sir-rs

SIR infectious disease modelling CLI

Example Usage

The CLI takes 5 input parameters to the application to run the simulation.

• Recovery Rate (gamma)
• Infection Rate (beta)
• Time Steps (t)
• Initial Susceptible (S₀)
• Initial Infectious (I₀)
• Initial Recovered (R₀)

cargo run -- {gamma} {beta} {t} {S} {I} {R}

Note: Please replace the {} values with your corresponding values.

Running this command will write a csv file to the directory in which the executable was running from called results.csv.

The schema for the csv is as follows:

Column Index	Description
0	Time step / day
1	Number of susceptible people
2	Number of infectious people
3	Number of recovered people

Example

Running the following command results in the following data being generated:

cargo run -- 0.05 0.0001 100 10000 1000 0

or if you've compiled the binary on Linux:

./target/release/sir-rs 0.05 0.0001 100 10000 1000 0

And on Windows:

.\target\release\sir-rs 0.05 0.0001 100 10000 1000 0

0,10000,1000,0
1,9000,1950,50
2,7245,3607.5,147.5
3,4631.36625,6040.75875,327.875
4,1833.6696300857811,8536.417432414219,629.9129375
5,268.3726905305018,9674.893500348788,1056.733809120711
6,8.724970602034944,9450.796545259815,1540.4784841381504
7,0.47917839971441367,8986.502510199145,2013.018311401141
8,0.048564610527734864,8537.607998478374,2462.3434369110983
9,0.007102049799277241,8110.769061115184,2889.223836835017
10,0.0013417412210295259,7705.236368368003,3294.7622898907766

This dataset can then be visualized by the tool of your choice, but I will display an example in Power BI.

Compiled Binary

To get the compile this project into a binary, run:

cargo build --release

The binary will be located in ./target/release/sir-rs. If you are on a Windows machine, the binary will be a .exe file.

Running the compiled binary

Ensure the binary has file permission to be executed.

Linux/macOS Command to run the binary:

cd ./target/release && ./sir-rs {gamma} {beta} {t} {S} {I} {R}

Windows command to run binay:

cd .\target\release && sir.exe {gamma} {beta} {t} {S} {I} {R}

Model

Please visit https://en.wikipedia.org/wiki/Compartmental_models_in_epidemiology#SIR for details.