On Fri, 29 Apr 2011, Thomas Lumley wrote:
On Fri, Apr 29, 2011 at 8:01 AM, Mike Miller <mbmille...@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:
http://cran.r-project.org/web/packages/coin/
To estimate very small p-values properly, one must resample many more
times.
Mike
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