On Dec 10, 2013, at 6:55 PM, bakerwl wrote: > David, > > Thanks for your reply--I appreciate your thoughts. I will look at prop.test. > > The reason I chose fisher.test over chisq.test is that fisher.test is more > appropriate when observed counts are not numerous--empty cells and cells > with counts < 5 are less a problem. > > Expected values are needed to test a null hypothesis against observed > counts, but if total observed counts are 20 for 3 categories, then a null > hypothesis of a random effect would use expected values = 6.67 in each of > the 3 categories (20/3). > > Yes, fisher.test is for count data and so is chisq.test, but chisq.test > allows 6.67 to be input as expected values in each of 3 categories, while > fisher.test does not seem to allow this? > > I don't think it is inherent in Fisher's exact test itself that expected > values must be integers, but not sure.
I see it differently, although I could be further educated on the subject and I've been wrong on Rhelp before. I think it _is_ inherent in Fisher's Exact Test. FET is essentially a permutation test built on the hypergeometric distribution (a discrete distribution) and it is unclear what to do with 1.33 of an entity under conditions of permutation. The "chi-square test" (one of many so-called chi-square tests) is a pretty good approximation to the discrete counterparts despite the fact that the chi-square distribution takes continuous arguments and generally holds well down to expected counts of 5. The link between the chi-square and binomial distributions is through there variances: npq vs sum(o-e)^2/n. You can develop arguments "in the limit" that converge fairly quickly. > -- > View this message in context: > http://r.789695.n4.nabble.com/fisher-test-can-I-use-non-integer-expected-values-tp4681976p4681989.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > 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. David Winsemius Alameda, CA, USA ______________________________________________ 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.
