Pooled Testing of Traced Contacts Under Superspreading Dynamics

This repository contains the code used in the paper Pooled Testing of Traced Contacts Under Superspreading Dynamics, published at PLOS Computational Biology.

Dependencies

All the experiments were performed using Python 3.9. In order to create a virtual environment and install the project dependencies you can run the following commands:

python3 -m venv env
source env/bin/activate
pip install -r requirements.txt

Code organization

The directory src contains the source code for performing simulation experiments with our method and classic Dorfman's method.

The directory scripts contains bash scripts that use the aforementioned code and pass parameter values required for the various experiments.

The directory notebooks contains jupyter notebooks producing the figures appearing in the paper. Each notebook reads output files which first need to be generated by executing the corresponding script of the same name.

The directory figures is used for saving the figures produced by the notebooks.

The directory outputs is used for saving the json outputs produced by the scripts.

The directory temp-outputs is used for saving intermediate output files used by the notebooks.

Citation

If you use parts of the code in this repository for your own research, please consider citing:

@article{tsirtsis2022group,
    title={Pooled Testing of Traced Contacts Under Superspreading Dynamics},
    author={Tsirtsis, Stratis and De, Abir and Lorch, Lars and Gomez-Rodriguez, Manuel},
    journal={PLOS Computational Biology},
    year={2022}
}