Tal and David, thanks for your messages. I should have added that I tried all variations of true/false values for the exact and correct parameters. Running with correct=FALSE makes only a tiny change, resulting in W = 485, p-value = 0.0002481.
At one point, I also thought that the discrepancy between R and these online calculators might come from how ties are handled, but the fact that R and two of the online calcultors reach the same U/W values seems to indicate that ties aren't the issue, since (I believe) the U or W values contain all of the information needed to calculate the p-value, assuming the number of samples is also known for each condition. (However, it's been a while since I looked into how MWU tests work, so maybe now's the time to refresh.) If that's correct, the discrepancy seems to be based in what R does with the W value that is identical to the U values of two of the online calculators. (I'm also assuming that U and W have the same meaning, which seems likely.) - Brad ____________________ W. Bradley Knox, PhD http://bradknox.net bradk...@mit.edu On Wed, Sep 3, 2014 at 9:10 AM, David L Carlson <dcarl...@tamu.edu> wrote: > That does not change the results. The problem is likely to be the way ties > are handled. The first sample has 25 values of which 23 are identical > (359). The second sample has 26 values of which 12 are identical (359). The > difference between the implementations may be a result of the way the ties > are ranked. For example the R function rank() offers 5 different ways of > handling the rank on tied observations. With so many ties, that could make > a substantial difference. > > Package coin has wilxon_test() which uses Monte Carlo simulation to > estimate the confidence limits. > > ------------------------------------- > David L Carlson > Department of Anthropology > Texas A&M University > College Station, TX 77840-4352 > > > -----Original Message----- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] > On Behalf Of Tal Galili > Sent: Wednesday, September 3, 2014 5:24 AM > To: W Bradley Knox > Cc: r-help@r-project.org > Subject: Re: [R] wilcox.test - difference between p-values of R and online > calculators > > It seems your numbers has ties. What happens if you run wilcox.test with > correct=FALSE, will the results be the same as the online calculators? > > > > ----------------Contact > Details:------------------------------------------------------- > Contact me: tal.gal...@gmail.com | > Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | > www.r-statistics.com (English) > > ---------------------------------------------------------------------------------------------- > > > > On Wed, Sep 3, 2014 at 3:54 AM, W Bradley Knox <bradk...@mit.edu> wrote: > > > Hi. > > > > I'm taking the long-overdue step of moving from using online calculators > to > > compute results for Mann-Whitney U tests to a more streamlined system > > involving R. > > > > However, I'm finding that R computes a different result than the 3 online > > calculators that I've used before (all of which approximately agree). > These > > calculators are here: > > > > http://elegans.som.vcu.edu/~leon/stats/utest.cgi > > http://vassarstats.net/utest.html > > http://www.socscistatistics.com/tests/mannwhitney/ > > > > An example calculation is > > > > > > > *wilcox.test(c(359,359,359,359,359,359,335,359,359,359,359,359,359,359,359,359,359,359,359,359,359,303,359,359,359),c(332,85,359,359,359,220,231,300,359,237,359,183,286,355,250,105,359,359,298,359,359,359,28.6,359,359,128))* > > > > which prints > > > > > > > > > > > > > > > > > > > > *Wilcoxon rank sum test with continuity correction data: c(359, 359, > 359, > > 359, 359, 359, 335, 359, 359, 359, 359, 359, and c(332, 85, 359, 359, > 359, > > 220, 231, 300, 359, 237, 359, 183, 359, 359, 359, 359, 359, 359, 359, > 359, > > 359, 303, 359, 359, and 286, 355, 250, 105, 359, 359, 298, 359, 359, 359, > > 28.6, 359, 359) and 359, 128) W = 485, p-value = 0.0002594 alternative > > hypothesis: true location shift is not equal to 0 Warning message: In > > wilcox.test.default(c(359, 359, 359, 359, 359, 359, 335, 359, : cannot > > compute exact p-value with ties* > > > > > > However, all of the online calculators find p-values close to 0.0025, 10x > > the value output by R. All results are for a two-tailed case. > Importantly, > > the W value computed by R *does agree* with the U values output by the > > first two online calculators listed above, yet it has a different > p-value. > > > > Can anyone shed some light on how and why R's calculation differs from > that > > of these online calculators? Thanks for your time. > > > > ____________________ > > W. Bradley Knox, PhD > > http://bradknox.net > > bradk...@mit.edu > > > > [[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. > > > > [[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. > [[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.
