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

Martin Maechler maechler at stat.math.ethz.ch
Sat Jun 4 19:17:47 CEST 2005

```>>>>> "UweL" == Uwe Ligges <ligges at 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:
>>
>>> 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) <Ted.Harding at nessie.mcc.ac.uk>
>> Fax-to-email: +44 (0)870 094 0861
>> Date: 04-Jun-05                                       Time: 00:02:32
>> ------------------------------ XFMail ------------------------------

```