Updates to match JHU sims and port to R

[mccorvie]

There are two parts to this update. The first updates the JHU processing script to adapt to changes in the input simulation:

1. read parquet files instead of csv files
2. don't rely on the sim_num field, this is duplicated in different simulation paths, instead use the number in the filename
3. add new scenarios file paths
4. add a rundate argument to allow for processing of old sims

The second part ports the whole python script to R. Future development will probably all be in R.