{
  "_id": "6a1d3ad81d7bb097a0a3ec22",
  "Package": "avotrex",
  "Version": "1.3.1",
  "Type": "Package",
  "Title": "A Global Dataset of Anthropogenic Extinct Birds and their\nTraits: Phylogeny Builder",
  "Description": "Grafts the extinct bird species from the 'Avotrex'\ndatabase (Sayol et al., in review) on to the 'BirdTree'\nphylogenies <https://birdtree.org>, using a set of different\ncommands.",
  "Authors@R": "c(person(\"Joseph\", \"Wayman\", email = \"j.wayman@bham.ac.uk\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-3122-8070\")),\nperson(\"Thomas J.\", \"Matthews\", email = \"txm676@gmail.com\",\nrole = c(\"aut\"), comment = c(ORCID = \"0000-0002-7624-244X\")),\nperson(\"Paul\", \"Dufour\", role = c(\"ctb\")),\nperson(\"Ferran\", \"Sayol\", role = c(\"ctb\")),\nperson(\"Pedro\", \"Cardoso\", role = c(\"ctb\")))",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.1",
  "biocViews": "",
  "LazyData": "true",
  "License": "GPL-3",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev",
  "Repository": "https://joe-wayman.r-universe.dev",
  "Date/Publication": "2025-06-04 19:04:24 UTC",
  "RemoteUrl": "https://github.com/joe-wayman/avotrex",
  "RemoteRef": "HEAD",
  "RemoteSha": "b54613155bf5a80b5061b5f3959e19ab7e381a33",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-01 07:49:13 UTC",
    "User": "root"
  },
  "Author": "Joseph Wayman [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-3122-8070>),\nThomas J. Matthews [aut] (ORCID:\n<https://orcid.org/0000-0002-7624-244X>),\nPaul Dufour [ctb],\nFerran Sayol [ctb],\nPedro Cardoso [ctb]",
  "Maintainer": "Joseph Wayman <j.wayman@bham.ac.uk>",
  "MD5sum": "7f8fab961c50718d998d1b970c9fc330",
  "_user": "joe-wayman",
  "_type": "src",
  "_file": "avotrex_1.3.1.tar.gz",
  "_fileid": "a04655149f5e07b23526833f403b6b76e5cef79eda27bf8890b7697614077d4d",
  "_filesize": 3519865,
  "_sha256": "a04655149f5e07b23526833f403b6b76e5cef79eda27bf8890b7697614077d4d",
  "_created": "2026-06-01T07:49:13.000Z",
  "_published": "2026-06-01T07:55:04.256Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78808529989,
      "time": 172,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7326085525"
    },
    {
      "job": 78808529921,
      "time": 171,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7326085017"
    },
    {
      "job": 78808529976,
      "time": 222,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7326092137"
    },
    {
      "job": 78808529953,
      "time": 159,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7326075089"
    },
    {
      "job": 78807916198,
      "time": 257,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7326030957"
    },
    {
      "job": 78808529962,
      "time": 142,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7326076046"
    },
    {
      "job": 78808529929,
      "time": 126,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7326071539"
    },
    {
      "job": 78808529937,
      "time": 118,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7326069376"
    },
    {
      "job": 78808529924,
      "time": 125,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7326071529"
    }
  ],
  "_buildurl": "https://github.com/r-universe/joe-wayman/actions/runs/26741950725",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/joe-wayman/avotrex",
  "_commit": {
    "id": "b54613155bf5a80b5061b5f3959e19ab7e381a33",
    "author": "Tom Matthews <txm676@gmail.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Update README.md",
    "time": 1749063864
  },
  "_maintainer": {
    "name": "Joseph Wayman",
    "email": "j.wayman@bham.ac.uk",
    "login": "joe-wayman",
    "orcid": "0000-0002-3122-8070",
    "description": "Macroecologist. Research associate at the University of Birmingham (see website for current research and interests).",
    "uuid": 63051678
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0.0",
      "role": "Depends"
    },
    {
      "package": "ape",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "doSNOW",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "phytools",
      "role": "Imports"
    },
    {
      "package": "snow",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "tidytree",
      "version": ">= 0.4.6",
      "role": "Imports"
    },
    {
      "package": "TreeTools",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "markdown",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    }
  ],
  "_owner": "joe-wayman",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-23",
      "n": 1
    }
  ],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "txm676",
      "count": 42,
      "uuid": 24476402
    },
    {
      "user": "joe-wayman",
      "count": 34,
      "uuid": 63051678
    }
  ],
  "_userbio": {
    "uuid": 63051678,
    "type": "user",
    "name": "Joe Wayman",
    "description": "Macroecologist. Research associate at the University of Birmingham (see website for current research and interests)."
