Hello Henric, Thank you so much for the detailed responses and helpful information. Much appreciated.
Regards Janh On Mon, Jun 3, 2013 at 6:15 AM, Henric Winell <nilsson.hen...@gmail.com>wrote: > Janh, > > Janh Anni skrev 2013-06-01 19:47: > > Hello All, >> Thanks a lot for the helpful suggestions. I wonder how ties are handled >> for the rank sum test by wilcox_test and wilcox.exact? For instance, >> > > Ties handling was mainly a problem back in the day when recursion formulas > were used for the computation of exact p-values. (When no ties are > present, the form of the exact null distribution of the Wilcoxon rank-sum > statistic depends only on the total number of observations in the two > groups.) > > > other software such as Minitab correct for ties by adjusting the >> variance of the test statistic, and actually provide the p values before >> and after adjustment for ties. >> > > Adjusting the variance only matters when approximating the exact > distribution with its asymptotic Gaussian distribution. And only when at > least one tie is shared between the two groups. And yes, the standardized > statistic in 'coin' accounts for ties. If ties are present, why would you > want to know the unadjusted p-value? > > > IIf neither wilcox_test nor wilcox.exact >> expressly corrects for ties in the Wilcoxon rank sum test, then perhaps >> one should just use the conventional wilcox.test which is the simplest >> > > of them all? Thanks again > > If this was true, the 'wilcox.exact' function would be completely > pointless since 'wilcox.test' just falls back on the asymptotic > approximation when ties are present. > > Software like 'StatXact', 'exactRankTests', and 'coin' use algorithms that > compute the exact p-value for any ties configuration. Take a look at > Torsten Hothorn's "On Exact Rank Tests in R" article from the very first > issue of R News > http://www.r-project.org/doc/**Rnews/Rnews_2001-1.pdf<http://www.r-project.org/doc/Rnews/Rnews_2001-1.pdf> > . > > > Henric > > > > Janh >> >> >> On Sat, Jun 1, 2013 at 8:41 AM, Henric Winell <nilsson.hen...@gmail.com >> <mailto:nilsson.henric@gmail.**com <nilsson.hen...@gmail.com>>> wrote: >> >> Janh, >> >> Janh Anni skrev 2013-06-01 04:27: >> >> Hello peter, >> >> >> Thanks for the comment. wilcox.exact is simpler as you pointed >> out but the >> fact that it is no longer being developed is somewhat concerning. >> >> >> Admittedly, 'coin' is being actively developed and has a lot more >> bells and whistles. But for something as simple as this, that >> wouldn't bother me at all. In any case, the 'exactRankTests' >> package still gets bug fixes and the algorithm used in the Wilcoxon >> case is exactly the same for both packages. >> >> However, if you want to stay with 'coin' you can just wrap up Greg's >> proposal in a function: >> >> wilcox_test.default <- function(x, y, ...) { >> data <- >> data.frame(values = c(x, y), >> group = rep(c("x", "y"), c(length(x), length(y)))) >> wilcox_test(values ~ group, data = data, ...) >> } >> >> Assuming that both 'coin' and 'exactRankTests are loaded, we can now >> check that it works: >> >> > set.seed(123) >> > x <- rpois(10, 3) >> > y <- rpois(11, 3.1) >> > >> > wilcox_test(x, y, alternative = "less", distribution = "exact") >> >> Exact Wilcoxon-Mann-Whitney Test >> >> data: values by group (x, y) >> Z = -0.0715, p-value = 0.4844 >> alternative hypothesis: true mu is less than 0 >> >> > wilcox.exact(x, y, alternative = "less") >> >> Exact Wilcoxon rank sum test >> >> data: x and y >> W = 54, p-value = 0.4844 >> alternative hypothesis: true mu is less than 0 >> >> >> HTH, >> Henric >> >> >> >> >> Regards >> Janh >> >> >> On Fri, May 31, 2013 at 6:50 PM, Peter Ehlers >> <ehl...@ucalgary.ca <mailto:ehl...@ucalgary.ca>> wrote: >> >> On 2013-05-30 20:20, Janh Anni wrote: >> >> Hello Greg, >> >> Thank you so much for your kind assistance. It looks >> like there's no way >> around using the formula format. I longed in vain for a >> simpler script >> more like the wilcox.test format. Thanks again. >> >> Janh >> >> >> I don't see why the formula syntax would be a problem, but >> to avoid it >> you could use exactRankTests::wilcox.exact() which, I >> believe, was >> written by the same author. It uses the same syntax as >> wilcox.test(). >> Note, though, that the package is no longer >> being developed. >> >> Peter Ehlers >> >> >> >> >> On Thu, May 30, 2013 at 6:21 PM, Greg Snow >> <538...@gmail.com <mailto:538...@gmail.com>> wrote: >> >> Ok, it looks like the function mainly works through >> the formula syntax. >> >> It still would have been nice to have a >> reproducible example of what >> your >> data may look like, but I can show an example with >> simulated x and y: >> >> x <- rpois(10, 3) >> >> y <- rpois(11, 3.1) >> mydf <- data.frame( vals = c(x,y), >> >> + group=rep( c('x','y'), c( length(x), length(y) ) >> ) ) >> >> wilcox_test( vals ~ group, data=mydf ) >> >> >> Asymptotic Wilcoxon-Mann-Whitney Test >> >> data: vals by group (x, y) >> Z = -1.3718, p-value = 0.1701 >> alternative hypothesis: true mu is not equal to 0 >> >> Does that help? (maybe I am the heedlessness >> theorist after all) >> >> >> >> On Thu, May 30, 2013 at 4:14 PM, Janh Anni >> <annij...