Re: [R] hypergeometric vs fisher.test
On Aug 13, 2010, at 3:47 PM, Andrea Franceschini wrote: Dear R team, I have a simple question. I tried this command: phyper(17,449,19551,181, FALSE) [1] 1.47295e-07 and then I tried this command: (fisher.test(matrix(c(17,449,181,19551),2,2), alternative='greater'))$p.value [1] 3.693347e-06 Shouldn't be identical the results of the two commands ? What is the difference ? Just read the phyper docs more carefully (and perhaps revisit the theory), and you'll see that phyper is using margin totals of the table, where fisher.test is using the individual entries. Also beware of left/right continuity issues with tails of discrete distributions: The convention is that the lower and the upper tail sums to 1, so your 17 is NOT included in the upper tail. Thx a lot -- View this message in context: http://r.789695.n4.nabble.com/hypergeometric-vs-fisher-test-tp2324223p2324223.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. -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.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.
Re: [R] hypergeometric vs fisher.test
I ask the question also because I found this line in Wikipedia: The test (see above) based on the hypergeometric distribution (hypergeometric test) is identical to the corresponding one-tailed version of Fisher's exact test. Is this wrong ? May I kindly ask a friendly explanation for not-experts in statistics ? Thx a lot, -- View this message in context: http://r.789695.n4.nabble.com/hypergeometric-vs-fisher-test-tp2324223p2324429.html Sent from the R help mailing list archive at Nabble.com. [[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.
Re: [R] hypergeometric vs fisher.test
Andrea Franceschini wrote: I ask the question also because I found this line in Wikipedia: The test (see above) based on the hypergeometric distribution (hypergeometric test) is identical to the corresponding one-tailed version of Fisher's exact test. Is this wrong ? May I kindly ask a friendly explanation for not-experts in statistics ? Thx a lot, You never said you were a non-expert. A question like that might very well have come from a student, or an incompetent claiming to have found a bug in fisher.test... The point was that Fisher's test takes the 2x2 table a b c d and interprets the situation under the null hypothesis as taking a sample of size a+c from an urn with a+b white balls and c+d black balls. Once you read the docs for phyper properly (it _is_ tricky to get it right), you arrive at phyper(16,17+181,449+19551,17+449, lower.tail=FALSE) [1] 3.693347e-06 -- Peter Dalgaard Center for Statistics, Copenhagen Business School Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.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.
Re: [R] hypergeometric vs fisher.test
or an incompetent Such harsh words Peter. You're not making this a friendly environment for people to ask questions. Is there a less competent attribute mailing list so that some of us don't offend you with our questions? On Aug 13, 2010, at 2:11 PM, Peter Dalgaard wrote: Andrea Franceschini wrote: I ask the question also because I found this line in Wikipedia: The test (see above) based on the hypergeometric distribution (hypergeometric test) is identical to the corresponding one-tailed version of Fisher's exact test. Is this wrong ? May I kindly ask a friendly explanation for not-experts in statistics ? Thx a lot, You never said you were a non-expert. A question like that might very well have come from a student, or an incompetent claiming to have found a bug in fisher.test... The point was that Fisher's test takes the 2x2 table a b c d and interprets the situation under the null hypothesis as taking a sample of size a+c from an urn with a+b white balls and c+d black balls. Once you read the docs for phyper properly (it _is_ tricky to get it right), you arrive at phyper(16,17+181,449+19551,17+449, lower.tail=FALSE) [1] 3.693347e-06 -- Peter Dalgaard Center for Statistics, Copenhagen Business School Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.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. __ 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.
