Re: [Rd] Re: [R] p-value > 1 in fisher.test()
On 04-Jun-05 Martin Maechler wrote:
>> "UweL" == Uwe Ligges <[EMAIL PROTECTED]>
>> 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) <[EMAIL PROTECTED]>
Fax-to-email: +44 (0)870 094 0861
Date: 05-Jun-05 Time: 11:40:21
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Re: [Rd] Re: [R] p-value > 1 in fisher.test()
> "UweL" == Uwe Ligges <[EMAIL PROTECTED]>
> on Sat, 04 Jun 2005 11:43:34 +0200 writes:
UweL> (Ted Harding) wrote:
>> On 03-Jun-05 Ted Harding wrote:
>>
>>> And on mine
>>>
>>> (A: PII, Red Had 9, R-1.8.0):
>>>
>>> ff <- c(0,10,250,5000); dim(ff) <- c(2,2);
>>>
>>> 1-fisher.test(ff)$p.value
>>> [1] 1.268219e-11
>>>
>>> (B: PIII, SuSE 7.2, R-2.1.0beta):
>>>
>>> ff <- c(0,10,250,5000); dim(ff) <- c(2,2);
>>>
>>> 1-fisher.test(ff)$p.value
>>> [1] -1.384892e-12
>>
>>
>> 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
UweL> Uwe Ligges
>> Best wishes to all,
>> Ted.
>>
>>
>>
>> E-Mail: (Ted Harding) <[EMAIL PROTECTED]>
>> Fax-to-email: +44 (0)870 094 0861
>> Date: 04-Jun-05 Time: 00:02:32
>> -- XFMail --
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