https://github.com/networks-learning/pooled-testing
Code for "Pooled Testing of Traced Contacts Under Superspreading Dynamics", PLOS Computational Biology
https://github.com/networks-learning/pooled-testing
coronavirus covid-19 group-testing overdispersion pooled-testing superspreading-events
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Code for "Pooled Testing of Traced Contacts Under Superspreading Dynamics", PLOS Computational Biology
- Host: GitHub
- URL: https://github.com/networks-learning/pooled-testing
- Owner: Networks-Learning
- Created: 2021-01-25T13:55:34.000Z (about 5 years ago)
- Default Branch: master
- Last Pushed: 2022-04-06T08:03:13.000Z (almost 4 years ago)
- Last Synced: 2025-03-11T08:31:41.173Z (about 1 year ago)
- Topics: coronavirus, covid-19, group-testing, overdispersion, pooled-testing, superspreading-events
- Language: Jupyter Notebook
- Homepage:
- Size: 1.13 MB
- Stars: 1
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# 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](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010008), published at [PLOS Computational Biology](https://journals.plos.org/ploscompbiol/).
## 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:
```bash
python3 -m venv env
source env/bin/activate
pip install -r requirements.txt
```
## Code organization
The directory [src](src/) contains the source code for performing simulation experiments with our method and classic Dorfman's method.
The directory [scripts](scripts/) contains bash scripts that use the aforementioned code and pass parameter values required for the various experiments.
The directory [notebooks](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](figures/) is used for saving the figures produced by the notebooks.
The directory [outputs](outputs/) is used for saving the json outputs produced by the scripts.
The directory [temp-outputs](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}
}