{
  "_id": "6a4793ab2f27a93436c0d365",
  "Package": "Rogue",
  "Title": "Identify Rogue Taxa in Sets of Phylogenetic Trees",
  "Version": "2.2.1.9000",
  "Authors@R": "c(\nperson(\"Martin R.\", 'Smith',\nemail = \"martin.smith@durham.ac.uk\",\nrole = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0001-5660-1727\")),\nperson(given = \"Andre J.\", family=\"Aberer\",\nrole = c(\"aut\", \"cph\"),\nemail = \"andre.aberer@googlemail.com\",\ncomment = \"RogueNaRok\"\n)\n)",
  "License": "GPL (>= 3)",
  "Description": "Rogue (\"wildcard\") taxa are leaves with uncertain\nphylogenetic position. Their position may vary from tree to\ntree under inference methods that yield a tree set (e.g.\nbootstrapping, Bayesian tree searches, maximum parsimony). The\npresence of rogue taxa in a tree set can potentially remove all\ninformation from a consensus tree. The information content of a\nconsensus tree - a function of its resolution and branch\nsupport values - can often be increased by removing rogue tips.\n'Rogue' provides an explicitly information-theoretic approach\nto rogue detection (Smith 2022) <doi:10.1093/sysbio/syab099>,\nan interface to 'RogueNaRok' (Aberer et al. 2013)\n<doi:10.1093/sysbio/sys078>, and heuristics for measuring leaf\ninstability.",
  "URL": "https://ms609.github.io/Rogue/",
  "BugReports": "https://github.com/ms609/Rogue/issues/",
  "Config/Needs/github-actions": "callr, pkgbuild, rcmdcheck,",
  "Config/Needs/coverage": "covr",
  "Config/Needs/memcheck": "devtools",
  "Config/Needs/metadata": "codemetar",
  "Config/Needs/website": "pkgdown",
  "Config/roxygen2/version": "8.0.0",
  "RdMacros": "Rdpack",
  "SystemRequirements": "C++17",
  "ByteCompile": "true",
  "Encoding": "UTF-8",
  "Language": "en-GB",
  "VignetteBuilder": "knitr",
  "Roxygen": "list(markdown = TRUE)",
  "Config/pak/sysreqs": "cmake make libuv1-dev zlib1g-dev",
  "Repository": "https://ms609.r-universe.dev",
  "Date/Publication": "2026-06-29 08:52:46 UTC",
  "RemoteUrl": "https://github.com/ms609/rogue",
  "RemoteRef": "HEAD",
  "RemoteSha": "573cf9b63ffd0fb9be61f898e9073eef6ac0c200",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-07-02 17:31:22 UTC",
    "User": "root"
  },
  "Author": "Martin R. Smith [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0001-5660-1727>),\nAndre J. Aberer [aut, cph] (RogueNaRok)",
  "Maintainer": "Martin R. Smith <martin.smith@durham.ac.uk>",
  "_user": "ms609",
  "_type": "src",
  "_file": "Rogue_2.2.1.9000.tar.gz",
  "_fileid": "https://r2.ropensci.org/b7c85bdc7a35a292427b5196bb6e634ad605b16e44986e90db2eff3457de4f9f",
  "_filesize": 1427794,
  "_sha256": "b7c85bdc7a35a292427b5196bb6e634ad605b16e44986e90db2eff3457de4f9f",
  "_expires": "2026-10-11T10:49:14.000Z",
  "_created": "2026-07-02T17:31:22.000Z",
  "_published": "2026-07-03T10:49:15.337Z",
  "_jobs": [
    {
      "job": 84984005353,
      "time": 201,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8046867754"
    },
    {
      "job": 84984005008,
      "time": 188,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8046862531"
    },
    {
      "job": 84984005563,
      "time": 214,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8046873159"
    },
    {
      "job": 84984004953,
      "time": 183,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8046859894"
    },
    {
      "job": 84984005266,
      "time": 119,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8046833926"
    },
    {
      "job": 84984005360,
      "time": 237,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8046882367"
    },
    {
      "job": 84984004943,
      "time": 136,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8046840429"
    },
    {
      "job": 84984005326,
      "time": 220,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8046875260"
