[R] fisher exact for > 2x2 table

Mike Miller mbmiller+l at gmail.com
Fri Apr 29 23:20:26 CEST 2011


Your biostatistician has not disagreed with the rest of us about anything 
except for his preferred name for the test.  He wants to call it the 
Freeman-Halton test, some people call it the Fisher-Freeman-Halton test, 
but most people call it the Fisher Exact test -- all are the same test. 
When he was "adamant you could not do > 2x2", what he was being adamant 
about was the name you should use when referring to the test for tables 
larger than 2x2.  Why he was doing that, I don't know, but I think it is 
silly -- he confused you and the rest of us.

He goes on to tell you that to get the Freeman-Halton test in SAS, you use 
"tables a * b / fisher".  In other words, SAS calls the test "Fisher" 
instead of calling it Freeman-Halton.  R also calls it "Fisher" and not 
Freeman-Halton.  I'm like R and SAS and unlike your biostatistician, but 
to each his own.

You say that he is "exceptionally clear on this point," which may be true, 
but what is the point?  The point is that he prefers a different *name* 
for the test than the rest of us.  Everyone agrees on the math/stat.


Michael B. Miller, Ph.D.
Minnesota Center for Twin and Family Research
Department of Psychology
University of Minnesota

On Fri, 29 Apr 2011, viostorm wrote:

> After I shared comments form the forum yesterday with the biostatistician he
> indicated this:
> "Fisher's exact test is the non-parametric analog for the Chi-square
> test for 2x2 comparisons. A version (or extension) of the Fisher's Exact
> test, known as the Freeman-Halton test applies to comparisons for tables
> greater than 2x2. SAS can calculate both statistics using the following
> instructions.
>  proc freq; tables a * b / fisher;"
> Do people here still stand by position fisher exact test can be used for RxC
> contingency tables ?  Sorry to both you all so much it is just important for
> a paper I am writing and planning to submit soon. ( I have a 4x2 table but
> does not meet expected frequencies requirements for chi-squared.)
> I guess people here have suggested R implements, the following, which
> unfortunately are unavailable at least easily at my library but  at least by
> the titles indicates it is extending it to RxC
> Mehta CR, Patel NR. A network algorithm for performing Fisher's exact test
> in r c contingency tables. Journal of the American Statistical Association
> 1983;78:427-34.
> Mehta CR, Patel NR. Algorithm 643: FEXACT: A FORTRAN subroutine for Fisher's
> exact test on unordered r x c contingency tables. ACM Transactions on
> Mathematical Software 1986;12:154-61.
> The only reason I ask again is he is exceptionally clear on this point.
> Thanks again,
> -Rob

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