[Rd] fisher.test(... , simulate.p.value=TRUE) (PR#10558)

[r . hankin]

Full_Name: Robin Hankin
Version: R-2.6.1
OS: macosx 10.5.1
Submission from: (NULL) (139.166.245.10)


fisher.test() with a matrix a <- diag(1:3) has a p-value of 1/60 ~= 0.01

Setting the simulate.p.value flag to TRUE gives a very incorrect answer:

> fisher.test(a,simulate.p.value=TRUE)$p.value
[1] 0.0004997501
> fisher.test(a,simulate.p.value=TRUE,B=1)$p.value
[1] 9.999e-05
> 


These values are repeatable [there is no variability].  The relevant line in
fisher.test() is reproduced below; it is the one where PVAL is set:


   n <- sum(sc)
STATISTIC <- -sum(lfactorial(x))
tmp <- .C("fisher_sim", as.integer(nr), as.integer(nc), 
as.integer(sr), as.integer(sc), as.integer(n), 
as.integer(B), integer(nr * nc), double(n + 1), 
integer(nc), results = double(B), PACKAGE = "stats")$results
almost.1 <- 1 + 64 * .Machine$double.eps
PVAL <- (1 + sum(tmp <= almost.1 * STATISTIC))/(B + 
1)
}


the problem is sum(tmp <= almost.1 * STATISTIC).  This line would be correct if
tmp (and STATISTIC) were positive, but they are negative (or zero).  The
fisher.test() is returning 1/(B+1) because *no* element of tmp satisfies tmp <=
almost.1 * STATISTIC.


 Changing the line to read 

PVAL <- (1 + sum(tmp <=  STATISTIC/almost.1))/(B +  1)


fixes the problem:


> myfish(a,simulate.p.value=TRUE,B=1)$p.value
[1] 0.01749825
> myfish(a,simulate.p.value=TRUE,B=1)$p.value
[1] 0.01779822
> myfish(a,simulate.p.value=TRUE,B=1)$p.value
[1] 0.01559844
> myfish(a,simulate.p.value=TRUE,B=1)$p.value
[1] 0.01739826
> 


See how the p-values agree with the theoretical value of 1/60 (more or less).

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[Rd] Trig.Rd typo (PR#9269)

[r . hankin]

Full_Name: Robin Hankin
Version: 2.4.0 RC
OS: MacOSX 10.4.7
Submission from: (NULL) (139.166.242.29)


The first cut line described in Trig.Rd for asin() is incorrect in the ascii
version of the manpage.

The Rd file reads:

 For \code{asin()} and \code{acos()}, there are two cuts, both along
   the real axis: \eqn{\left(-\infty, -1\right]}{\(-Inf, 1\]} and
 
Note the inconsistency between the ascii and latex equations.
It should read:

 For \code{asin()} and \code{acos()}, there are two cuts, both along
   the real axis: \eqn{\left(-\infty, -1\right]}{\(-Inf, -1\]} and


where the final "1" has been changed to a "-1".  Ref:  AMS-55, page 79,
figure 4.4.


It's very difficult to catch this kind of error: thanks to Kjetil Halvorson for
his sharp-eyed comment.

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