print p
> > On Sun, Dec 20, 2009 at 10:37 AM, <josef.pktd@gmail.com> wrote:
> >>
> >> On Sun, Dec 20, 2009 at 12:26 PM, Pete Shepard <peter.shepard@gmail.com
> >
> >> wrote:
> >> > Hello,
> >> >
> >> > I am using a fisher exact test I got from
> >> > http://projects.scipy.org/scipy/attachment/ticket/956/fisher.py. This
> >> > program takes in two tuples and returns an odds ratio and a  p-value.
> >> > Most
> >> > tuples are handled nicely by the script but certain tuples eg "[[6,
> 1],
> >> > [1,
> >> > 6]]" return "None". I am wondering if anyone knows why this is true?
> >>
> >> I get this, with and without the patch of thomas in the comments
> >>
> >> >>> fisherExact([[6, 1], [1, 6]])
> >> (36.0, 0.029137529137528768)
> >>
> >> Do you have an exact example? Which version of numpy and scipy?
> >> Looking at the code, I don't see any reason why it should return None.
> >>
> >> Josef
> >> >
> >> > TIA
> >> >
> >> > _______________________________________________
> >> > SciPy-User mailing list
> >> > SciPy-User@scipy.org
> >> > http://mail.scipy.org/mailman/listinfo/scipy-user
> >> >
> >> >
> >> _______________________________________________
> >> SciPy-User mailing list
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> >> http://mail.scipy.org/mailman/listinfo/scipy-user
> >
> >
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> >
> >
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