General
USDOS is comprised of 3 stages: pre-processing, simulation, and post-processing. The details of each stage are listed below. Each of these stages has been partially automated to make the process streamlined and efficient. Pre-processing includes the selection of parameters and control type, and the generation of config, batch, and a job file for simulation. Simulation is completed with either a C code compiled version of USDOS or USDOS within the R package, and encompasses the simulation of the given number of outbreak runs. Finally, the results from these simulations are analyzed during post-processing and pre-determined maps and graphics are automatically generated.