On Fri, 13 Jan 2006 [EMAIL PROTECTED] wrote: > 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").
As statistics is usually taught, significance tests are always one-tailed. The two-sided t-test is one-tailed, the test statistic being |T|. In any case, the `two-sided' is part of the arguments given to the function, so this para is just using the already-established terminology. >> 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. Well, if you had given the R version number the problem would have been much more obvious. > 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 ------------------------------ > > ______________________________________________ > 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.html > -- 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 ______________________________________________ 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.html