From ligges at statistik.uni-dortmund.de  Sat Jun  4 11:43:34 2005
From: ligges at statistik.uni-dortmund.de (Uwe Ligges)
Date: Sat Jun  4 11:40:39 2005
Subject: [Rd] Re: [R] p-value > 1 in fisher.test()
In-Reply-To: <XFMail.050604003317.Ted.Harding@nessie.mcc.ac.uk>
References: <XFMail.050604003317.Ted.Harding@nessie.mcc.ac.uk>
Message-ID: <42A177C6.8030705@statistik.uni-dortmund.de>

(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!

[moved to R-devel]

Ted, my (naive?) objection:
Many errors in the underlying code have been detected by a function 
returning a nonsensical value, but if the probability is silently set to 
0 or 1 .......
Hence I would agree to do so in special cases where it makes sense 
because of numerical issues, but please not globally.

Uwe Ligges





> Best wishes to all,
> Ted.
> 
> 
> --------------------------------------------------------------------
> E-Mail: (Ted Harding) <Ted.Harding@nessie.mcc.ac.uk>
> Fax-to-email: +44 (0)870 094 0861
> Date: 04-Jun-05                                       Time: 00:02:32
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[Rd] Re: [R] p-value > 1 in fisher.test()
Uwe Ligges