Question

Is there a simple way to plot the difference between two probability density functions?

I can plot the pdfs of my data sets (both are one-dimensional vectors with roughly 11000 values) on the same plot together to get an idea of the overlap/difference but it would be more useful to me if I could see a plot of the difference.

something along the lines of the following (though this obviously doesn’t work):

> plot(density(data1)-density(data2))

I’m relatively new to R and have been unable to find what I’m looking for on any of the forums.

Thanks in advance

Answer 1

This should work:

plot(x =density(data1, from= range(c(data1, data2))[1], 
                       to=range(c(data1, data2))[2] )$x, 
  y=  density(data1, from= range(c(data1, data2))[1], 
                     to=range(c(data1, data2))[2] )$y-
       density(data2,  from= range(c(data1, data2))[1], 
                      to=range(c(data1, data2))[2] )$y )

The trick is to make sure the densities have the same limits. Then you can plot their differences at the same locations.My understanding of the need for the identical limits comes from having made the error of not taking that step in answering a similar question on Rhelp several years ago. Too bad I couldn’t remember the right arguments.