Split functions from run time of code

[seabbs]

In R it is usual to split function loading from calling the functions (i.e run-region-updates.R which is currently more C or Python like). It would make sense to make all functions in covid-rt-estimates part of an R package that can then be unit tested. This would also help with documentation and discoverability.

This would also allow the underlying framework to be separated from this particular list of datasets to run against and this particular data verse config etc.