[R] Change Confidence Limits on a plot

Dieter Menne dieter.menne at menne-biomed.de
Fri Nov 14 17:53:12 CET 2008

Robin Clark wrote:
> 	mult<-glht(lm(effectModel, data=statdata, na.action = na.omit),
> linfct=mcp(mainEffect="Means"))
> 	meanPlot <- sub(".html", "meanplot.jpg", htmlFile)
> 	jpeg(meanPlot)
> 	plot(mult, main=NA, xlab=unlist(strsplit(Args[4],"~"))[1]) 
> This produces 95% CIs by default but I would like to produce 99% CIs - How
> do I do this?

See documentation under plot.confint.glht. Finding the function doing the
job can be a bit 
tricky in R, because plot(mult,) does not call a generic plot routine in
this case, but it tries 
the "best matching" for the object generated. 

Frequently, you can expect something like plot.glht being called, but the
docs of 
multcompt show that this does not exist, so plot.confint.glht comes close.

Using str(mult) and methods() you can formalize this search, but in most
cases good
guesses are faster.

(Note: no sample provided, since you example is not self-contained)


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