Jeff and others: Paul Mielke and Ken Berry at Colorado State University developed very fast Fortran routines for doing Fisher exact tests (as well as some others like Chi-square and Zelterman's statistics). Their book (Permutation Methods: A Distance Function Approach, 2nd ed. 2007. Springer) indicates that these algorithms were only efficient for <= 5 conditional loops so 2x2, 3x2, 4x2, 5x2, 6x2, 3x3, and 2x2x2 were feasible back in the 1990's. I'm not sure whether more recent computing capability permits larger tables now.
Brian Brian S. Cade U. S. Geological Survey Fort Collins Science Center 2150 Centre Ave., Bldg. C Fort Collins, CO 80526-8818 email: [EMAIL PROTECTED] tel: 970 226-9326 "Dr. Jeff Miller" <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 05/07/2008 09:56 AM To "'Greg Snow'" <[EMAIL PROTECTED]>, "'David Winsemius'" <[EMAIL PROTECTED]>, <[EMAIL PROTECTED]> cc Subject Re: [R] categorical data analysis - fisher.exact for 2x2 and greater Hi Simon and all, I'm pretty sure that you are correct about this. I think it is a misconception to say that the fisher exact test is only for a 2 by 2 table. It is presented that way in textbooks because, for a 2x2 table, it is easy to perform. For larger tables, it becomes complex quickly due to the rate at which the permutations increase. When I use it for larger tables, it is hit or miss as to whether R will be able to do it. It's not uncommon to get an error implying that R is out of memory. Check out Agresti's Categorical Data Analysis on the use of the fisher exact for larger than 2x2 tables, and check out the R archives (and Google search) for all the posts about the error message people run into sometimes. On April 29th, Marc Schwartz replied to my question about this as follows: Take a look at the 'workspace' argument in ?fisher.test and review the second paragraph in Details: "For 2 by 2 cases, p-values are obtained directly using the (central or non-central) 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 and Joe (1993). The FORTRAN code can be obtained from http://www.netlib.org/toms/643. Note this fails (with an error message) when the entries of the table are too large. (It transposes the table if necessary so it has no more rows than columns. One constraint is that the product of the row marginals be less than 2^31 - 1.)" Thank you, Jeff -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Greg Snow Sent: Wednesday, May 07, 2008 9:55 AM To: David Winsemius; [EMAIL PROTECTED] Subject: Re: [R] categorical data analysis The last example in ?fisher.test is not a 2x2 table, in fact it uses levels with a natural ordering similar to the original question. Why would this not be applicable to the situation? ________________________________________ From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of David Winsemius [EMAIL PROTECTED] Sent: Wednesday, May 07, 2008 7:34 AM To: [EMAIL PROTECTED] Subject: Re: [R] categorical data analysis Simon Blomberg <[EMAIL PROTECTED]> wrote in news:[EMAIL PROTECTED]: > But see these posts: > > http://finzi.psych.upenn.edu/R/Rhelp02a/archive/119079.html > > http://finzi.psych.upenn.edu/R/Rhelp02a/archive/119080.html > > Simon. Interesting reading, but the OP specifically said he was not dealing with 2x2 tables, so neither fisher.test nor the suggested alternatives would be applicable to his data situation. -- David Winsemius ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Internal Virus Database is out-of-date. 11:27 AM Internal Virus Database is out-of-date. 11:27 AM ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
