{"id":55899,"name":"epidemics","description":"A library of published compartmental epidemic models, and classes to represent demographic structure, non-pharmaceutical interventions, and vaccination regimes, to compose epidemic scenarios.","url":"https://github.com/epiverse-trace/epidemics","last_synced_at":"2025-09-05T14:03:32.038Z","repository":{"id":65903034,"uuid":"586911007","full_name":"epiverse-trace/epidemics","owner":"epiverse-trace","description":"A library of published compartmental epidemic models, and classes to represent demographic structure, non-pharmaceutical interventions, and vaccination regimes, to compose epidemic scenarios.","archived":false,"fork":false,"pushed_at":"2025-08-06T11:26:57.000Z","size":32914,"stargazers_count":11,"open_issues_count":24,"forks_count":5,"subscribers_count":7,"default_branch":"main","last_synced_at":"2025-08-06T11:30:31.305Z","etag":null,"topics":["decision-support","epidemic-modelling","epidemic-simulations","epidemiology","epiverse","infectious-disease-dynamics","model-library","non-pharmaceutical-interventions","r","r-package","rcpp","rcppeigen","scenario-analysis","vaccination"],"latest_commit_sha":null,"homepage":"https://epiverse-trace.github.io/epidemics/","language":"R","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/epiverse-trace.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2023-01-09T14:20:16.000Z","updated_at":"2025-08-06T09:33:01.000Z","dependencies_parsed_at":"2023-09-28T15:56:13.072Z","dependency_job_id":"2e195c3c-7b3c-4680-9178-8d15954a4d12","html_url":"https://github.com/epiverse-trace/epidemics","commit_stats":{"total_commits":700,"total_committers":11,"mean_commits":63.63636363636363,"dds":"0.14714285714285713","last_synced_commit":"14b38b8ffbda1ddfdf1d90b2d26d6570e1830d89"},"previous_names":[],"tags_count":4,"template":false,"template_full_name":"epiverse-trace/packagetemplate","purl":"pkg:github/epiverse-trace/epidemics","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiverse-trace%2Fepidemics","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiverse-trace%2Fepidemics/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiverse-trace%2Fepidemics/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiverse-trace%2Fepidemics/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/epiverse-trace","download_url":"https://codeload.github.com/epiverse-trace/epidemics/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiverse-trace%2Fepidemics/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273768126,"owners_count":25164464,"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":"2025-09-05T02:00:09.113Z","response_time":402,"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"}},"owner":{"login":"epiverse-trace","name":"Epiverse-TRACE","uuid":"101338582","kind":"organization","description":"","email":null,"website":"https://epiverse.org","location":null,"twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/101338582?v=4","repositories_count":17,"last_synced_at":"2023-03-06T22:51:50.116Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/epiverse-trace","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-16T23:02:56.947Z","updated_at":"2023-03-06T22:51:50.140Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/epiverse-trace","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/epiverse-trace/repositories"},"packages":[],"commits":{"id":1368612,"full_name":"epiverse-trace/epidemics","default_branch":"main","committers":[{"name":"Pratik Gupte","email":"pratik.gupte@lshtm.ac.uk","login":null,"count":597},{"name":"GitHub Action","email":"action@github.com","login":"actions-user","count":32},{"name":"James Azam","email":"james.m.azam@gmail.com","login":null,"count":18},{"name":"jamesaazam","email":"james.azam@lshtm.ac.uk","login":null,"count":17},{"name":"Pratik Gupte","email":"pratikgupte16@gmail.com","login":null,"count":11},{"name":"Hugo Gruson","email":"Bisaloo","login":"Bisaloo","count":9},{"name":"bahadzie","email":"bahadzie@gmail.com","login":null,"count":7},{"name":"Edwin van Leeuwen","email":"edwinvanl@tuta.io","login":null,"count":5},{"name":"adamkucharski","email":"adam.kucharski@lshtm.ac.uk","login":null,"count":2},{"name":"Tim