Fisher Fast Fisher's Exact Test
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Python library Python testing EXACT exact test

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Fast Fisher's Exact Test Fisher is a simple and fast implementation of Fisher's exact test. For example, for the following table: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 foldereasy_install .from pypieasy_install fisheror from github (contributions welcomed)git clone git://github.com/brentp/fishers_exact_test.gitUsage: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 = , ]>>> 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: 3000.62526381calling rpy fisher...iterations/sec: 289.225902364calling R directly...iterations/sec: 244.36542276So the cython fisher is up to 10 times faster than rpy or R version. Requirements: · Python

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