Use fisher.test(). Yates' correction compensates for a tendency for Chi-square
to be overestimated in a 2x2 table, but Yates' can overcompensate, reducing
Chi-square too much. It's main advantage was when computers were expensive and
Fisher's Exact was hard to compute by hand. You can see from the following
that Fisher's Exact estimates the p-value as .717, a bit less than .7477.
> M <- matrix(c(8, 12, 4, 10), 2, 2)
> fisher.test(M)
Fisher's Exact Test for Count Data
data: M
p-value = 0.717
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
0.3160571 9.7976232
sample estimates:
odds ratio
1.641969
An alternative would be to let chisq.test() use simulations to estimate the
p-value:
> chisq.test(M, simulate.p.value=TRUE)
Pearson's Chi-squared test with simulated p-value (based on 2000
replicates)
data: M
X-squared = 0.471, df = NA, p-value = 0.7141
Which agrees pretty well with fisher.test(). The X-squared value of 0.471 is
the uncorrected value so you can see that the Yates' correction reduced it
substantially (to .1035).
-------------------------------------
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77840-4352
-----Original Message-----
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Jomy Jose
Sent: Tuesday, February 21, 2017 4:48 AM
To: r-help@r-project.org
Subject: [R] Yates correction
I tried to do chi square test for the following observed frequencies
---------------------------------------------------------------------------------------------
A B
A 8 4
B 12 10
R gave the following output:
-------------------------------------------------------------------------------------------
Pearson's Chi-squared test with Yates' continuity correction
data: M
X-squared = 0.10349, df = 1, p-value = 0.7477
Warning message:
In chisq.test(M) : Chi-squared approximation may be incorrect
---------------------------------------------------------------------------------------------------------------
Whether this result can be relied or we have to use Fishers exact test ?
Jose
[[alternative HTML version deleted]]
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______________________________________________
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