fisher-rxc 0.9.0

Fast multithreaded implementation for calculating Fisher's exact test for any RxC sized table

Fisher RxC

Fast multithreaded implementation of calculating Fisher's exact test for any RxC size table. Written in Rust using Maturin.

Installation

pip install fisher-rxc

import fisher

Usage

fisher.exact(table, workspace=None)

Calculate Fisher's exact test for 2D list according to Mehta & Patel's Network Algorithm. If workspace size is not provided, it will be "guessed" dynamically.

Workspace size of 2e8 takes ~800MB of RAM.

fisher.sim(table, iterations)

Calculate Fisher's exact test for 2D list by Monte Carlo simulation. This multithreaded implementation can be more than 100x faster than using R through rpy2.

A modern CPU can quickly do 10^8 iterations and get very accurate results.

fisher.recursive(table)

Calculate Fisher's exact test by a simple multithreaded recursive algorithm. This is generally much slower than the fisher.exact function. Only use for small tables with low numbers.

Return values

0 <= x <= 1: p-value

x < 0: error code number, message printed to stdout

References

Contingency table generator (ASA159): https://people.sc.fsu.edu/~jburkardt/c_src/asa159/asa159.html

Fisher' exact test - network algorithm (ASA643): https://netlib.org/toms/643.gz

Fisher's exact test - recursive: https://stackoverflow.com/questions/25368284/fishers-exact-test-for-bigger-than-2-by-2-contingency-table

Fortran to C transpiler: https://www.netlib.org/toms/

C to Rust transpiler: https://github.com/immunant/c2rust