>>>>> 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`
Martin Maechler
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