rZeroORing

Code for paper by van den Bosch, Helps and Cunniffe on using the O-ring statistic to calculate R0 for spatially structured epidemic models.

The pipeline for creating landscape(s), running epidemics and calculating R0 is described below.

1. Compile EpidemicSim.exe from EpidemicSim.c and mt19937ar.c
2. Create directory to do the runs
3. Copy the following files to directory created in step 2
   • EpidemicSim.cfg
   • EpidemicSim.exe
   • create_LS.R
   • rZero_From_Sims.R
   • rZero_Function.R
4. Create the following subdirectories of directory created in step 2
   • Inputs
   • Outputs
5. Start R and change to the directory created in step 2 using setwd()
6. Run create_LS.R
   • Options for landscape generation are in the R file
   • Running it will fill up Inputs subdirectory
7. Run EpidemicSim.exe on command line
   • Options for epidemics are in the EpidemicSim.cfg files
   • will fill up Outputs subdirectory
8. Run rZero_From_Sims.R
   • will print estimated and calculated rZero to the screen