[R] Shading area under density curves

[Marc Schwartz]

On Wed, 2007-10-03 at 14:21 -0700, rominger at stanford.edu wrote:
> Hello,
> 
> I have a question regarding shading regions under curves to display  
> 95% confidence intervals.  I generated bootstrap results for the slope  
> and intercept of a simple linear regression model using the following  
> code (borrowed from JJ Faraway 2005):
> 
> > attach(allposs.nine.d)
> > x<-model.matrix(~log(d.dist,10))[,-1]
> > bcoef<-matrix(0,1000,2)
> > for(i in 1:1000){
> + newy<-predict(all.d.nine.lm)+residuals(all.d.nine.lm)[sample(1002,rep=TRUE)]
> + brg<-lm(newy~x)
> + bcoef[i,]<-brg$coef
> + }
> 
> Where "allposs.nine.d" is a data file composed of two columns: (1)  
> geographical distances between sample points ("d.dist") and (2) their  
> respective pairwise percent similarity in species composition  
> ("d.sim").  The expression "all.d.nine.lm" equals lm(d.sim~d.dist).
> 
> I saved the bootstrap results for each coefficient as:
> 
> > dist.density.b1<-density(bcoef[,2])
> > dist.density.b0<-density(bcoef[,1])
> 
> Along with their 95% confidence intervals:
> 
> > dist.quant.b1<-quantile(bcoef[,2],c(.025,.975))
> > dist.quant.b0<-quantile(bcoef[,1],c(.025,.975))
> 
> I then could plot smooth density curves along with their 95% CI's:
> 
> > plot(dist.density.b1)
> > abline(v=dist.quant.b1)
> 
> Now finally for my question:  Instead of drawing vertical lines to  
> represent the 95% CI's, I'd much prefer to somehow shade in the region  
> under the curve corresponding the to 95% CI.  I tried using the  
> polygon() function for this but did not get very far as I couldn't  
> figure out how to define limits for x and y coordinates.
> 
> Any suggestions would be great.  Thanks very much--
> Andy Romigner

You might want to review this post on shading critical regions (my reply
to question #3):

  http://tolstoy.newcastle.edu.au/R/help/03b/2475.html

or perhaps this entry by Thomas Lumley from the R Graph Gallery:

  http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=88

HTH,

Marc Schwartz