Fixed some bugs in Chapter 3 R code:

* Use 'ggsave' instead of 'pdf' (was not actually saving PDF files before)
* replaced deprecated 'opts' with 'theme'
* use 'stat="identity" in the geom_bar calls
* use 'colMeans' instead of 'mean' for data frame

Not fixed here, but worth noting: the naming convention in the code is a bit confusing. Eg, it's not clear from the text of the published e-book what example3-10b.rb is, as opposed to just example3-10. Ditto for the 3-11 examples.