Project creating individual based simulator for running epidemics. Can handle individual-based and raster-based simulations.

For help on command line arguments, run python .\simulator.py -h.

Running the simulator always requires three main files:

1. Configuration file (e.g. config.ini)
2. Host position file (e.g. hosts.txt)
3. Host initial conditions file (e.g. hosts_init.txt)

The configuration file is a .ini key = value file giving many options for the simulations. An example file with the minimal number of default parameters can be generated by running python .\simulator.py -d, or alternatively, with the -k flag the keyfile detailing all possible options is generated.

The first line of the two host files gives the number of hosts. There is then one line per host with space delimited x,y positions or initial state string, as appropriate.

For a simple example see the example/ folder.

• README.md This document
• simulator.py Main module for simulator project. Can be imported or run from command line
• code/ Directory containing majority of code for the simulator
• example/ Basic example of simulator usage
• test/ Testing code
• utilities/ Helpful modules for using the simulator

1. Documentation
2. Testing