On 2010-02-18 8:22, fussel wrote:
Hey hey, I`m analyzing a data set containing the element contentrations of various samples... I wanted to construct notched boxplots and got quite ugly results for some of the boxplots. The notches are often larger then the hinges which resulted in weird looking edges (even though I`m using a log-boxplot). To avoid this problem I thought about using "normal" log-boxplots and adding some kind of parantheses for showing the confidence interval. I found an option to do this with the help of the package "psych". It works beautifully for sth like that: x<- replicate(20,rnorm(50)) boxplot(x,notch=TRUE,main="Notched boxplot with error bars") error.bars(x,add=TRUE) abline(h=0)
Beautifully? To me, that's one of the ugliest plots I've seen in a while. But, as they say, it's in the eye of the beholder. Anyway, what is the purpose of the notches? It's not clear to me that you understand them. There's a good reason why the notches sometimes stick out beyond the box. This is usually the result of a small sample. If you have variable sample sizes you might find variable-width boxplots somewhat informative. Personally, I don't have much for use notched boxplots.
I tried to apply this to my own dataset: ## Ag boxplotDAS(log10(Ag)~Aquifer,ylab="",xlab="Ag (mg/l)", main="", data=samples, notch=TRUE, horizontal=TRUE, xaxt="n", col="gray85") error.bars(samples,add=TRUE) axis(1,at=log10(a<-sort(c((10^(-50:50))%*%t(c(1,5))))),labels=a, tick=T) abline(v=log10(a),lty=3,col='gray') I end up with lots of error messages - all of them saying: Warning in arrows(s[s], x.stats$mean[s] - ci[s] * x.stats$se[s], s[s], x.stats$mean[s] + : zero-length arrow is of indeterminate angle and so skipped What does that mean and how can I get rid of it? Any ideas?
These warning (not 'error') messages come from error.bars(). Why not try to plot the error bars without any boxplots to see where the problems might lie. As a check, I would also do the confidence interval calculations 'by hand'. Or you could provide a *reproducible* example, preferably minimal (i.e. skip the xlab= , etc stuff) and someone might try the code and tell you where the problems lie. -Peter Ehlers
Thanks a lot, fussel
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