Re: [Rd] Re: [R] p-value > 1 in fisher.test()

From: Ted Harding <Ted.Harding_at_nessie.mcc.ac.uk>
Date: Sun 05 Jun 2005 - 10:40:34 GMT


On 04-Jun-05 Martin Maechler wrote:

>>>>>> "UweL" == Uwe Ligges <ligges@statistik.uni-dortmund.de>
>>>>>>     on Sat, 04 Jun 2005 11:43:34 +0200 writes:

>
> UweL> (Ted Harding) wrote:
> >> On 03-Jun-05 Ted Harding wrote:
> >> [...]
> >> I have a suggestion (maybe it should also go to R-devel).
> >>
> >> There are many functions in R whose designated purpose is
> >> to return the value of a probability (or a probability
> >> density). This designated purpose is in the mind of the
> >> person who has coded the function, and is implicit in its
> >> usage.
> >>
> >> Therefore I suggest that every such function should have
> >> a built-in internal check that no probability should be
> >> less than 0 (and if the primary computation yields such
> >> a value then the function should set it exactly to zero),
> >> and should not exceed 1 (in which case the function should
> >> set it exactly to 1). [And, in view of recent echanges,
> >> I would suggest exactly +0, not -0!]
> >>
> >> Similar for any attempts to return a negative probability
> >> density; while of course a positive value can be allowed
> >> to be anything.
> >>
> >> All probabilities would then be guaranteed to be "clean"
> >> and issues like the Fisher exact test above would no longer
> >> be even a tiny problem.
> >>
> >> Implementing this in the possibly many cases where it is
> >> not already present is no doubt a long-term (and tedious)
> >> project.
> >>
> >> Meanwhile, people who encounter problems due to its absence
> >> can carry out their own checks and adjustments!
>
> UweL> [moved to R-devel]
>
> UweL> Ted, my (naive?) objection:
> UweL> Many errors in the underlying code have been detected by a
> function
> UweL> returning a nonsensical value, but if the probability is
> silently set to
> UweL> 0 or 1 .......
> UweL> Hence I would agree to do so in special cases where it makes
> sense
> UweL> because of numerical issues, but please not globally.
>
> I agree very much with Uwe's point.
>
> Further to fisher.test(): This whole thread is
> re-hashing a pretty recent bug report on fisher.test()
> { "negative p-values from fisher's test (PR#7801)", April '05}
> I think that only *because* of the obviously wrong P-values have
> we found and confirmed that the refereed and published code
> underlying fisher.test() is bogous. Such knowledge would have
> been harder to gain if the P-values would have been cut into [0,1].
>
> Martin Maechler

Uwe, Martin: Those are very pertinent comments, and they lead me to agree with you!

I really had in mind the case where the code for a function was not in question, but the usual "rounding errors" could generate an "impossible" result.

So I think that perhaps the best solution is the one I proposed as "interim", namely that people carry out their own checks and adjustments.

Best wishes,
Ted.



E-Mail: (Ted Harding) <Ted.Harding@nessie.mcc.ac.uk> Fax-to-email: +44 (0)870 094 0861
Date: 05-Jun-05                                       Time: 11:40:21
------------------------------ XFMail ------------------------------

______________________________________________
R-devel@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel Received on Sun Jun 05 20:53:27 2005

This archive was generated by hypermail 2.1.8 : Mon 24 Oct 2005 - 22:26:57 GMT