I'm really pleased to see you're using Pander[1] in your tool chain. I think this is one of the most useful literate programming tools in the R ecosystem. Although, having read Part 6 (briefly), it looks like you might only be using it for tables and plots. I think Pander's literate programming functionality, in conjunction with Brew, is worth further exploration[2].
Also, if you're using R-base plots, there's an excellent tutorial[3] and theme library[4] which can help make those plots look really excellent.
Also, if you're using R-base plots, there's an excellent tutorial[3] and theme library[4] which can help make those plots look really excellent.
[1] http://rapporter.github.io/pander/
[2] https://github.com/Rapporter/pander/tree/master/inst/example...
[3] http://karolis.koncevicius.lt/posts/r_base_plotting_without_...
[4] https://github.com/KKPMW/basetheme