Make the document work in LaTeX/PDF

[bvkrauth]

• Make the graphs have correct alignment
• Make the code fit the page
• Make the cross references work
• Add shaded boxes

[bvkrauth]

The LaTeX engine will only put an R generated graph in a figure environment with caption if the code chunk is separated by an empty line (double spaces at the end of the line won't do it).

I have fixed this in the cases where there was a bad reference, but should also do it wherever fig.cap is used.