[R] Fast version of Fisher's Exact Test

Stefan Evert stefanML at COLLOCATIONS.DE
Tue Apr 12 16:14:47 CEST 2011

> Is anyone aware of a fast way of doing fisher's exact test for a series of 2
> x 2 tables in R? The fisher.test is really slow if n1=1000 and n2 = 1000.

If you don't require exact two-sided p-values (determined according to a likelihood criterion as in fisher.test), you can use the vectorised fisher.pval() function from the 'corpora' package.

The function is just a wrapper around the hypergeometric distribution; it doesn't compute confidence intervals, which are much more difficult to obtain.


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