  },
  "_downloads": {
    "count": 199,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/avotrex"
  },
  "_devurl": "https://github.com/joe-wayman/avotrex",
  "_searchresults": 9,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/avotrex.html",
    "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",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/joe-wayman/avotrex",
  "_realowner": "joe-wayman",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2024-04-12"
    },
    {
      "version": "1.1.0",
      "date": "2024-05-31"
    },
    {
      "version": "1.2.0",
      "date": "2024-06-08"
    },
    {
      "version": "1.3.0",
      "date": "2024-07-30"
    }
  ],
  "_exports": [
    "AvoBind",
    "AvoPhylo"
  ],
  "_datasets": [
    {
      "name": "AvotrexPhylo",
      "title": "Avotrex phylo dataset",
      "object": "AvotrexPhylo",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "sp_id",
        "phylo_id",
        "per_fixed",
        "time_fixed",
        "group",
        "species",
        "order",
        "family",
        "genus",
        "jetz_order",
        "jetz_family",
        "jetz_genus",
        "type",
        "sister_order",
        "sister_clade",
        "sister_family",
        "sister_genus",
        "sister_species",
        "sister_species_group"
      ],
      "rows": 610,
      "table": true,
      "tojson": true
    },
    {
      "name": "BirdTree_tax",
      "title": "Bird Tree taxonomic data",
      "object": "BirdTree_tax",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Genus",
        "Species",
        "TipLabel",
        "English",
        "Taxonomy",
        "Clade",
        "BLFamilyLatin",
        "BLFamilyEnglish",
        "FamSequID",
        "Order",
        "OscSubOsc"
      ],
      "rows": 9993,
      "table": true,
      "tojson": true
    },
    {
      "name": "BirdTree_trees",
      "title": "Bird Tree trees",
      "object": "BirdTree_trees",
      "class": [
        "multiPhylo"
      ],
      "fields": [],
      "table": true,
      "tojson": false
    },
    {
      "name": "treesEx",
      "title": "A set of three AvoPhylo trees",
      "object": "treesEx",
      "class": [
        "multiAvophylo",
        "multiPhylo"
      ],
      "fields": [],
      "table": true,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "AvoBind",
      "title": "AvoBind - Bind extinct species to the tree",
      "topics": [
        "AvoBind"
      ]
    },
    {
      "page": "AvoPhylo",
      "title": "AvoPhylo: Building phylogenies based on the AvoTrex extinct bird trait database and BirdTree backbone",
      "topics": [
        "AvoPhylo"
      ]
    },
    {
      "page": "AvotrexPhylo",
      "title": "Avotrex phylo dataset",
      "topics": [
        "AvotrexPhylo"
      ]
    },
    {
      "page": "BirdTree_tax",
      "title": "Bird Tree taxonomic data",
      "topics": [
        "BirdTree_tax"
      ]
    },
    {
      "page": "BirdTree_trees",
      "title": "Bird Tree trees",
      "topics": [
        "BirdTree_trees"
      ]
    },
    {
      "page": "plot.avophylo",
      "title": "Plot Model Fits for an 'avophylo' Object",
      "topics": [
        "plot.avophylo"
      ]
    },
    {
      "page": "plot.multiAvophylo",
      "title": "Plot Model Fits for an 'multiAvophylo' Object",
      "topics": [
        "plot.multiAvophylo"
      ]
    },
    {
      "page": "treesEx",
      "title": "A set of three AvoPhylo trees",
      "topics": [
        "treesEx"
      ]
    }
  ],
  "_readme": "https://github.com/joe-wayman/avotrex/raw/HEAD/README.md",
  "_rundeps": [
    "ape",
    "bit",
    "bit64",
    "cli",
    "clusterGeneration",
    "coda",
    "codetools",
    "combinat",
    "cpp11",
    "DEoptim",
    "digest",
    "doParallel",
    "doSNOW",
    "dplyr",
    "expm",
    "fastmatch",
    "foreach",
    "fs",
    "generics",
    "glue",
    "igraph",
    "iterators",