    },
    {
      "job": 84984004794,
      "time": 189,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8046785030"
    },
    {
      "job": 84984005270,
      "time": 144,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8046843504"
    },
    {
      "job": 84984005328,
      "time": 123,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8046836583"
    },
    {
      "job": 84984005045,
      "time": 108,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8046829232"
    },
    {
      "job": 84984004906,
      "time": 159,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8046849686"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/ms609/actions/runs/28609162162",
  "_status": "success",
  "_upstream": "https://github.com/ms609/rogue",
  "_commit": {
    "id": "573cf9b63ffd0fb9be61f898e9073eef6ac0c200",
    "author": "GitHub Actions <actions@github.com>",
    "committer": "GitHub Actions <actions@github.com>",
    "message": "Update codemeta.json\n",
    "time": 1782723166
  },
  "_maintainer": {
    "name": "Martin R. Smith",
    "email": "martin.smith@durham.ac.uk",
    "login": "ms609",
    "bluesky": "@palaeosmith.bsky.social",
    "orcid": "0000-0001-5660-1727",
    "description": "Professor in palaeontology, interested in phylogenetic methods ",
    "uuid": 1695515
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "ape",
      "version": ">= 5.0",
      "role": "Imports"
    },
    {
      "package": "cli",
      "version": ">= 3.0",
      "role": "Imports"
    },
    {
      "package": "fastmatch",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "Rdpack",
      "version": ">= 0.7",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "TreeDist",
      "version": "> 2.2.0",
      "role": "Imports"
    },
    {
      "package": "TreeTools",
      "version": ">= 1.9.1.9003",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "PlotTools",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "spelling",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "ms609",
  "_selfowned": true,
  "_usedby": 2,
  "_updates": [
    {
      "week": "2025-27",
      "n": 3
    },
    {
      "week": "2025-36",
      "n": 1
    },
    {
      "week": "2025-37",
      "n": 2
    },
    {
      "week": "2025-47",
      "n": 1
    },
    {
      "week": "2026-06",
      "n": 12
    },
    {
      "week": "2026-07",
      "n": 1
    },
    {
      "week": "2026-08",
      "n": 1
    },
    {
      "week": "2026-12",
      "n": 3
    },
    {
      "week": "2026-13",
      "n": 2
    },
    {
      "week": "2026-25",
      "n": 5
    },
    {
      "week": "2026-26",
      "n": 4
    },
    {
      "week": "2026-27",
      "n": 4
    }
  ],
  "_tags": [
    {
      "name": "2.2.0",
      "date": "2026-03-20"
    },
    {
      "name": "2.2.1",
      "date": "2026-06-24"
    }
  ],
  "_topics": [
    "consensus-tree",
    "phylogenetic-trees",
    "phylogenetics",
    "cpp"
  ],
  "_stars": 4,
  "_contributors": [
    {
      "user": "ms609",
      "count": 131,
      "uuid": 1695515
    }
  ],
  "_userbio": {
    "uuid": 1695515,
    "type": "user",
    "name": "Martin R. Smith",
    "followers": 62,
    "description": "Professor in palaeontology, interested in phylogenetic methods "
  },
  "_downloads": {
    "count": 1215,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/Rogue"
  },
  "_devurl": "https://github.com/ms609/rogue",
  "_pkgdown": "https://ms609.github.io/Rogue/",
  "_searchresults": 163,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/Rogue.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/ms609/rogue",
  "_realowner": "ms609",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2021-07-01"
    },
    {
      "version": "2.0.0",
