[R] help on fisher.test(stats)?

[Stefan Grosse]

-------- Original Message  --------
Subject: [R] help on fisher.test(stats)?
From: zhijie zhang <epistat at gmail.com>
To: R-help at stat.math.ethz.ch
Date: 09.07.2007 09:03
> Dear friends,
>   My dataset have many zeros, so i must use fisher exact test .
> Unfortunately, the fisher.test(stats) function fail to do it.
>   Anybody knows how to do the fisher exact test with many zeros in the
> dataset?
> My dataset is:
> a<-matrix(c(0,1,0,0,0,0,1,0,1,0,0,0,0,1,0,1,1,0,2,1,5,1,1,6,4,4,1,17,2,8,5,7,1,1,24,3,6,1,1,3,2,16,7,4,0,2,4,0,17,0,1,0,0,0,1,2),nrow=8,byrow=TRUE)
> data.frame(a)
> b<-a[,-7]
> as.matrix(b)
> c<-as.matrix(b)
>
>   
>> c
>>     
>      [,1] [,2] [,3] [,4] [,5] [,6]
> [1,]    0    1    0    0    0    0
> [2,]    0    1    0    0    0    0
> [3,]    0    1    1    0    2    1
> [4,]    1    1    6    4    4    1
> [5,]    2    8    5    7    1    1
> [6,]    3    6    1    1    3    2
> [7,]    7    4    0    2    4    0
> [8,]    0    1    0    0    0    1
>   
>> fisher.test(c,workspace=200000000000000000)
>>     
> ŽíÎóÓÚfisher.test(c, workspace = 2e+17) :
>         ÍâœÓº¯Êýµ÷ÓÃʱ²»ÄÜÓÐNA(arg10)
> ŽËÍâ: Warning message:
> Ç¿Öƞıä¹ý³ÌÖвúÉúÁËNA
>
> Any suggestion or help are greatly appreciated.
>   
Your workspace is by far to large. I have done it with
> fisher.test(c,workspace=40000000)

        Fisher's Exact Test for Count Data

data:  c
p-value = 0.01548
alternative hypothesis: two.sided

(btw. it took half an hour...)

Simulation would also be an alternative approach:

> fisher.test(c,simulate=T)

        Fisher's Exact Test for Count Data with simulated p-value (based
on 2000 replicates)

data:  c
p-value = 0.01349
alternative hypothesis: two.sided

As you see the p-value is not that different, you could use more
replications:

> fisher.test(c,simulate=T,B=1000000)

        Fisher's Exact Test for Count Data with simulated p-value (based
on 1e+06 replicates)

data:  c
p-value = 0.01514
alternative hypothesis: two.sided

and it is still much faster...

Stefan
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