Hi Tom, Thank you for the friendly and informative answer. It does explain a lot of things, actually. As with any good answer, it inevitably leads to other questions. In the first place, I need the arithmetic mean. It's what we base our calculations on...
My code is currently this: Metall<-c("Cu","Cu","Cu","Cu","Cu","Cu","Cu","Cu","Cu","Cr","Cr","Cr","Cr"," Cr","Cr","Cr","Cr","Cr","As","As","As","As","As","As","As","As","As","Pb","P b","Pb","Pb","Pb","Pb","Pb","Pb","Pb","Zn","Zn","Zn","Zn","Zn","Zn","Zn","Zn ","Zn") Halt<-c(85,13,13,340,18,13,88,24,12,216,33,21,454,20,18,88,30,21,1254,22,4.2 ,1081,35,6,1772,192,7.6,43,20,12,3107,21,12,30,24,19,1109,57,46,269,68,50,58 5,131,52) beanplot(Halt~Metall, log = "y", yaxt = "n", ylab="Halt (mg/kg)",cex.lab=1.2) axis(2,c(1,10,100,1000,10000)) polygon(c(0.2966510,0.2966510,1.4832033,1.4832033,3.6160162,3.6160162,4.4921 444,4.4921444,5.6968371,5.6968371),c(2.763021e-01,10,10,80,80,40,40,250,250, 2.763021e-01),col="#66FF0090", border="#66FF0090") text(5.58,10,"<KM", cex=1.2, font=2) polygon(c(0.2966510,0.29665101,1.4832033,1.4832033),c(10,25,25,10),col="#FFF F0090",border="#FFFF0090") polygon(c(1.4832033,1.4832033,2.5027348,2.5027348,3.6160162,3.6160162,4.4921 444,4.4921444,5.6968371,5.6968371,4.4921444,4.4921444,3.6160162,3.6160162,1. 4832033),c(80,150,150,200,200,400,400,500,500,250,250,40,40,80,80),col="#FFF F0090",border="#FFFF0090") text(5.54,350,"<MKM", cex=1.2, font=2) polygon(c(0.2966510,0.2966510,5.6968371,5.6968371,4.4921444,4.4921444,3.6160 162,3.6160162,2.5027348,2.5027348,1.4832033,1.4832033),c(25,30085.997183,300 85.997183,500,500,400,400,200,200,150,150,25),col="#FF000090",border="#FF000 090") text(5.54,2500,">MKM", cex=1.2, font=2) The polygons convey information on whether each sample is higher than the soil guideline value. If I take away, the log scale, the vast difference in values obscures the polygons... Ideally I'd like the average beanline to be the arithmetic mean or to be gone altogether. Can't seem to make beanplot do this... Sincerely, Michael Hopgood -----Ursprungligt meddelande----- Från: Tom Wainwright [mailto:thomas.wainwri...@noaa.gov] Skickat: den 24 november 2009 18:43 Till: Michael Hopgood Kopia: r-help@r-project.org Ämne: Re: [R] Help: Beanplots calculating wrong average Hi Michael, Looking at the help for beanplot(), note that the 'log' option defaults to 'auto' which means the function will automatically log-transform data like yours. This also implies that the mean it shows is the geometric mean, not the arithmetic mean. As you note, the transformation doesn't affect the median. If you don't want this behavior, I think setting log="" will do the trick. Hope this helps. Tom Wainwright On 11/24/2009 03:52 AM, Michael Hopgood wrote: > Hi there, > > I have a set of data that looks like this: > > As1988<-c(1254.0, 22.0, 4.2, 1081.0, 35.0, 6.0, 1772.0, 192.0, 7.6) > > The mean of this (as calculated by R) is: 485.9778 > > The median of this (as calculated by R) is: 35 > > > > If I then make a beanplot(As1988), I find that the beanline (average) is now > 77.68561 while the beanline (median) is 35.39739 (using the locator function > to check the graph and log axis). > > > > While I can understand the small discrepancy of the median(mouse hovering > over the line), I am at a loss to explain the huge difference between the > means. Is this a flaw in the package or is there something I am missing? > > > > My gut feeling is that the log scales are affecting the calculations > somehow. > > > > Sincerely, > > Michael Hopgood > > > > > [[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. > -- Tom Wainwright NOAA Northwest Fisheries Science Center Newport, Oregon ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The contents of this message are mine personally and do not necessarily reflect any position of the Government or the National Oceanic and Atmospheric Administration. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ______________________________________________ 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.