Running CovidSim in R

Purpose

These are scripts in R that take the data generated by the spatial simulation and summarize it graphically.

Download and install R.. These scripts have been tested for R 3.4.4, but other versions should work as well.

You will need the R library sp, but if this is missing, the scripts will prompt you to install it themselves.

If you generated data with run_UK_100th.sh, you can type

Rscript Rscripts/CompareScenarios.R

or

Rscript Rscripts/PlotsSpatial.R

If you have generated data with the ./run_sample.py, inside the data folder, you can type

Rscript Rscripts/PlotRuns.R data

More generally, the syntax is:

Rscript [path-to-one-of-the-scripts.R] [folder-where-the-data-is]

If the second argument is omitted, it will try to pull the data from the current directory.