    "lattice",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "maps",
    "MASS",
    "Matrix",
    "mnormt",
    "nlme",
    "numDeriv",
    "optimParallel",
    "phangorn",
    "phytools",
    "pillar",
    "pkgconfig",
    "PlotTools",
    "purrr",
    "quadprog",
    "R6",
    "rappdirs",
    "rbibutils",
    "Rcpp",
    "Rdpack",
    "rlang",
    "scatterplot3d",
    "snow",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "tidytree",
    "TreeTools",
    "utf8",
    "vctrs",
    "withr",
    "yulab.utils"
  ],
  "_vignettes": [
    {
      "source": "avotrex-r-package.Rmd",
      "filename": "avotrex-r-package.html",
      "title": "avotrex R Package",
      "author": "Joseph P. Wayman and Thomas J. Matthews",
      "engine": "knitr::rmarkdown",
      "headings": [
        "BACKGROUND",
        "METHODOLOGY AND FUNCTIONS",
        "Tree building - AvoPhylo()",
        "ADDING NEW SPECIES",
        "PLOTTING",
        "REFERENCES"
      ],
      "created": "2024-03-28 15:14:25",
      "modified": "2024-07-10 22:13:48",
      "commits": 8
    }
  ],
  "_score": 3.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "avotrex",
  "_universes": [
    "joe-wayman"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.3.1",
      "date": "2026-06-01T07:51:41.000Z",
      "distro": "noble",
      "commit": "b54613155bf5a80b5061b5f3959e19ab7e381a33",
      "fileid": "87dac0162da239b42fbed55f01d5e72ae45bc683429fab2aeb8c1b4675567cff",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joe-wayman/actions/runs/26741950725"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.3.1",
      "date": "2026-06-01T07:51:42.000Z",
      "distro": "noble",
      "commit": "b54613155bf5a80b5061b5f3959e19ab7e381a33",
      "fileid": "56c54c5ea826a1916dee7d20a025971bcc82bf4544402e949862dc200c248dab",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joe-wayman/actions/runs/26741950725"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.3.1",
      "date": "2026-06-01T07:52:22.000Z",
      "commit": "b54613155bf5a80b5061b5f3959e19ab7e381a33",
      "fileid": "70339a76bebb86cbdc210b30485c21dc9014a9ff8bc415d9e9043022b2865aeb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joe-wayman/actions/runs/26741950725"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.3.1",
      "date": "2026-06-01T07:51:22.000Z",
      "commit": "b54613155bf5a80b5061b5f3959e19ab7e381a33",
      "fileid": "2c8549fdc11c9fa8b49ada578bc87179738bbd16fdabe54a757a8903a6a396e6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joe-wayman/actions/runs/26741950725"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.3.1",
      "date": "2026-06-01T07:51:56.000Z",
      "commit": "b54613155bf5a80b5061b5f3959e19ab7e381a33",
      "fileid": "1b8d601aa502adfbc31c35aa00e3661862559364efb1ee797e236be3bd453039",
      "status": "success",
      "buildurl": "https://github.com/r-universe/joe-wayman/actions/runs/26741950725"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.3.1",
      "date": "2026-06-01T07:50:44.000Z",
      "commit": "b54613155bf5a80b5061b5f3959e19ab7e381a33",
      "fileid": "e61a7606f48767ca83cb5374b10fdd60d4088e2e7e7470bd1b4349867be5ef3c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joe-wayman/actions/runs/26741950725"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.3.1",
      "date": "2026-06-01T07:50:40.000Z",
      "commit": "b54613155bf5a80b5061b5f3959e19ab7e381a33",
      "fileid": "12a9c870df113b3d7e91c0ee71e5853329679b70f180dd0b23c1bd36176ac1c7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joe-wayman/actions/runs/26741950725"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.3.1",
      "date": "2026-06-01T07:50:44.000Z",
      "commit": "b54613155bf5a80b5061b5f3959e19ab7e381a33",
      "fileid": "d6a8c86ceb924562e37beee350269fd30c9bd6c62e98d490e1f9236f5f1768fc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joe-wayman/actions/runs/26741950725"
    }
  ]
}