@gmail.com <mailto:annij...@gmail.com>> >> wrote: >> >> I thought (hoped) wilcox_test(x,y) would do it >> but it doesn't and the >> >> package maintainer says the data have to be >> rearranged but does not >> specify >> how. Thanks >> >> Janh >> >> >> >> On Thu, May 30, 2013 at 6:05 PM, Greg Snow >> <538...@gmail.com <mailto:538...@gmail.com>> >> wrote: >> >> What have you tried so far? Have you read >> the help page? have you run >> >> the examples on that page? >> >> I would expect that it is something as simple >> as >> >> library(coin) >> wilcox_test(x,y) >> >> or >> >> wilcox_test( y ~ group ) >> >> But you should trust the help page more than >> the expectations of >> someone >> who has not read it recently (see >> fortune(14)). >> >> If that does not answer your question then >> give us more detail on what >> you tried, what you expected the results to >> be, what the results >> actually >> were, and how they differed. Without that >> information we have to >> resort to >> mind reading and the current implementation >> of the esp package is still >> very pre-alpha, it suggests that the answer >> to your question is: >> >> esp() >> >> >> [1] "selflessly vigilantly pigeon theorist >> heedlessness" >> >> Which is either much to profound for the >> likes of me to understand or >> is >> complete gibberish (which is only slightly >> less helpful than an overly >> general question without a reproducible >> example). >> >> >> On Thu, May 30, 2013 at 2:07 PM, Janh Anni >> <annij...@gmail.com >> <mailto:annij...@gmail.com>> wrote: >> >> Dear All, >> >> >> I have two simple data samples (no >> groups or factors, etc.) and would >> just >> like to compute the two-sample Wilcoxon >> Rank Sum test using the >> wilcox_test >> function contained in the coin package, >> which is reportedly better >> than >> the >> regular wilcox.test function because it >> performs some adjustment for >> ties. >> Would anyone know how to craft a script >> to perform this task? Much >> appreciated. >> >> Janh >> >> [[alternative HTML version >> deleted]] >> >> ______________________________** >> __**________________ >> R-help@r-project.org >> <mailto:R-help@r-project.org> mailing >> list >> https://stat.ethz.ch/mailman/*** >> __*listinfo/r-help <https://stat.ethz.ch/mailman/*__*listinfo/r-help> >> <https://stat.ethz.ch/mailman/** >> **listinfo/r-help <https://stat.ethz.ch/mailman/**listinfo/r-help>>< >> https://**stat__ethz.ch/mailman/**listinfo/r-__help<https://stat__ethz.ch/mailman/listinfo/r-__help> >> >> <https://stat.ethz.ch/mailman/** >> listinfo/r-help <https://stat.ethz.ch/mailman/listinfo/r-help>>> >> >> PLEASE do read the posting guide >> http://www.R-project.org/**__** >> posting-guide.html <http://www.R-project.org/**__posting-guide.html> >> <http://www.R-project.org/**** >> posting-guide.html <http://www.R-project.org/**posting-guide.html>>< >> http://**www. <http://www.>__R-project.org/posting-**guide.__html >> >> <http://www.R-project.org/** >> posting-guide.html <http://www.R-project.org/posting-guide.html>>> >> >> and provide commented, minimal, >> self-contained, reproducible code. >> >> >> >> >> -- >> Gregory (Greg) L. Snow Ph.D. >> 538...@gmail.com <mailto:538...@gmail.com> >> >> >> >> >> >> >> -- >> Gregory (Greg) L. Snow Ph.D. >> 538...@gmail.com <mailto:538...@gmail.com> >> >> >> [[alternative HTML version deleted]] >> >> ______________________________**__**________________ >> R-help@r-project.org <mailto:R-help@r-project.org> >> mailing list >> >> https://stat.ethz.ch/mailman/***__*listinfo/r-help<https://stat.ethz.ch/mailman/*__*listinfo/r-help> >> >> <https://stat.ethz.ch/mailman/****listinfo/r-help<https://stat.ethz.ch/mailman/**listinfo/r-help> >> ><https://**stat__ethz.ch/mailman/**listinfo/r-__help<https://stat__ethz.ch/mailman/listinfo/r-__help> >> >> >> <https://stat.ethz.ch/mailman/**listinfo/r-help<https://stat.ethz.ch/mailman/listinfo/r-help> >> >> >> PLEASE do read the posting guide >> http://www.R-project.org/** >> posting-guide.html >> >> <http://www.R-project.org/__**posting-guide.html<http://www.R-project.org/__posting-guide.html> >> >> >> <http://www.R-project.org/**posting-guide.html<http://www.R-project.org/posting-guide.html> >> >> >> >> and provide commented, minimal, self-contained, >> reproducible code. >> >> >> >> >> >> [[alternative HTML version deleted]] >> >> ______________________________**__________________ >> R-help@r-project.org <mailto:R-help@r-project.org> mailing list >> >> https://stat.ethz.ch/mailman/_**_listinfo/r-help<https://stat.ethz.ch/mailman/__listinfo/r-help> >> >> >> <https://stat.ethz.ch/mailman/**listinfo/r-help<https://stat.ethz.ch/mailman/listinfo/r-help> >> > >> PLEASE do read the posting guide >> >> http://www.R-project.org/__**posting-guide.html<http://www.R-project.org/__posting-guide.html> >> >> >> <http://www.R-project.org/**posting-guide.html<http://www.R-project.org/posting-guide.html> >> > >> and provide commented, minimal, self-contained, reproducible code. >> >> >> >> > [[alternative HTML version deleted]] ______________________________________________ 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.