Taylor","email":"tim.taylor@hiddenelephants.co.uk","login":null,"count":1},{"name":"banky","email":"41001537+bahadzie","login":"bahadzie","count":1}],"total_commits":700,"total_committers":11,"total_bot_commits":0,"total_bot_committers":0,"mean_commits":63.63636363636363,"dds":0.14714285714285713,"past_year_committers":[{"name":"Pratik Gupte","email":"pratik.gupte@lshtm.ac.uk","login":null,"count":596},{"name":"GitHub Action","email":"action@github.com","login":"actions-user","count":32},{"name":"James Azam","email":"james.m.azam@gmail.com","login":null,"count":18},{"name":"jamesaazam","email":"james.azam@lshtm.ac.uk","login":null,"count":17},{"name":"Pratik Gupte","email":"pratikgupte16@gmail.com","login":null,"count":10},{"name":"Hugo Gruson","email":"Bisaloo","login":"Bisaloo","count":9},{"name":"bahadzie","email":"bahadzie@gmail.com","login":null,"count":7},{"name":"Edwin van Leeuwen","email":"edwinvanl@tuta.io","login":null,"count":5},{"name":"adamkucharski","email":"adam.kucharski@lshtm.ac.uk","login":null,"count":2},{"name":"Tim Taylor","email":"tim.taylor@hiddenelephants.co.uk","login":null,"count":1},{"name":"banky","email":"41001537+bahadzie","login":"bahadzie","count":1}],"past_year_total_commits":698,"past_year_total_committers":11,"past_year_total_bot_commits":0,"past_year_total_bot_committers":0,"past_year_mean_commits":63.45454545454545,"past_year_dds":0.14613180515759316,"last_synced_at":"2024-01-26T20:02:36.528Z","last_synced_commit":"14b38b8ffbda1ddfdf1d90b2d26d6570e1830d89","created_at":"2023-09-13T14:51:22.437Z","updated_at":"2024-01-26T20:02:36.528Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiverse-trace%2Fepidemics/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-08-27T00:00:29.048Z","repositories_count":5479765,"commits_count":853308191,"contributors_count":31095157,"owners_count":906558,"icon_url":"https://github.com/github.png","host_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories"}},"issues_stats":{"full_name":"epiverse-trace/epidemics","html_url":"https://github.com/epiverse-trace/epidemics","last_synced_at":"2025-08-31T15:30:51.689Z","status":null,"issues_count":153,"pull_requests_count":105,"avg_time_to_close_issue":5424127.0227272725,"avg_time_to_close_pull_request":1033241.125,"issues_closed_count":132,"pull_requests_closed_count":96,"pull_request_authors_count":10,"issue_authors_count":13,"avg_comments_per_issue":1.6339869281045751,"avg_comments_per_pull_request":1.7619047619047619,"merged_pull_requests_count":89,"bot_issues_count":0,"bot_pull_requests_count":6,"past_year_issues_count":7,"past_year_pull_requests_count":9,"past_year_avg_time_to_close_issue":10288024.5,"past_year_avg_time_to_close_pull_request":3338644.5,"past_year_issues_closed_count":2,"past_year_pull_requests_closed_count":2,"past_year_pull_request_authors_count":4,"past_year_issue_authors_count":4,"past_year_avg_comments_per_issue":4.571428571428571,"past_year_avg_comments_per_pull_request":0.0,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":2,"past_year_merged_pull_requests_count":1,"created_at":"2023-09-13T14:51:39.370Z","updated_at":"2025-09-02T19:41:44.797Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiverse-trace%2Fepidemics","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiverse-trace%2Fepidemics/issues","issue_labels_count":{"Discussion":22,"R frontend":21,"ODE model":19,"Documentation":17,"Helper functions":12,"Enhancement":10,"Interventions":9,"R code":9,"C++ backend":8,"Bug":7,"Vaccination":7,"good first issue":6,"Stale":6,"Cleanup":6,"C++":5,"Population":4,"question":4,"New model":3,"Infection":2,"CI":2,"Active":2,"known-issue":1,"Stochastic models":1,"Testing":1},"pull_request_labels_count":{"CI":9,"Documentation":6,"Enhancement":5,"ODE model":5,"Helper functions":5,"C++ backend":4,"Bug":4,"Vaccination":4,"R frontend":3,"New