      "date": "2021-09-13"
    },
    {
      "version": "2.1.0",
      "date": "2022-01-13"
    },
    {
      "version": "2.1.1",
      "date": "2022-07-20"
    },
    {
      "version": "2.1.2",
      "date": "2022-08-16"
    },
    {
      "version": "2.1.3",
      "date": "2022-09-26"
    },
    {
      "version": "2.1.4",
      "date": "2023-01-16"
    },
    {
      "version": "2.1.5",
      "date": "2023-03-20"
    },
    {
      "version": "2.1.6",
      "date": "2023-11-29"
    },
    {
      "version": "2.1.7",
      "date": "2025-07-01"
    },
    {
      "version": "2.2.0",
      "date": "2026-03-25"
    },
    {
      "version": "2.2.1",
      "date": "2026-06-24"
    }
  ],
  "_exports": [
    "C_RogueNaRok",
    "ColByStability",
    "Cophenetic",
    "GraphGeodesic",
    "QuickRogue",
    "RogueTaxa",
    "TipInstability",
    "TipVolatility"
  ],
  "_help": [
    {
      "page": "RogueTaxa",
      "title": "Drop rogue taxa to generate a more informative consensus",
      "topics": [
        "C_RogueNaRok",
        "QuickRogue",
        "RogueTaxa"
      ]
    },
    {
      "page": "TipInstability",
      "title": "Tip instability",
      "concept": [
        "tip instability functions"
      ],
      "topics": [
        "ColByStability",
        "TipInstability"
      ]
    },
    {
      "page": "TipVolatility",
      "title": "Detect rogue taxa using phylogenetic information distance",
      "concept": [
        "tip instability functions"
      ],
      "topics": [
        "TipVolatility"
      ]
    }
  ],
  "_readme": "https://github.com/ms609/rogue/raw/HEAD/README.md",
  "_rundeps": [
    "ape",
    "base64enc",
    "bit",
    "bit64",
    "bslib",
    "cachem",
    "cli",
    "commonmark",
    "digest",
    "fastmap",
    "fastmatch",
    "fontawesome",
    "fs",
    "glue",
    "htmltools",
    "httpuv",
    "jquerylib",
    "jsonlite",
    "later",
    "lattice",
    "lifecycle",
    "magrittr",
    "matrixStats",
    "memoise",
    "mime",
    "nlme",
    "otel",
    "PlotTools",
    "promises",
    "R6",
    "rappdirs",
    "rbibutils",
    "Rcpp",
    "Rdpack",
    "rlang",
    "sass",
    "shiny",
    "shinyjs",
    "sourcetools",
    "TreeDist",
    "TreeTools",
    "withr",
    "xtable"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "Bayesian.Rmd",
      "filename": "Bayesian.html",
      "title": "Detecting rogue taxa in Bayesian posterior tree sets",
      "author": "Martin R. Smith, Durham University",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Set up",
        "Select trees to analyse",
        "Initial appraisal",
        "Detect rogue taxa",
        "Visualize results",
        "References"
      ],
      "created": "2022-01-12 15:37:52",
      "modified": "2023-11-28 13:52:49",
      "commits": 5
    }
  ],
  "_score": 7.455126374433539,
  "_indexed": true,
  "_nocasepkg": "rogue",
  "_universes": [
    "ms609"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.2.1.9000",
      "date": "2026-07-02T17:34:45.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "573cf9b63ffd0fb9be61f898e9073eef6ac0c200",
      "fileid": "https://r2.ropensci.org/9da4e210db70a81cba946fd3c9614876a81be626b85740419531f8b3d4ac964c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ms609/actions/runs/28609162162"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.2.1.9000",
      "date": "2026-07-02T17:34:22.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "573cf9b63ffd0fb9be61f898e9073eef6ac0c200",
      "fileid": "https://r2.ropensci.org/a2eda1a628f5e01a4ce7d476ec697942597a04a6450e10564480cb7045e08d27",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ms609/actions/runs/28609162162"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2.2.1.9000",
