{"id":20723585,"url":"https://github.com/networks-learning/pooled-testing","last_synced_at":"2025-08-10T13:13:08.034Z","repository":{"id":68767293,"uuid":"332763887","full_name":"Networks-Learning/pooled-testing","owner":"Networks-Learning","description":"Code for \"Pooled Testing of Traced Contacts Under Superspreading Dynamics\", PLOS Computational Biology","archived":false,"fork":false,"pushed_at":"2022-04-06T08:03:13.000Z","size":1187,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-03-11T08:31:41.173Z","etag":null,"topics":["coronavirus","covid-19","group-testing","overdispersion","pooled-testing","superspreading-events"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Networks-Learning.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2021-01-25T13:55:34.000Z","updated_at":"2022-03-29T07:16:05.000Z","dependencies_parsed_at":null,"dependency_job_id":"3063198b-c512-4011-88b1-bd04e520edd5","html_url":"https://github.com/Networks-Learning/pooled-testing","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/Networks-Learning/pooled-testing","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Networks-Learning%2Fpooled-testing","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Networks-Learning%2Fpooled-testing/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Networks-Learning%2Fpooled-testing/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Networks-Learning%2Fpooled-testing/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Networks-Learning","download_url":"https://codeload.github.com/Networks-Learning/pooled-testing/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Networks-Learning%2Fpooled-testing/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":269729344,"owners_count":24465813,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-08-10T02:00:08.965Z","response_time":71,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["coronavirus","covid-19","group-testing","overdispersion","pooled-testing","superspreading-events"],"created_at":"2024-11-17T04:09:09.323Z","updated_at":"2025-08-10T13:13:08.025Z","avatar_url":"https://github.com/Networks-Learning.png","language":"Jupyter Notebook","readme":"# Pooled Testing of Traced Contacts Under Superspreading Dynamics\n\nThis 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/).\n\n## Dependencies\n\nAll 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:\n\n```bash\npython3 -m venv env\nsource env/bin/activate\npip install -r requirements.txt\n```\n\n## Code organization\n\nThe directory [src](src/) contains the source code for performing simulation experiments with our method and classic Dorfman's method.\n\nThe directory [scripts](scripts/) contains bash scripts that use the aforementioned code and pass parameter values required for the various experiments.\n\nThe 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.\n\nThe directory [figures](figures/) is used for saving the figures produced by the notebooks.\n\nThe directory [outputs](outputs/) is used for saving the json outputs produced by the scripts.\n\nThe directory [temp-outputs](temp-outputs/) is used for saving intermediate output files used by the notebooks.\n\n## Citation\n\nIf you use parts of the code in this repository for your own research, please consider citing:\n\n    @article{tsirtsis2022group,\n        title={Pooled Testing of Traced Contacts Under Superspreading Dynamics},\n        author={Tsirtsis, Stratis and De, Abir and Lorch, Lars and Gomez-Rodriguez, Manuel},\n        journal={PLOS Computational Biology},\n        year={2022}\n    }\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnetworks-learning%2Fpooled-testing","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnetworks-learning%2Fpooled-testing","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnetworks-learning%2Fpooled-testing/lists"}