Digital Proximity Tracing in the COVID-19 Pandemic on Empirical Contact Networks

This repository contains the code for the simulations and experiments in the paper

G. Cencetti, G. Santin, A. Longa, E. Pigani, A. Barrat, C. Cattuto, S. Lehmann, M. Salathe, B. Lepri, Digital Proximity Tracing in the COVID-19 Pandemic on Empirical Contact Network, DOI: 10.1101/2020.05.29.20115915.

Basic usage:

For a basic usage of this code, you may consider the following steps.

First, the simulations on the network can be launched using the notebooks:

• Digital-Contact-Tracing on DTU to run the simulation on the DTU dataset¹.
• Digital-Contact-Tracing on SocioPattern to run the simulation on some Sociopattern datasets².

Second, the simulation of the continuous model can be launched using the notebook:

• Generate_model_predictions.ipynb.

These notebooks compute outputs that are stored in RESULTS and RESULTS_Model. As an example, these folders already contain the outputs for the case R_0=1.5 with app_adoption=80%.

Finally, the outputs of the simulations may be visualized using the notebooks:

• Visualize effectivity.ipynb to visualize the effect of the tracing policies and check if they contain the spread.
• Visualize quarantines.ipynb to visualize the temporal evolution of the number of quarantined people (both false positive and false negative).

Documentation:

The official documentation can be found here.

How to cite:

If you use this code in your work, please consider citing the paper:

@techreport{Cencetti2020,
	author = {Cencetti, Giulia and Santin, Gabriele and Longa, Antonio and Pigani, Emanuele and Barrat, Alain and Cattuto, Ciro and Lehmann, Sune and Salathe, Marcel and Lepri, Bruno},
	title = {Digital Proximity Tracing in the COVID-19 Pandemic on Empirical Contact Networks},
	elocation-id = {2020.05.29.20115915},
	year = {2020},
	doi = {10.1101/2020.05.29.20115915},
	publisher = {Cold Spring Harbor Laboratory Press},
	URL = {https://www.medrxiv.org/content/early/2020/07/02/2020.05.29.20115915},
	eprint = {https://www.medrxiv.org/content/early/2020/07/02/2020.05.29.20115915.full.pdf},
	journal = {medRxiv}
}

The version v.1.0.0 of this code is published here .

Contacts:

If you have any question or comment, please feel free to drop us an email.

Datasets used in the simulations:

1: Interaction data from the Copenhagen Networks Study.

2: Contact Patterns in a High School: A Comparison between Data Collected Using Wearable Sensors, Contact Diaries and Friendship Surveys, and Can co-location be used as a proxy for face-to-face contacts?.