On Thu, 12 Jan 2006 [EMAIL PROTECTED] 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>. No, it *also* says 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, [EMAIL PROTECTED] 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 ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
