-------- Original Message -------- Subject: [R] help on fisher.test(stats)? From: zhijie zhang <[EMAIL PROTECTED]> To: R-help@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 -=-=- ... The most incomprehensible thing about the world is that it is comprehensible. (A. Einstein) ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.