nolanbconaway/poisson-etest

A poisson e-test for python.

Python Poisson E-Test

This library contains a function to compute a two-sample poisson E-test, as defined in Krishnamoorthy & Thomson (2004). I simply edited the fortran code posted on Krishnamoorthy's website so that numpy could wrap it. You can look at the edits in one of the early commits to this repo.

The code as it stands has a few problems, but I figured it'd be worth getting a direct implementation up. Here are some problems that I have noticed:

1. Floats not supported for k and n values.
2. Odd behavior with large numbers (I saw it at k = n = 10000).
3. Odd behavior at k = 0.

One day I'll fix these issues by reimplementing in pure python, assuming that doesn't also require a big hit in efficiency.

Install

Numpy is a requirement for poisson-etest, so make sure that's installed first. Then:

pip install poisson-etest

Usage

Test whether two samples of Poisson data were drawn from the same distribution.

>>> from poisson_etest import poisson_etest
>>> sample1_k, sample1_n = 10, 20
>>> sample2_k, sample2_n = 15, 20
>>> poisson_etest(sample1_k, sample2_k, sample1_n, sample2_n)
0.33116214285801826

poisson-etest's Issues

Installing poisson-etest doesn't work

Hi,

I would like to use the Poisson-etest package to compare my datasets but I can't install the package, can someone help me out (I'm not really experienced in programming)?

When I try to install via the PyCharm Termin using pip install poisson-etest, I get this error: extension 'poisson_etest.poisson_etest_fortran' has Fortran sources but no Fortran compiler found.
So I guess I need to install Fortran which I tried as suggested here: https://github.com/NickHilton/poisson-etest (brew install gcc) but then I get the error: The command "brew" is either misspelled or could not be found.

How can I now install Fortran and the poisson-etest package?

Cheers,
Tobi

Can't install

Hi Nolan,
I want to use this code to count the P value, But when i install your package, i met these error:
ERROR: Command errored out with exit status 1:
command: /zs32/home/a1lian/miniconda3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-w5049sut/poisson-etest/setup.py'"'"'; file='"'"'/tmp/pip-install-w5049sut/poisson-etest/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-_ad47rto
cwd: /tmp/pip-install-w5049sut/poisson-etest/
Complete output (5 lines):
Traceback (most recent call last):
File "", line 1, in
File "/tmp/pip-install-w5049sut/poisson-etest/setup.py", line 1, in
from numpy.distutils.core import Extension
ModuleNotFoundError: No module named 'numpy'
----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

Would you please tell me how can i fix this problem?
Thanks,
Aojie