{"id":24182966,"url":"https://github.com/ms609/tci","last_synced_at":"2026-06-08T12:04:04.219Z","repository":{"id":54818959,"uuid":"54549731","full_name":"ms609/tci","owner":"ms609","description":"R package to calculate the Total Cophenetic Index of Mir et al. 2013","archived":false,"fork":false,"pushed_at":"2021-06-23T18:14:41.000Z","size":47,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-12-09T19:32:32.234Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"R","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/ms609.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}},"created_at":"2016-03-23T10:08:18.000Z","updated_at":"2021-06-23T07:08:11.000Z","dependencies_parsed_at":"2022-08-14T03:50:11.382Z","dependency_job_id":null,"html_url":"https://github.com/ms609/tci","commit_stats":null,"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"purl":"pkg:github/ms609/tci","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2Ftci","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2Ftci/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2Ftci/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2Ftci/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ms609","download_url":"https://codeload.github.com/ms609/tci/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2Ftci/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":34061125,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-06-08T02:00:07.615Z","response_time":111,"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":[],"created_at":"2025-01-13T08:45:51.621Z","updated_at":"2026-06-08T12:04:04.203Z","avatar_url":"https://github.com/ms609.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![CRAN Status Badge](https://www.r-pkg.org/badges/version/TotalCopheneticIndex)](https://cran.r-project.org/package=TotalCopheneticIndex)\n[![CRAN Downloads](https://cranlogs.r-pkg.org/badges/TotalCopheneticIndex)](https://cran.r-project.org/package=TotalCopheneticIndex)\n[![DOI](https://zenodo.org/badge/54549731.svg)](https://zenodo.org/badge/latestdoi/54549731)\n[![Project Status: Inactive - The project has reached a stable, usable state but is no longer being actively developed; support/maintenance will be provided as time allows.](https://www.repostatus.org/badges/latest/inactive.svg)](https://www.repostatus.org/#inactive)\n\n# TotalCopheneticIndex\nR package implementing the Total Cophenetic Index measure of Mir _et al._ (2013).\nThis package is now simply a wrapper for the function `TotalCopheneticIndex()`\nin the package '[TreeTools](https://ms609.github.io/TreeTools/)'.\n\nThe total cophenetic index describes how balanced a phylogenetic tree is,\nby measuring the how deep the most recent common ancestor of each pair of leaves\nlies within the tree.\n\n# See also\n\nThis functionality is now available via the function [`TotalCopheneticIndex()`](https://ms609.github.io/TreeTools/reference/TotalCopheneticIndex.html) in the\n'[TreeTools](https://ms609.github.io/TreeTools/)' package, and via Rotger's\n(unmaintained?) package \n'[CollessLike](https://github.com/LuciaRotger/CollessLike)'.\n\n# References\n\nA. Mir, F. Rossello, L. A. Rotger, A new balance index for phylogenetic trees.\n  _Math. Biosci._ 241, 125-136 (2013).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fms609%2Ftci","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fms609%2Ftci","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fms609%2Ftci/lists"}