{"id":24182990,"url":"https://github.com/ms609/rogue","last_synced_at":"2026-02-17T23:36:12.259Z","repository":{"id":45049121,"uuid":"376830950","full_name":"ms609/Rogue","owner":"ms609","description":"Identify rogue taxa in phylogenetic trees within R","archived":false,"fork":false,"pushed_at":"2025-09-08T09:47:42.000Z","size":10804,"stargazers_count":3,"open_issues_count":11,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-10-11T22:49:32.245Z","etag":null,"topics":["consensus-tree","phylogenetic-trees","phylogenetics","r-package"],"latest_commit_sha":null,"homepage":"https://ms609.github.io/Rogue","language":"Bluespec","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":"NEWS.md","contributing":"CONTRIBUTING.md","funding":null,"license":null,"code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":"codemeta.json","zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2021-06-14T13:22:35.000Z","updated_at":"2025-09-08T09:47:45.000Z","dependencies_parsed_at":"2024-12-16T02:22:30.499Z","dependency_job_id":"a2f8461d-0120-498f-aa66-bff89af7946d","html_url":"https://github.com/ms609/Rogue","commit_stats":{"total_commits":211,"total_committers":5,"mean_commits":42.2,"dds":"0.44075829383886256","last_synced_commit":"25f9d7700f58642e6ad78c29fc653ce039273e7a"},"previous_names":[],"tags_count":11,"template":false,"template_full_name":null,"purl":"pkg:github/ms609/Rogue","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2FRogue","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2FRogue/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2FRogue/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2FRogue/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ms609","download_url":"https://codeload.github.com/ms609/Rogue/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2FRogue/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279296822,"owners_count":26142419,"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":"2025-10-17T02:00:07.504Z","response_time":56,"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":["consensus-tree","phylogenetic-trees","phylogenetics","r-package"],"created_at":"2025-01-13T08:45:56.412Z","updated_at":"2025-10-17T06:45:11.553Z","avatar_url":"https://github.com/ms609.png","language":"Bluespec","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Rogue\n\n[![Codecov test coverage](https://codecov.io/gh/ms609/Rogue/branch/main/graph/badge.svg)](https://codecov.io/gh/ms609/Rogue?branch=main)\n[![CRAN Status Badge](http://www.r-pkg.org/badges/version/Rogue)](https://cran.r-project.org/package=Rogue)\n[![CRAN Downloads](http://cranlogs.r-pkg.org/badges/Rogue)](https://cran.r-project.org/package=Rogue)\n[![DOI](https://zenodo.org/badge/376830950.svg)](https://zenodo.org/badge/latestdoi/376830950)\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.](http://www.repostatus.org/badges/latest/inactive.svg)](http://www.repostatus.org/#inactive)\n\n\"Rogue\" implements approaches to identify rogue taxa in phylogenetic analysis.\nRogues are wildcard leaves whose uncertain position reduces the resolution of\nconsensus trees. Consensus trees that omit rogue taxa can be more informative.\n\n\"Rogue\" allows the user to select a concept of \"information\" by which the\nquality of consensus trees should be evaluated, and a heuristic approach\nby which rogue taxa should be identified.\n\nRogue detection using the phylogenetic and clustering information content\nmeasures (Smith, 2022) is implemented using a quick heuristic that drops\nthe least \"stable\" leaves one at a time,\nusing an _ad hoc_ definition of stability (Smith, 2022);\nand by a more exhaustive (and time-consuming) approach that considers dropping\nall possible sets of up to _n_ leaves (Aberer _et al._ 2013).\n\nThe latter heuristic is implemented for the relative bipartition \n\"information\" content and Pattengale's criterion\n_via_ [RogueNaRok](https://rnr.h-its.org/about) (Aberer _et al._ 2013).\n\n\n[![Detecting rogue taxa with information theory](man/figures/Rogue_talk.png)](https://durham.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=86c175f1-6e20-499c-bcf2-adeb0137a4a7)\n\n# Installation\n\nInstall and load the stable version from CRAN as normal:\n```r\ninstall.packages(\"Rogue\")\nlibrary(\"Rogue\")\n```\n\nAlternatively, install the development version from GitHub with \n```r\ndevtools::install_github(\"ms609/Rogue\", args = \"--recursive\")\n```\n(Requires [git](https://git-scm.com/) to be installed and added to\nyour PATH system environment variable; you may also require the \"curl\" R package.)\n\n\n# Citing 'Rogue'\n\nIf you find this package useful in your work, please consider citing\nSmith (2021).\n\nTo cite the underlying methods, please cite Aberer _et al._ (2013) ('RogueNaRok')\nor Smith (2022), as appropriate.\n\n\n# References\n\nA.J. Aberer, D. Krompass, A. Stamatakis (2013): Pruning rogue taxa improves\n  phylogenetic accuracy: an efficient algorithm and webservice. _Systematic Biology_ 62(1):\n  162-166, [doi:10.1093/sysbio/sys078](https://dx.doi.org/10.1093/sysbio/sys078).\n\nM.R. Smith (2021): Rogue: Identify rogue taxa in sets of phylogenetic trees.\n  _Zenodo_,\n  [doi:10.5281/zenodo.5037327](https://dx.doi.org/10.5281/zenodo.5037327).\n\nM.R. Smith (2022): Using information theory to detect rogue taxa and improve\n  consensus trees. _Systematic Biology_ 71(5): 986–1008,\n  [doi:10.1093/sysbio/syab099](https://dx.doi.org/10.1093/sysbio/syab099)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fms609%2Frogue","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fms609%2Frogue","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fms609%2Frogue/lists"}