model":2,"Cleanup":2,"C++":2,"Interventions":1,"Testing":1,"Scenarios":1},"issue_author_associations_count":{"MEMBER":126,"NONE":6,"COLLABORATOR":6,"CONTRIBUTOR":3},"pull_request_author_associations_count":{"MEMBER":96,"COLLABORATOR":28,"NONE":13,"CONTRIBUTOR":2},"issue_authors":{"pratikunterwegs":109,"adamkucharski":11,"jamesmbaazam":4,"TimTaylor":3,"Degoot-AM":3,"avallecam":2,"rozeggo":2,"Bisaloo":1,"joshwlambert":1,"Karim-Mane":1,"amanda-minter":1,"CarmenTamayo":1,"roberthinch":1,"sdwfrost":1},"pull_request_authors":{"pratikunterwegs":103,"github-actions[bot]":10,"bahadzie":8,"Bisaloo":5,"chartgerink":2,"adamkucharski":2,"sbaptist":2,"avallecam":2,"TimTaylor":2,"jamesmbaazam":2,"roberthinch":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-03T00:00:08.273Z","repositories_count":10061379,"issues_count":31059648,"pull_requests_count":94180017,"authors_count":10686068,"icon_url":"https://github.com/github.png","host_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories","owners_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/owners","authors_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors"},"past_year_issue_labels_count":{},"past_year_pull_request_labels_count":{},"past_year_issue_author_associations_count":{"MEMBER":5,"NONE":2,"COLLABORATOR":1},"past_year_pull_request_author_associations_count":{"NONE":5,"MEMBER":3},"past_year_issue_authors":{"adamkucharski":4,"amanda-minter":1,"avallecam":1,"Degoot-AM":1,"roberthinch":1},"past_year_pull_request_authors":{"bahadzie":3,"sbaptist":2,"github-actions[bot]":2,"roberthinch":1},"maintainers":[{"login":"pratikunterwegs","count":212,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/pratikunterwegs"},{"login":"adamkucharski","count":13,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/adamkucharski"},{"login":"bahadzie","count":8,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/bahadzie"},{"login":"jamesmbaazam","count":6,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/jamesmbaazam"},{"login":"Bisaloo","count":6,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/Bisaloo"},{"login":"avallecam","count":4,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/avallecam"},{"login":"chartgerink","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/chartgerink"},{"login":"rozeggo","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/rozeggo"},{"login":"Karim-Mane","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/Karim-Mane"},{"login":"joshwlambert","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/joshwlambert"},{"login":"amanda-minter","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/amanda-minter"}],"active_maintainers":[{"login":"adamkucharski","count":4,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/adamkucharski"},{"login":"bahadzie","count":3,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/bahadzie"},{"login":"amanda-minter","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/amanda-minter"},{"login":"avallecam","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/avallecam"}]},"events":{"total":{"CreateEvent":6,"IssuesEvent":10,"WatchEvent":4,"DeleteEvent":4,"MemberEvent":1,"IssueCommentEvent":57,"PushEvent":94,"PullRequestReviewCommentEvent":14,"PullRequestReviewEvent":29,"PullRequestEvent":14,"ForkEvent":10},"last_year":{"CreateEvent":6,"IssuesEvent":10,"WatchEvent":4,"DeleteEvent":4,"MemberEvent":1,"IssueCommentEvent":57,"PushEvent":94,"PullRequestReviewCommentEvent":14,"PullRequestReviewEvent":29,"PullRequestEvent":14,"ForkEvent":10}},"keywords":["decision-support","epidemic-modelling","epidemic-simulations","epidemiology","epiverse","infectious-disease-dynamics","model-library","non-pharmaceutical-interventions","r","r-package","rcpp","rcppeigen","scenario-analysis","vaccination"],"dependencies":[{"ecosystem":"actions","filepath":".github/workflows/Cpp-lint-check.yaml","sha":null,"kind":"manifest","created_at":"2023-02-20T20:31:24.146Z","updated_at":"2023-02-20T20:31:24.146Z","repository_link":"https://github.com/epiverse-trace/epidemics/blob/main/.github/workflows/Cpp-lint-check.yaml","dependencies":[{"id":7802086044,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":7802086047,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/R-CMD-check.yaml","sha":null,"kind":"manifest","created_at":"2023-02-20T20:31:24.340Z","updated_at":"2023-02-20T20:31:24.340