SPIR (Susceptible-Prophylactic-Infected-Recovered) Agent-Based Simulation Model

Software Pre-requisites

• Python 3.0+
• Python Libraries: argparse, matplotlib, os.path, sys, time

Download Project from GitHub

• Open a terminal
• Navigate to the directory where you want to download the SPIR code
• Type: git clone https://github.com/bertybaums/SPIR.git

Configure

You can configure the simulation for running by changing the values of the parameters in the config.txt file.

Execute

To execute the simulation,

• Open a terminal
• Navigate to the SPIR root directory
• Type: python SPIR/Main.py -v -g configFile config.txt

You should see as a result a graphic with the dynamics of agents in the Susceptible, Prophylactic, Infectious, Recovered state.

Scripts

There are several R Statistics scripts available in the directory scripts. These scripts have different aims:

• ode-sir-model.R - Traditional SIR ODE model
• ode-spir-model.R - SPIR model as ODE
• decision-landscape-analysis.R - 3D visualization of the Susceptible and Prophylactic Expected Utility values in relation to the proportion of infected and time horizon for the decision-making
• switching-point-analysis.R - Calculus of the precise switching point location and a comparison with a possible linear approximation
• disease-analysis.R - Analysis of specific diseases