{
  "_id": "6abcd82699f7aa8c6aa4cc58",
  "Type": "Package",
  "Package": "closesamples",
  "Title": "Gets feasible taxon samples on a tree",
  "Version": "1.0",
  "Date": "2020-02-25",
  "Author": "Brian C. O'Meara",
  "Maintainer": "Brian C. O'Meara <omeara.brian@gmail.com>",
  "Description": "Often you want to pick species at random, but don't have\naccess to all the possible species, and your group might be a\nnonrandom set. However, you might have a taxonomy, perhaps a\nbad one, for all the species. This will let you pick species at\nrandom on that full taxonomy and then pick a species out of the\npossible set closest to this. You could still have a biased\nsample, but way less biased.",
  "License": "GPL 3.0",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.1.0",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libxml2-dev\nlibssl-dev",
  "Repository": "https://phylotastic.r-universe.dev",
  "Date/Publication": "2021-11-08 16:01:32 UTC",
  "RemoteUrl": "https://github.com/bomeara/closesamples",
  "RemoteRef": "HEAD",
  "RemoteSha": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-09-30 09:04:53 UTC",
    "User": "root"
  },
  "_user": "phylotastic",
  "_type": "src",
  "_file": "closesamples_1.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/47108fd1d219f89f4dd04bf2ee96dc30c2085a5dd8706e92a913c3ef87af3777",
  "_filesize": 106651,
  "_sha256": "47108fd1d219f89f4dd04bf2ee96dc30c2085a5dd8706e92a913c3ef87af3777",
  "_expires": "2027-01-08T09:36:36.000Z",
  "_created": "2026-09-30T09:04:53.000Z",
  "_published": "2026-09-30T09:36:38.883Z",
  "_jobs": [
    {
      "job": 109816945513,
      "time": 164,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "11087210630"
    },
    {
      "job": 109816945410,
      "time": 166,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11087420036"
    },
    {
      "job": 109816945388,
      "time": 86,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "11087379937"
    },
    {
      "job": 109816945613,
      "time": 123,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11088123862"
    },
    {
      "job": 109815244143,
      "time": 287,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11086024667"
    },
    {
      "job": 109816945315,
      "time": 162,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11087085596"
    },
    {
      "job": 109816945530,
      "time": 91,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "11086124759"
    },
    {
      "job": 109816945470,
      "time": 104,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "11087220049"
    },
    {
      "job": 109816945551,
      "time": 97,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11087085437"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/phylotastic/actions/runs/36693231811",
  "_status": "success",
  "_upstream": "https://github.com/bomeara/closesamples",
  "_commit": {
    "id": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30",
    "author": "Brian O'Meara <omeara.brian@gmail.com>",
    "committer": "Brian O'Meara <omeara.brian@gmail.com>",
    "message": "requires Rfast2\n",
    "time": 1636387292
  },
  "_maintainer": {
    "name": "Brian C. OMeara",
    "email": "omeara.brian@gmail.com",
    "login": "bomeara",
    "mastodon": "@omearabrian@mastodon.social",
    "bluesky": "@omearabrian.bsky.social",
    "orcid": "0000-0002-0337-5997",
    "description": "",
    "uuid": 1612612
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "ape",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "phangorn",
      "role": "Imports"
    },
    {
      "package": "taxize",
      "role": "Imports"
    },
    {
      "package": "Rfast2",
      "role": "Imports"
    },
    {
      "package": "anRpackage",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 2.1.0",
      "role": "Suggests"
    }
  ],
  "_owner": "bomeara",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "bomeara",
      "count": 16,
      "uuid": 1612612
    }
  ],
  "_userbio": {
    "uuid": 1652822,
    "type": "organization",
    "name": "phylotastic",
    "followers": 5
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/closesamples"
  },
  "_devurl": "https://github.com/bomeara/closesamples",
  "_searchresults": 0,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/closesamples.html",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE"
  ],
  "_cranurl": false,
  "_exports": [
    "GetClosestSamples",
    "GetEnclosingTaxonomy",
    "LabelNodesWithFeasibleDescendants",
    "SubsampleTree"
  ],
  "_datasets": [
    {
      "name": "ORCID_TOKEN",
      "title": "",
      "object": "ORCID_TOKEN",
      "file": "ORCID_TOKEN.rda",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "r",
      "title": "",
      "object": "r",
      "file": "r.rda",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "GetClosest",
      "title": "Get the closest taxon to the focal taxon",
      "topics": [
