Write tests and create more robust and maintainable architecture

[vicfabienne]

Most of the scripts need tests. For further information contact @rekado

Also, there is a lot of processing currently done within the rmd reports which should be moved to individual files.

[rekado]

These two parts are linked: in order to simplify the tests we should move most processing out of the Rmd files and into scripts (or libraries). Once that's done we can test those scripts or libraries without having to process rmarkdown.

[rekado]

One of the issues relating to moving code out of Rmd files is #19