From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>

Date: Fri 13 Jan 2006 - 13:00:37 EST

Date: Fri 13 Jan 2006 - 13:00:37 EST

On Thu, 12 Jan 2006 Ted.Harding@nessie.mcc.ac.uk wrote:

> I want to ascertain the basis of the table ranking,

*> i.e. the meaning of "extreme", in Fisher's Exact Test
**> as implemented in 'fisher.test', when applied to RxC
**> tables which are larger than 2x2.
**>
**> One can summarise a strategy for the test as
**>
**> 1) For each table compatible with the margins
**> of the observed table, compute the probability
**> of this table conditional on the marginal totals.
**>
**> 2) Rank the possible tables in order of a measure
**> of discrepancy between the table and the null
**> hypothesis of "no association".
**>
**> 3) Locate the observed table, and compute the sum
**> of the probabilties, computed in (1), for this
**> table and more "extreme" tables in the sense of
**> the ranking in (2).
**>
**> The question is: what "measure of discrepancy" is
**> used in 'fisher.test' corresponding to stage (2)?
**>
**> (There are in principle several possibilities, e.g.
**> value of a Pearson chi-squared, large values being
**> discrepant; the probability calculated in (2),
**> small values being discrepant; ... )
**>
**> "?fisher.test" says only:
*

[That following is not a quote from a current version of R.]

> In the one-sided 2 by 2 cases, p-values are obtained

*> directly using the hypergeometric distribution.
**> Otherwise, computations are based on a C version of
**> the FORTRAN subroutine FEXACT which implements the
**> network developed by Mehta and Patel (1986) and
**> improved by Clarkson, Fan & Joe (1993). The FORTRAN
**> code can be obtained from
**> <URL: http://www.netlib.org/toms/643>.
*

Two-sided tests are based on the probabilities of the tables, and take as 'more extreme' all tables with probabilities less than or equal to that of the observed table, the p-value being the sum of such probabilities.

which answers the question (there are only two-sided tests for such tables).

Now, what does the posting guide say about stating the R version and updating before posting?

-- Brian D. Ripley, ripley@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.htmlReceived on Fri Jan 13 13:06:49 2006

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