Z","repository_link":"https://github.com/epiverse-trace/epidemics/blob/main/.github/workflows/R-CMD-check.yaml","dependencies":[{"id":7802086830,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7802086831,"package_name":"r-lib/actions/setup-pandoc","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7802086832,"package_name":"r-lib/actions/setup-r","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7802086833,"package_name":"r-lib/actions/setup-r-dependencies","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7802086834,"package_name":"r-lib/actions/check-r-package","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/pkgdown.yaml","sha":null,"kind":"manifest","created_at":"2023-02-20T20:31:24.388Z","updated_at":"2023-02-20T20:31:24.388Z","repository_link":"https://github.com/epiverse-trace/epidemics/blob/main/.github/workflows/pkgdown.yaml","dependencies":[{"id":7802086841,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7802086842,"package_name":"r-lib/actions/setup-pandoc","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7802086843,"package_name":"r-lib/actions/setup-r","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7802086844,"package_name":"r-lib/actions/setup-r-dependencies","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7802086845,"package_name":"JamesIves/github-pages-deploy-action","ecosystem":"actions","requirements":"4.1.4","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/render_readme.yml","sha":null,"kind":"manifest","created_at":"2023-02-20T20:31:24.431Z","updated_at":"2023-02-20T20:31:24.431Z","repository_link":"https://github.com/epiverse-trace/epidemics/blob/main/.github/workflows/render_readme.yml","dependencies":[{"id":7802086857,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7802086858,"package_name":"r-lib/actions/setup-r","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7802086859,"package_name":"r-lib/actions/setup-pandoc","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7802086860,"package_name":"r-lib/actions/setup-r-dependencies","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/test-coverage.yaml","sha":null,"kind":"manifest","created_at":"2023-02-20T20:31:24.479Z","updated_at":"2023-02-20T20:31:24.479Z","repository_link":"https://github.com/epiverse-trace/epidemics/blob/main/.github/workflows/test-coverage.yaml","dependencies":[{"id":7802086980,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7802086981,"package_name":"r-lib/actions/setup-r","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7802086982,"package_name":"r-lib/actions/setup-r-dependencies","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"cran","filepath":"DESCRIPTION","sha":null,"kind":"manifest","created_at":"2023-02-20T20:31:24.612Z","updated_at":"2023-02-20T20:31:24.612Z","repository_link":"https://github.com/epiverse-trace/epidemics/blob/main/DESCRIPTION","dependencies":[{"id":7802087992,"package_name":"data.table","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":7802088003,"package_name":"deSolve","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":7802088078,"package_name":"Rcpp","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":7802088084,"package_name":"covr","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":7802088108,"package_name":"testthat","ecosystem":"cran","requirements":"\u003e= 3.0.0","direct":true,"kind":"suggests","optional":false}]}],"score":5.953243334287784,"created_at":"2025-09-04T15:51:31.992Z","updated_at":"2025-10-07T08:22:06.433Z","avatar_url":"https://github.com/epiverse-trace.png","language":"R","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["stan","real-time-infectious-disease-modelling","pandemic-preparedness","outbreak-analysis","nowcasting","infectious-disease-surveillance","effective-reproduction-number-estimation","cmdstanr","transmission-chain-reconstruction","transmission-chain"],"project_url":"https://science.ecosyste.ms/api/v1/projects/55899","html_url":"https://science.ecosyste.ms/projects/55899","bibtex_url":"https://science.ecosyste.ms/projects/55899/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/55899/export.apalike"}