In R: http://robjhyndman.com/index.php?option=com_content&view=article&id=233:r-graph-with-two-y-axes&catid=32:mbr&Itemid=103

In Stata: http://www.ats.ucla.edu/stat/stata/library/GraphExamples/code/twobar.htm

Also, R package "plotrix" has a function "twoord.plot" designed specifically for this.

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