On 13-Jan-06 Prof Brian Ripley wrote: > On Thu, 12 Jan 2006 [EMAIL PROTECTED] wrote: >>[...] >> "?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).
Thanks for the above information, which is indeed the definitive straightforward answer to my question! (Not sure that I quite agree with the "two-sided" terminology, though, since the ranking is unidirectional based on decreasing probability, and the P-value is that of the least-probability tail -- i.e. analagous to the "large (-2*loglik)" tail of a likelihood-ratio test -- which I've always visualised as a 1-tailed test (depite the fact that the "other tail" can on occasion be indicative of a fit "too good to be true"). > Now, what does the posting guide say about stating the R version and > updating before posting? Well, I plead that in practice there is necessarily a grey area here! My quotation was from "?fisher.test" in R-2.1.0beta of 2004/04/08, the most recent version installed on any of my machines. Admittedly a bit behind the times, but not grossly; and that help page has not changed in this respect since the earliest version I have installed, which is R-1.2.3 of 2001/04/26. Contents of help pages can change overnight as R evolves. While it is better to be up-to-date than behind the times (even slightly), there is a compromise to be struck between upgrading to the latest R every time one has a question which might be answered thereby, or going on-line to read the latest PDF documentation from CRAN, on the one hand, and on the other asking a straightforward question to the list. Thanks again, and best wishes, Ted. -------------------------------------------------------------------- E-Mail: (Ted Harding) <[EMAIL PROTECTED]> Fax-to-email: +44 (0)870 094 0861 Date: 13-Jan-06 Time: 08:55:11 ------------------------------ XFMail ------------------------------ ______________________________________________ [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
