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)´íÎóÓÚfisher.test(c, workspace = 2e+17) : Íâ½Óº¯Êýµ÷ÓÃʱ²»ÄÜÓÐNA(arg10) ´ËÍâ: Warning message: Ç¿ÖƸıä¹ý³ÌÖвúÉúÁËNA Any suggestion or help are greatly appreciated. -- With Kind Regards, oooO::::::::: (..)::::::::: :\.(:::Oooo:: ::\_)::(..):: :::::::)./::: ::::::(_/:::: ::::::::::::: [***********************************************************************] Zhi Jie,Zhang ,PHD Tel:86-21-54237149 Dept. of Epidemiology,School of Public Health,Fudan University Address:No. 138 Yi Xue Yuan Road,Shanghai,China Postcode:200032 Email:epistat@gmail.com Website: www.statABC.com [***********************************************************************] oooO::::::::: (..)::::::::: :\.(:::Oooo:: ::\_)::(..):: :::::::)./::: ::::::(_/:::: ::::::::::::: [[alternative HTML version deleted]]
-------- 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) >> > ??????fisher.test(c, workspace = 2e+17) : > ????????????????????NA(arg10) > ????: Warning message: > ????????????????????NA > > 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)