# Fisher\'s Exact Test
[](https://github.com/brentp/fishers_exact_test/actions/workflows/package.yml)
[](https://pypi.org/project/fisher)
Simple, fast implementation of [Fisher\'s exact
test](http://en.wikipedia.org/wiki/Fisher's_exact_test). For example,
for the following table:
| | 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 :
git clone git://github.com/brentp/fishers_exact_test.git
pip install .
From PyPI :
pip install fisher
Or install the development version :
pip install git+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 # doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS
(0.04455473783507..., 0.994525206021..., 0.0802685520741...)
## 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.
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"description": "# Fisher\\'s Exact Test\n\n[](https://github.com/brentp/fishers_exact_test/actions/workflows/package.yml)\n[](https://pypi.org/project/fisher)\n\nSimple, fast implementation of [Fisher\\'s exact\ntest](http://en.wikipedia.org/wiki/Fisher's_exact_test). For example,\nfor the following table:\n\n| | Having the property | Not having the property |\n| ------------ | ------------------- | ----------------------- |\n| Selected | 12 | 5 |\n| Not selected | 29 | 2 |\n\nPerhaps we are interested in whether there is any difference of property\nin selected vs. non-selected groups, then we can do the Fisher\\'s exact\ntest.\n\n## Installation\n\nWithin this folder :\n\n git clone git://github.com/brentp/fishers_exact_test.git\n pip install .\n\nFrom PyPI :\n\n pip install fisher\n\nOr install the development version :\n\n pip install git+git://github.com/brentp/fishers_exact_test.git\n\n## Usage\n\n`fisher.pvalue()` accepts 4 values corresponding to the 2-by-2\ncontingency table, returns an object with attributes for left_tail,\nright_tail, and two_tail p-values :\n\n >>> from fisher import pvalue\n >>> mat = [[12, 5], [29, 2]]\n >>> p = pvalue(12, 5, 29, 2)\n >>> p.left_tail, p.right_tail, p.two_tail # doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS\n (0.04455473783507..., 0.994525206021..., 0.0802685520741...)\n\n## Benchmark\n\nA simple benchmark that calls the Fisher\\'s exact test 1000 times (in\n`scripts/rfisher.py`):\n\n calling python fisher...\n iterations/sec: 3000.62526381\n calling rpy fisher...\n iterations/sec: 289.225902364\n calling R directly...\n iterations/sec: 244.36542276\n\nSo the cython fisher is up to 10 times faster than rpy or R version.\n",
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