janalasser / school_seirx

Assessing the impact of SARS-CoV-2 prevention measures in Austrian schools by means of agent-based simulations calibrated to clustertracing data

Author: Jana Lasser, Graz University of Technology ([email protected])

Simulations using the scseirx (small-community-SEIRX) package to simulate disease spread in small communities and under a range of different interventions. This repository is an application to schools, presented in this preprint.

This software is under development and intended to respond rapidly to the current situation. Please use it with caution and bear in mind that there might be bugs.

Reference:

Lasser, J., Sorger, J., Richter, L., Thurner, S., Schmid, D., Klimek, P. (2022). Assessing the impact of SARS-CoV-2 prevention measures in schools by means of agent-based simulations calibrated to cluster tracing data. Nature Communications. DOI: 10.1038/s41467-022-28170-6

Contents

The content of this repository is structured into four main parts, also reflected in the folder structure of the code subfolder.

1. Model calibration
2. Analysis of intervention measures
3. Sensitivity analysis
4. Analysis of vaccination scenarios
5. Visualizations

Each of the four parts has its own README file, giving instructions on how to reproduce the simulations and analyses presented in the paper.

Note: to run the scripts listed here, you will need to download the necessary data from the OSF repository corresponding to this project. Please download the folder data from the repository and place it in the same directory of the repository as this README file.

Requirements

This project requires Python and Jupyter Notebooks as well as the scseirx Python package (v1.4.1) to run. The scseirx python package can be installed using pip. This should satisfy all other package dependencies.

pip install -Iv scseirx==1.4.1

The installation of the package takes about one minute on a modern laptop with a fast internet connection, depending on how many dependencies need to be downloaded.

In the README of the scseirx simulation repository you can find

• A detailed description of the simulation design and implementation
• Easy-to-follow usage examples for the simulation package (specifically relevant for the school application is this example notebook).
• Installation instructions for linux