[SciPy-Dev] Contingency Table Model

Bruce Southey bsouthey@gmail....
Mon Aug 9 15:35:34 CDT 2010


On 08/09/2010 02:31 PM, Anthony Scopatz wrote:
> Hello All,
>
> I have just opened a ticket 
> (http://projects.scipy.org/scipy/ticket/1258) that adds a general 
> contingency table class to the the stats package.  This class includes 
> methods to slice and collapse the table as well a calculate metrics 
> such as chi-squared and entropy.
>
> This implementation came out of Warren Weckesser and me working on 
> this over the SciPy 2010 statistics sprint.
>
> Please take a look!  Comments and suggestions are always welcome.
> Be Well,
> Anthony
>
>
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Some points:

1) You can not use numpy's asarray function without checking the input 
type. You must be aware of at least masked arrays and Matrix inputs as 
well as new data types.

2) You can not force a dtype on the user -  on line 54 when you can 
provide optional precision.

3) Can you please clarify lines 112-113?
"  scipy.stats.chisquare -- one-way chi-square test (which is not the same
as the n-way test with n=1)."
This needs to be a little more clear because the exact same test 
statistic is being used. In fact the function must give the correct 
answer with 1d array.

4) Related to point 3, lines 72-74 are not correct, see
http://en.wikipedia.org/wiki/Pearson's_chi-square_test 
<http://en.wikipedia.org/wiki/Pearson%27s_chi-square_test>

5) You must allow the user to provide their own expected values

6) Users need to be able to control the output - really I don't want to 
see the table of expected values unless requested. Also a user might 
just want the table of expected values and nothing else.

7) You should not need the chi2 function.

8) More generally, what is the need for having an ContingencyTable object?


Bruce





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