[R] Previously attainable fisher's exact test

[peter dalgaard]

On Apr 14, 2011, at 16:55 , Jim Silverton wrote:

> What Ted and Peter did were Fisher's exact test, To get the previous attainable p-value, what you do is  the the fisher exact test p-values of ALL the possible tables with margins fixed and choose the p-value that is just below the one for fisher's exact test of the original table.

Well, you might have said so...

For one-sided tests, just add/subtract matrix(c(1,-1,1,1),2) and recompute. Otherwise, I guess that you get to play with dhyper and phyper because you need to know where the opposite tail starts. Check the internals of fisher.test.


> 
> n Thu, Apr 14, 2011 at 3:01 AM, peter dalgaard <pdalgd at gmail.com> wrote:
> 
> On Apr 14, 2011, at 01:29 , (Ted Harding) wrote:
> 
> > On 13-Apr-11 17:40:53, Jim Silverton wrote:
> >> I have a matrix say,
> >>
> >> 1  4
> >> 23  30
> >>
> >> and I want to find the previously attainable fisher's exact test
> >> p-value. Is there a way to do this in R?
> >> --
> >> Thanks,
> >> Jim.
> >
> > I do not understand what you mean by "previously attainable".
> >
> > As far as that particular matrix is concerned, the fisher.test()
> > function will yield its exact Fisher P-value:
> >
> >  M <- matrix(c(1, 4, 23, 30), byrow=TRUE, nrow=2)
> >  M
> >  #      [,1] [,2]
> >  # [1,]    1    4
> >  # [2,]   23   30
> >  fisher.test(M)
> >  #         Fisher's Exact Test for Count Data
> >  # data:  M
> >  # p-value = 0.3918
> >  # alternative hypothesis: true odds ratio is not equal to 1
> >  # 95 percent confidence interval:
> >  #  0.006355278 3.653391412
> >  # sample estimates:
> >  # odds ratio
> >  #  0.3316483
> >
> > So the P-value is 0.3918 (as attained now, and as attainable
> > at any time previously if you had done the above ... !).
> >
> 
> What Ted said, plus
> 
> f <- fisher.test(M)
> f$p.value
> # [1] 0.3917553
> 
> 
> --
> Peter Dalgaard
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com
> 
> 
> 
> 
> -- 
> Thanks,
> Jim.
> 

-- 
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com