[R] Fast version of Fisher's Exact Test

Steven McKinney smckinney at bccrc.ca
Sat Apr 9 00:44:53 CEST 2011

Do you mean a test something such as this?

> fisher.test(matrix(c(502,498,490, 510), nrow = 2))

	Fisher's Exact Test for Count Data

data:  matrix(c(502, 498, 490, 510), nrow = 2) 
p-value = 0.6228
alternative hypothesis: true odds ratio is not equal to 1 
95 percent confidence interval:
 0.8770113 1.2550998 
sample estimates:
odds ratio 

This runs quickly on my machine.

> system.time(fisher.test(matrix(c(502,498,490, 510), nrow = 2)))
   user  system elapsed 
  0.008   0.001   0.010 
> sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

[1] en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] tools_2.12.2

Can you provide an example that is running slowly for you?

Steven McKinney

From: r-help-bounces at r-project.org [r-help-bounces at r-project.org] On Behalf Of Jim Silverton [jim.silverton at gmail.com]
Sent: April 8, 2011 9:43 AM
To: r-help at r-project.org
Subject: Re: [R] Fast version of Fisher's Exact Test

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.


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