Hi, This report deals with p-values coming from chisq.test using the simulate.p=TRUE option. The issue is numerical accuracy and was brought up in previous bug reports 3486 and 3896. The bug was considered fixed but apparently was only mostly fixed. Just the typical problem of two values that are mathematically equal not ending up numerically equivalent.
Consider this series of three 2x2 tables: [1,] 1 7 [2,] 0 15 [1,] 1 7 [2,] 0 16 [1,] 1 7 [2,] 0 17 The pvals returned from chisq.test(m, sim=TRUE)$p.value are 0.3543228, 0.0004997501 and 0.3273363 respectively. The 2nd seems a bit unlikely, huh? I checked into it and the value I'm getting for the statistic (calculated in R code) is 4*.Machine$double.eps less than the value (which should be equal) that is returned from the C-code that does the simulation. Code for creating/testing the three matrices shown above: m <- matrix(c(1,0,7,15),2,2) ; chisq.test(m, sim=TRUE)$p.value m <- matrix(c(1,0,7,16),2,2) ; chisq.test(m, sim=TRUE)$p.value m <- matrix(c(1,0,7,17),2,2) ; chisq.test(m, sim=TRUE)$p.value Running SuSE9.3 on a AMD Athlon4000+ > version platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status Patched major 2 minor 1.1 year 2005 month 07 day 29 language R Thanks, Doug Douglas Grove Statistical Research Associate Fred Hutchinson Cancer Research Center Seattle WA 98109 ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
