Split code and data

[seabbs]

At the moment code is split over two repositories and data is embedded in both (in the form of set up lists, configs, and results etc).

From a reproducibility and testability standpoint it would be much better to move all processing code (both the R handling code and python batch set up code) to a new repo (for example EpiNow2.batch) and then make this repo have just the public config (dataset lists, scheduling etc) and encrypted (or otherwise secured) private config.

In the code repo using an R package structure would greatly improve the portability of the code as would the use of no global variables. It would also enable moving data read in (currently embedded in the code) into a single config list.

This issue would enable #151, #149,#143, #150