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Project Description

Fisher’s Exact Test

Simple, fast implementation of Fisher’s exact test. . For example, for the following table:

o Having the property Not having the property
Selected 12 5
Not selected 29 2

Perhaps we are interested in whether there is any difference of property in selected vs. non-selected groups, then we can do the Fisher’s exact test.

Installation

within this folder

easy_install .

from pypi

easy_install fisher

or from github (contributions welcomed)

git clone git://github.com/brentp/fishers_exact_test.git

Usage

fisher.pvalue() accepts 4 values corresponding to the 2-by-2 contingency table, returns an object with attributes for left_tail, right_tail, and two_tail p-values

>>> from fisher import pvalue
>>> mat = [[12, 5], [29, 2]]
>>> p = pvalue(12, 5, 29, 2)
>>> p.left_tail, p.right_tail, p.two_tail
(0.044554737835078267, 0.99452520602190897, 0.08026855207410688)

Benchmark

A simple benchmark that calls the Fisher’s exact test 1000 times (in scripts/rfisher.py):

calling python fisher...
iterations/sec: 3000.62526381
calling rpy fisher...
iterations/sec: 289.225902364
calling R directly...
iterations/sec: 244.36542276

So the cython fisher is up to 10 times faster than rpy or R version.

Release History

Release History

0.1.4

This version

History Node

TODO: Figure out how to actually get changelog content.

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0.1.2

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0.1.1

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Download Files

Download Files

TODO: Brief introduction on what you do with files - including link to relevant help section.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
fisher-0.1.4.tar.gz (45.0 kB) Copy SHA256 Checksum SHA256 Source Mar 30, 2010

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