Agent Based Model Mini-Project 2023

This project consists of an SIR model for N indidivuals in a closed room. The simulation begins with I_0 individuals with Infected Status and updates discretely each time step.

Installation

To install a copy of the simulator, open a terminal and run:

git clone [email protected]:SABS-R3-Epidemiology/abm-project-2023.git

To make sure all dependencies are installed, in the current directory run:

pip install ./abm-project-2023

Class Overview

Here is a UML class diagram for our project:

Produce data files

Move to the abm-project-2023 directory. In the command line, run

python abm_model/generate_data.py

This will run the simulation with pre-set parameter values, producing a .csv file containing the results of the simulation in the directory data/csv_files.

In order to change these parameter values, you will need to use commands within abm-project-2023 (see below).

generate_data.py commands

Entering commands in the terminal will allow you to set-up a specific simulation.

A comprehensive list of the commands is provided below:

Command	Command Shortcut	Description
--help	-h	Print help
--population-size=100	-N	Total number of individuals in the simulation
--total-time=20	-t	Number of time steps [days] that the simulation will run for
--beta=0.01	-b	Effective contact rate of the disease
--recovery-period=3.0	-D	Average number of time steps for which an individual is infected
--initial-infected=1	-I	Initial number of infected individuals
--title="test"	-T	Title attached to the output .csv file
--path="data"	-p	Path to the directory containing the .csv file and the plots

Plotting a data file

Still within the abm-project-2023 directory, run the following command to plot the data within a given .csv file

python abm_model/generate_plots.py -f "<file_name>.csv"

This will produce plots for the given SIR data, which will end up in the directory data/plots. You must either specify the file_name or enter "-h" or "--help" for help.

generate_plots.py commands

Here is a table of commands for generate_plots.py:

Command	Command Shortcut	Description
--help	-h	Print help
--csv-file-name	-f	The chosen .csv file containing the data of a simulation

Running Tests

Within the abm-project-2023/abm_model directory, run the following command to run tests

python -m unittest tests/test_status.py

This will run the tests in test_status.py. We can also run the other test scripts by replacing this with:

• test_gif_plot.py
• test_minicell.py
• test_person.py
• test_plot.py

Parameter Definitions

Parameter	Command Shortcut	Description
population_size	-N	Total number of individuals in the simulation
total_time	-t	Number of time steps [days] that the simulation will run for
beta	-b	Effective contact rate of the disease
recovery_period	-D	Average number of time steps for which an individual is infected
initial_infected	-I	Initial number of infected individuals
title	-T	Title attached to the output .csv file
path	-p	Path to the directory containing the .csv file and the plots