[R] fisher exact for > 2x2 table
mbmiller+l at gmail.com
Thu Apr 28 23:26:51 CEST 2011
On Fri, 29 Apr 2011, Thomas Lumley wrote:
> On Fri, Apr 29, 2011 at 8:01 AM, Mike Miller <mbmiller+l at gmail.com> wrote:
>> On Thu, 28 Apr 2011, viostorm wrote:
>>> I'm using fisher.exact on a 4x2 table and it seems to work.
>>> Does anyone know exactly what is going on? I thought fisher.exact is
>>> only for 2x2 tables.
>> You were wrong. I'm sure there's nothing wrong with the program. You
>> will find that with bigger tables and larger sample sizes the
>> computational cost becomes quite enormous.
> In fact, with large tables, roundoff error becomes significant before
> computational cost becomes prohibitive.
To avoid both of these problems one might use Monte Carlo resampling under
the null, maybe 10,000 times or more. I think independence_test() in the
coin package will do this:
To estimate very small p-values properly, one must resample many more
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