>>>>> "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 ------------------------------ ______________________________________________ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel