{"id":17358674,"url":"https://github.com/babak2/whd","last_synced_at":"2025-06-19T03:43:35.819Z","repository":{"id":172300645,"uuid":"649109072","full_name":"babak2/WHD","owner":"babak2","description":"Within Host Dynamics","archived":false,"fork":false,"pushed_at":"2023-11-21T19:03:50.000Z","size":19714,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-02-01T19:45:12.297Z","etag":null,"topics":["cpp","individual-based-modelling","infectious-disease-modeling","malaria-modeling","pk-pd-modelling"],"latest_commit_sha":null,"homepage":"","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/babak2.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","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":"2023-06-03T20:05:37.000Z","updated_at":"2025-01-16T00:30:07.000Z","dependencies_parsed_at":null,"dependency_job_id":"3ad68fe1-a818-4974-823b-08f3d4e8f50c","html_url":"https://github.com/babak2/WHD","commit_stats":null,"previous_names":["babak2/whd"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/babak2%2FWHD","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/babak2%2FWHD/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/babak2%2FWHD/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/babak2%2FWHD/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/babak2","download_url":"https://codeload.github.com/babak2/WHD/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245878924,"owners_count":20687297,"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","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":["cpp","individual-based-modelling","infectious-disease-modeling","malaria-modeling","pk-pd-modelling"],"created_at":"2024-10-15T19:06:28.237Z","updated_at":"2025-03-27T16:18:25.526Z","avatar_url":"https://github.com/babak2.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"# WHD model\n\n## To Build\n\n`g++` is the default compiler.\n\n\n```\nmake\n```\nFor more details please refer to the `Makefile`\nOr compile diretly by typing:\n./make.sh\n\n## To Run\n\n```\n./build/bin/malaria_model -c config.json -o outputs\n```\n\n### Mandatory Commandline Options\n\n- `-c [FILE]`, user specified simulation configuration file. A simplified (not complete) example `config_whd.json` is given below.\n\n```\n{\n    \"simulation\" : {\n        \"schema_file_name\" : \"schema.config.json\",\n        \"total_steps\" : 60,\n        \"total_population\" : 100\n    },\n\n    \"whd\" : {\n        \"whd_level\" : 0,\n        \"II50\" : 2000000000,\n        \"pmf\" : 11.0,\n        \"gamma\": 0.75,\n                     \n        \"transition_matrix\" : {\n            \"Jpk\" : {\n                \"CL\": 3.2500,\n                \"V2\": 5.3750\n            }\n        }\n    }\n}\n```\n\n- `-o [OUTPUT_DIRECTORY]`\n\n### Optional Commandline Options\n\n- `-i [OUTPUT_PREFIX]`, if given will be used as prefix for all outputs of this run, otherwise a timestamp will be used to identify outputs. \n\n\n## To Test\nWe use the [Catch2](https://github.com/catchorg/Catch2) framework.\n\n1. Build tests:\n```\nmake test\nOr compile diretly by typing:\n./make_4_test.sh\n```\n\n2. Run all tests:\n```\nmalaria_model$ ./build/bin/test\n```\n\n3. List all tests:\n```\nmalaria_model$ ./build/bin/test -l\n```\n\n4. Run a specific test:\n```\nmalaria_model$ ./build/bin/test [whd:test]\n```\n\n```\nmalaria_model$ ./build/bin/test [whd_multiple:test]\n```\n\n## Dependencies\nC++ Libraries and the version installed on the development machine:\n\n### .hpp Dependencies\nThese are header-only libraries that are included as part of this project. No installation is required.\n\n- [Eigen](https://eigen.tuxfamily.org), v3.3.9, for linear algebra / matrix operations. Included in include/third_party directory.\n- [Catch2](https://github.com/catchorg/Catch2), v2.1.2, a C++ test framework. `./test/third_party/`\n\n\n## License\n\nThe WHD model is licensed under the GNU GENERAL PUBLIC LICENSE. See LICENSE for more information.\n\n## Author\n\nBabak Mahdavi Ardestani\n\nbabak.m.ardestani@gmail.com\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbabak2%2Fwhd","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbabak2%2Fwhd","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbabak2%2Fwhd/lists"}