Andrea Onofri wrote: > Dear all, > > I'm using R to perform multiple comparison testing on agriculture > genotype trials. To perform the Duncan's MRT, I use the qtukey() > function with the following syntax: > > qtukey(p = ((1 - 0.05) ^ (pos - 1)), nmeans = pos, df = ni) > > I experience a strange behaviour when the number of means in the trial > and the number of residual degrees of freedom (ni) becomes high > (orientatively pos > 30 and ni > 60), i.e. the function returns NaN > together with the following message: > > convergence failed in 'qtukey' > > Running the code below should reproduce a statistical table for > Duncan's MRT, such those reported on old books of agricultural > statistics (ex. Steel and Torrie, 1960). > > table <- matrix(0, 28, 14) > pos <- c(10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 50, 100, 200) > df <- c(2:20, seq(22, 30, by = 2), 40, 60, 100, 1000) > for (i in 1:28) table [i, ] <- qtukey(p = ((1 - 0.05) ^ (pos - 1)), > nmeans = pos, df = df[i]) > colnames(table) <- pos > rownames(table) <- df > > Indeed, I get several NaN and some odd figures. > > Am I doing something wrong or is there any intrinsic limit for the > values of p, nmeans and df within the qtukey() function? Just in this > latter case, is it possible to raise those limits? Some genotype trials > can have more than thirty treatments under comparison. > > I thank you all for your attention. > > Andrea Onofri > Department of Agriculture and Environmental Sciences > University of Perugia (ITALY) > > ______________________________________________ > R-help@r-project.org 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. > Yes, this looks a bit suspicious, especially the fact that it worsens with increasing df. The core of the matter seems to be this
> qtukey(log(3.689754e-05),200,1000,log=T) [1] NaN Warning messages: 1: In qtukey(log(3.689754e-05), 200, 1000, log = T) : convergence failed in 'qtukey' 2: In qtukey(p, nranges, nmeans, df, lower.tail, log.p) : NaNs produced which presumably is from inverting ptukey, but > f <- Vectorize(function(x)ptukey(x,200,1000,log=T)-log(3.689754e-05)) > curve(f, from=3,to=5) > uniroot(f, c(3,5)) $root [1] 3.760707 $f.root [1] -5.756398e-05 $iter [1] 6 $estim.prec [1] 6.103516e-05 is looking perfectly nice. -- O__ ---- Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 ______________________________________________ R-help@r-project.org 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.
