Source Code for Module mvpa.misc.stats

 1  #emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*- 
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 4  # 
 5  #   See COPYING file distributed along with the PyMVPA package for the 
 6  #   copyright and license terms. 
 7  # 
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 9  """Little statistics helper""" 
10   
11  __docformat__ = 'restructuredtext' 
12   
13  from mvpa.base import externals 
14  externals.exists('scipy', raiseException=True) 
15   
16  import scipy.stats as stats 
17  import numpy as N 
18   
19 -def chisquare(obs, exp=None): 
20      """Compute the chisquare value of a contingency table with arbitrary 
21      dimensions. 
22   
23      If no expected frequencies are supplied, the total N is assumed to be 
24      equally distributed across all cells. 
25   
26      Returns: chisquare-stats, associated p-value (upper tail) 
27      """ 
28      obs = N.array(obs) 
29   
30      # get total number of observations 
31      nobs = N.sum(obs) 
32   
33      # if no expected value are supplied assume equal distribution 
34      if exp == None: 
35          exp = N.ones(obs.shape) * nobs / N.prod(obs.shape) 
36   
37      # make sure to have floating point data 
38      exp = exp.astype(float) 
39   
40      # compute chisquare value 
41      chisq = N.sum((obs - exp )**2 / exp) 
42   
43      # return chisq and probability (upper tail) 
44      return chisq, stats.chisqprob(chisq, N.prod(obs.shape) - 1) 
45