>>>>> Martin Maechler writes: >>>>> Stephanie Evert >>>>> on Sun, 17 May 2026 09:03:52 +0200 writes:
>>> I will revise my feature request to "have an >>> easily-discoverable fast p-value-only calculation" for >>> those who aren't using the odds ratio or confidence >>> interval. >> fisher.pval() in the "corpora" package. >> Best, Steph > Thank you Steph; > However, I still agree with Chris that it would be nice to have > an easy way to basically just get the p-value, in a case where > neither the ESTIMATE nor the confidence interval is needed. > Indeed, I've not unfrequently seen R code snippets > <some>.test(.........)$p.value > also in CRAN package R code and I think base R should provide > a simple documented way to get only the pvalue in cases where > the full test costs a factor of 1000 more, even if is still > only microseconds in case of small data sets. > My svn commit to the R sources, > 22 years ago (!) > r29551 | maechler | 2004-05-24 21:34 | > did introduce the optional argument 'conf.int = TRUE' for the > 2x2 case _and_ the NEWS entry (of svn rev 29551) has been >> o fisher.test(*, conf.int=FALSE) allows to skip the confidence interval >> computation > However, Chris is (indirectly) correct -- he did not mention the > 'conf.int' option -- but in this very large case, conf.int=FALSE > does not help much, as indeed, the unconditionalized > logdc <- dhyper(support, m, n, k, log = TRUE) > is already expensive, and also the computation of the sample OR (odds ratio) > ESTIMATE <- mle(x) > is costly. Indeed, I will add a new argument to fisher.test() to allow > skipping > the expensive parts and get the p.value and *still* a valid result > of class "htest". > For now, this will only be fast when as by default the null > hypothesis is `or = 1` Perhaps we could simply take `or = NULL` or `or = NA` to say "do not even estimate the OR"? -k > Martin Maechler > ______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
