[R] Help: Beanplots calculating wrong average

[Tom Wainwright]

On 11/26/2009 02:25 AM, Michael Hopgood wrote:
> 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
>

Hi Michael,

I don't know beanplot() well enough to know if it can be forced to do exactly 
what you want.  You should be able to use the "what" argument to suppress the 
mean lines, then you could add your own average lines using lines() or 
segments().  You could of course also modify the code to suit your needs (mybean 
<- beanplot; edit mybean), but it looks pretty complicated.

	Tom Wainwright

-- 
NOAA Northwest Fisheries Science Center
Newport, Oregon
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