R devel - May 2026 - Feature request: Fisher's 2x2, binomial (, others?) exact test efficiency improvements

>>>>> 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

>>>>> 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
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