Fast version of Fisher's Exact Test
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 1.049119 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) locale: [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
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.
--
Thanks,
Jim.
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