[R] Monte Carlo p-value (was "question")

[cfinet@ens-lyon.fr]

I thank you for your answer but I do not understand yet why the Fisher´s exact 
test does not work. And why is a "negative key".

Cédric Finet



En réponse à Spencer Graves <spencer.graves at pdf.com>:

>       What is the standard convention for a Monte Carlo p-value when the
> 
> observed outcome is more extreme than all simulations?  The example 
> provided by Cédric Fine produced a Monte Carlo p-value, according to 
> Kjetil Halvorsen, of "2.2e-16 (based on 2000 replicates)".  This seems
> 
> inappropriate to me. 
> 
>       By reading the code, I found that for this case,
> 
>             PVAL <- sum(tmp$results >= STATISTIC)/B
> 
> where STATISTIC is the observed chi-square while "tmp$results" is a 
> vector of length B of chi-squares from Monte Carlo simulated tables with
> 
> the same marginals.  Thus, PVAL ranges over seq(0, 1, length=(B+1)).  
> For the observed table, presumably, PVAL = 0.  The function "chisq.test"
> 
> apparently returns an object of class "htest", and "print.htest" calls
> 
> "format.pval(x$p.value, digits = digits)", for which "format.pval(0, 4)"
> 
> is "< 2.2e-16". 
> 
>       Can someone provide an appropriate reference or sense of the 
> literature on the appropriate number to report for a Monte Carlo p-value
> 
> when the observed is more extreme than all the simulations?  A value of
> 
> 0 or "< 2.2e-16" violates my sense of the logic of this situation.  If
> 
> the appropriate number is 0.5/B, then the line "PVAL <- sum(tmp$results
> 
>  >= STATISTIC)/B" could be followed immediately by something like the 
> following: 
> 
>       if(PVAL==0) PVAL <- 0.5/B
> 
>       Comments?
>       Best Wishes,
>       Spencer Graves
> 
> kjetil at entelnet.bo wrote:
> 
> >On 8 Mar 2004 at 16:38, cfinet at ens-lyon.fr wrote:
> >
> >  
> >
> >>I do not manage to make a Fisher´s exact test with the next matrix :
> >>
> >>    
> >>
> >
> >You can consider using chisq.test() with the argument sim=TRUE:
> >
> >  
> >
> >>mat <- matrix(scan(), 7, 12, byrow=TRUE)
> >>    
> >>
> >1:  1    3    0    1    2    9    0    0    2     5     8     6
> >13:    0    3    3    0    0    0    0    5    0     3     0     0
> >25:    0    0    0    0    0   10    0    0    0     0    10     0
> >37:    0    2    0    2    6   14    0    0    6     0    10     6
> >49:    0    5    0    0    0    7    0    0    0     2     8     0
> >61:    0    0    1    9    4    7    2    1    4     2    12     5
> >73:    0    6    0    0    0    0    0    0    0     5     1     3
> >85: 
> >Read 84 items
> >
> >  
> >
> >>chisq.test(mat, sim=TRUE)
> >>    
> >>
> >
> >        Pearson's Chi-squared test with simulated p-value (based
> >        on 2000 replicates)
> >
> >data:  mat 
> >X-squared = 218.3366, df = NA, p-value = < 2.2e-16
> >
> >Kjetil Halvorsen
> >
> >
> >
> >  
> >
> >>    [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
> >>[1,]    1    3    0    1    2    9    0    0    2     5     8     6
> >>[2,]    0    3    3    0    0    0    0    5    0     3     0     0
> >>[3,]    0    0    0    0    0   10    0    0    0     0    10     0
> >>[4,]    0    2    0    2    6   14    0    0    6     0    10     6
> >>[5,]    0    5    0    0    0    7    0    0    0     2     8     0
> >>[6,]    0    0    1    9    4    7    2    1    4     2    12     5
> >>[7,]    0    6    0    0    0    0    0    0    0     5     1     3
> >>
> >>but I do not understand why it does not work since I obtain the next
> >>error message :
> >>
> >>
> >>
> >>    
> >>
> >>>fisher.test(enfin.matrix)
> >>>      
> >>>
> >>Error in fisher.test(enfin.matrix) : Bug in FEXACT: gave negative
> key
> >>
> >>thank you for considering my application
> >>
> >>cédric finet
> >>
> >>______________________________________________
> >>R-help at stat.math.ethz.ch mailing list
> >>https://www.stat.math.ethz.ch/mailman/listinfo/r-help
> >>PLEASE do read the posting guide!
> >>http://www.R-project.org/posting-guide.html
> >>    
> >>
> >
> >______________________________________________
> >R-help at stat.math.ethz.ch mailing list
> >https://www.stat.math.ethz.ch/mailman/listinfo/r-help
> >PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html
> >  
> >
> 
>