Epidemics Suppression Model

This repository implements a mathematical model describing the suppression of an epidemic due to measures that identify and isolate infected individuals, possibly with the help of a mobile app. The output of the algorithm is the time evolution of the relative suppression of the effective reproduction number due to these measures.

The model is described in the paper Maiorana, A., Meneghelli, M. & Resnati, M. Effectiveness of isolation measures with app support to contain COVID-19 epidemics: a parametric approach. J. Math. Biol. 83, 46 (2021). https://doi.org/10.1007/s00285-021-01660-9 (arXiv preprint).

In section 4 of the paper we described the application of the model to the COVID-19 epidemic, and we reported the results of some computations that were made running the code contained in the package examples of this repository.

We refer to the paper for details about the model, the interpretation of the parameters appearing here, and the sources of the epidemiological features of COVID-19 that are used as an input of the model. Note that in this repository, like in the computations made in the paper, the "default" (i.e. without measures) effective reproduction number is taken constantly equal to 1, as we are interested in studying the relative suppression only.

Set-up and usage

To use the algorithm you should clone the repository by running

git clone https://github.com/BendingSpoons/epidemic-suppression-model.git
cd epidemics-suppression-model

The library runs on Python 3.8. The dependencies of the library are provided in the file pyproject.toml. To install them, you first need to install Poetry, and then run

poetry install

Examples

The directory examples contains some functions that, when executed, run the algorithm with certain specific choice of the input parameters, printing the results and generating the plots appearing in the paper. There are also some scripts running only small pieces of the algorithm to illustrate how they work, or displaying the epidemic data used by the algorithm.

How to cite this repository

Maiorana A and Meneghelli M 2021. Epidemics Suppression Model. https://github.com/BendingSpoons/epidemic-suppression-model.

@misc{mm2021epidemics,
    author = {Maiorana, Andrea and Meneghelli, Marco},
    title = {Epidemics Suppression Model},
    year={2021},
    publisher = {GitHub},
    journal = {GitHub repository},
    howpublished = "\url{https://github.com/BendingSpoons/epidemic-suppression-model}"
}