      "date": "2026-07-02T17:34:55.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "573cf9b63ffd0fb9be61f898e9073eef6ac0c200",
      "fileid": "https://r2.ropensci.org/adc29c88d5848450baa63365cfc535bc20a1b50de3969112073e1c71dfca33b6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ms609/actions/runs/28609162162"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2.2.1.9000",
      "date": "2026-07-02T17:34:21.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "573cf9b63ffd0fb9be61f898e9073eef6ac0c200",
      "fileid": "https://r2.ropensci.org/a3cce87920982c84da1cef38d33e76878269737ffb049c3a539af52725dabcd4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ms609/actions/runs/28609162162"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.2.1.9000",
      "date": "2026-07-02T17:33:06.000Z",
      "arch": "aarch64",
      "commit": "573cf9b63ffd0fb9be61f898e9073eef6ac0c200",
      "fileid": "https://r2.ropensci.org/9f4593a8127028bb6b1894add61572e309939b63395c71eed439f83c38854d61",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ms609/actions/runs/28609162162"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.2.1.9000",
      "date": "2026-07-02T17:34:41.000Z",
      "arch": "x86_64",
      "commit": "573cf9b63ffd0fb9be61f898e9073eef6ac0c200",
      "fileid": "https://r2.ropensci.org/2fba7894cfba47e0d750ac68d29995bb8fe6001a76e95c37689d20bdd85cc8b7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ms609/actions/runs/28609162162"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2.2.1.9000",
      "date": "2026-07-02T17:33:24.000Z",
      "arch": "aarch64",
      "commit": "573cf9b63ffd0fb9be61f898e9073eef6ac0c200",
      "fileid": "https://r2.ropensci.org/29f0f6d24466c2f3ba346452f65aba236832780f7989730565f9e7085e7ee4b1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ms609/actions/runs/28609162162"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2.2.1.9000",
      "date": "2026-07-02T17:34:31.000Z",
      "arch": "x86_64",
      "commit": "573cf9b63ffd0fb9be61f898e9073eef6ac0c200",
      "fileid": "https://r2.ropensci.org/293ecf65e138adc1b772b3811f765a3ce07d6071d0bc0fd7110204d6fad193a0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ms609/actions/runs/28609162162"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.2.1.9000",
      "date": "2026-07-02T17:34:02.000Z",
      "arch": "emscripten",
      "commit": "573cf9b63ffd0fb9be61f898e9073eef6ac0c200",
      "fileid": "https://r2.ropensci.org/aaa7c7628b2c0300179339c30f0ac96d35779a27590dbfd4a66140c317b790c9",
      "status": "success",
      "buildurl": "https://github.com/r-universe/ms609/actions/runs/28609162162"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.2.1.9000",
      "date": "2026-07-02T17:32:40.000Z",
      "arch": "x86_64",
      "commit": "573cf9b63ffd0fb9be61f898e9073eef6ac0c200",
      "fileid": "https://r2.ropensci.org/afde0e44c0ce02239f43f98d8a2c31b2162984cbb29b4823d5b20ee97a73937d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ms609/actions/runs/28609162162"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.2.1.9000",
      "date": "2026-07-02T17:32:39.000Z",
      "arch": "x86_64",
      "commit": "573cf9b63ffd0fb9be61f898e9073eef6ac0c200",
      "fileid": "https://r2.ropensci.org/da06990aebb75443b6564b36c615116306d96c62db1ef2339bbb7c64b165d3b7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ms609/actions/runs/28609162162"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "2.2.1.9000",
      "date": "2026-07-02T17:33:12.000Z",
      "arch": "x86_64",
      "commit": "573cf9b63ffd0fb9be61f898e9073eef6ac0c200",
      "fileid": "https://r2.ropensci.org/304a62b9d3f5191518425280a675dcc0e8abcecf45eb48e5e241b496fcad1800",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ms609/actions/runs/28609162162"
    }
  ]
}