Commenting out lots of setwd() commands that cause me trouble

Since you have the user set this in the Makefile.R, you don't need to do it in all the individual scripts. I realize they were probably helpful for development but they are not good once you distribute to others.
Nicer way to list the figure files
Improving the writing in the report
Merge pull request #1 from jennybc/master

JB suggestions for improvement