Re: [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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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