Thanks for your reply Pascal. The alpha argument in binconf() is "probability of a type I error, so confidence coefficient = 1-alpha". Alternately, binom::binom.confint() is given the argument as confidence level. The 'exact' method in both functions gives results as expected. It's just odd for me to go that way when binconf() help says: "Following Agresti and Coull, the Wilson interval is to be preferred and so is the default."
Cheers Michael ________________________________ From: skalp.oet...@gmail.com [mailto:skalp.oet...@gmail.com] On Behalf Of Pascal Oettli Sent: September 9, 2013 9:16 PM To: Folkes, Michael Cc: R help Subject: Re: [R] Hmisc binconf function value interpretation during narrow confidence intervals Hello, Are you sure of the alpha value? Regards, Pascal 2013/9/10 Folkes, Michael <michael.fol...@dfo-mpo.gc.ca> Hello all, I've been using binconf (package Hmisc) at a range of alpha values and noticed that using the 'Wilson' method when alpha is larger (i.e. narrow CI), results in the upper value being smaller than the lower value. The 'exact' and 'asymptotic' methods give results in the realm I'd expect. But the help file suggests: "Following Agresti and Coull, the Wilson interval is to be preferred and so is the default." Suggestions and clarifications gratefully received. The following code shows the curious results: #calc 5% CI's. require(Hmisc) alpha <-.95 bin.prob <- binconf(1, 100, alpha=alpha,method='all') colnames(bin.prob)[-1] <- paste('p',c(alpha/2,1-alpha/2),sep='') bin.prob ______________________________________ Michael Folkes Salmon Stock Assessment Canadian Dept. of Fisheries & Oceans Pacific Biological Station 3190 Hammond Bay Rd. Nanaimo, B.C., Canada V9T-6N7 michael.fol...@dfo-mpo.gc.ca ______________________________________________ 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. -- Pascal Oettli Project Scientist JAMSTEC Yokohama, Japan ______________________________________________ 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.