        "GetClosest"
      ]
    },
    {
      "page": "GetClosestSamples",
      "title": "Get n samples",
      "topics": [
        "GetClosestSamples"
      ]
    },
    {
      "page": "GetEnclosingTaxonomy",
      "title": "Get enclosing taxonomy for a feasible tree",
      "topics": [
        "GetEnclosingTaxonomy"
      ]
    },
    {
      "page": "GetSimilarity",
      "title": "Get similarity Uses ape's cophenetic.phylo to get patristic distances between pairs of taxa, then makes the diagonals Inf. If the tree has no branch lengths, makes every edge length 1.",
      "topics": [
        "GetSimilarity"
      ]
    },
    {
      "page": "LabelNodesWithChosenDescendants",
      "title": "Include descendant taxon ids in node labels",
      "topics": [
        "LabelNodesWithChosenDescendants"
      ]
    },
    {
      "page": "LabelNodesWithFeasibleDescendants",
      "title": "Include descendant taxon ids in node labels",
      "topics": [
        "LabelNodesWithFeasibleDescendants"
      ]
    },
    {
      "page": "SubsampleTree",
      "title": "Return a sampled tree",
      "topics": [
        "SubsampleTree"
      ]
    }
  ],
  "_readme": "https://github.com/bomeara/closesamples/raw/HEAD/README.md",
  "_rundeps": [
    "ape",
    "askpass",
    "backports",
    "BH",
    "checkmate",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "crul",
    "curl",
    "data.table",
    "digest",
    "dplyr",
    "future",
    "future.apply",
    "generics",
    "globals",
    "glue",
    "hms",
    "httpcode",
    "httr",
    "igraph",
    "jsonlite",
    "lattice",
    "lifecycle",
    "listenv",
    "magrittr",
    "Matrix",
    "mime",
    "natserv",
    "nlme",
    "openssl",
    "osqp",
    "parallelly",
    "phangorn",
    "pillar",
    "pkgconfig",
    "plyr",
    "prettyunits",
    "progress",
    "progressr",
    "R6",
    "Rcpp",
    "RcppArmadillo",
    "RcppParallel",
    "rentrez",
    "Rfast",
    "Rfast2",
    "ritis",
    "rlang",
    "Rnanoflann",
    "rncl",
    "rotl",
    "rredlist",
    "S7",
    "solrium",
    "stringi",
    "sys",
    "taxize",
    "tibble",
    "tidyselect",
    "triebeard",
    "urltools",
    "utf8",
    "vctrs",
    "WikipediR",
    "wikitaxa",
    "withr",
    "worrms",
    "XML",
    "xml2",
    "zigg",
    "zoo"
  ],
  "_score": 1.6989700043360187,
  "_indexed": false,
  "_nocasepkg": "closesamples",
  "_universes": [
    "phylotastic"
  ],
  "_indexurl": "https://bomeara.r-universe.dev/closesamples",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0",
      "date": "2026-09-30T09:08:16.000Z",
      "distro": "resolute",
      "commit": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30",
      "fileid": "https://r2.ropensci.org/283666daf028c5827e9700039feb44b8e41ba0a8872719b1656b46a778406ca9",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/36693231811"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.0",
      "date": "2026-09-30T09:07:42.000Z",
      "distro": "resolute",
      "commit": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30",
      "fileid": "https://r2.ropensci.org/ef9f831ffb33065096d69f65f6159b54ce4c03199fba5a3a15689cb092037e0b",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/36693231811"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0",
      "date": "2026-09-30T09:33:02.000Z",
      "commit": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30",
      "fileid": "https://r2.ropensci.org/694243d87514b7976b769f08d977101768994f3c8b7d3f8cad8990735f2b4148",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/36693231811"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.0",
      "date": "2026-09-30T09:35:56.000Z",
      "commit": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30",
      "fileid": "https://r2.ropensci.org/df9757a7f3834fea602eca1d69cd4ab71e665b43566e87340d191ee6524bc0fe",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/36693231811"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0",
      "date": "2026-09-30T09:07:52.000Z",
      "commit": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30",
      "fileid": "https://r2.ropensci.org/6c777e8ab41a092cecd56fc875e600751494fcfdf6ded19fa23b6f0193db0e8a",
      "status": "success",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/36693231811"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0",
      "date": "2026-09-30T09:06:25.000Z",
      "commit": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30",
      "fileid": "https://r2.ropensci.org/2720162fdfe54600d47bb2d82328b1690649d40b205ff56c390b81e27158e8ac",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/36693231811"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0",
      "date": "2026-09-30T09:06:34.000Z",
      "commit": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30",
      "fileid": "https://r2.ropensci.org/5ce9cc31db3da08f52b86db47039a7bc2a86f6fb746ec3d77ed7989d4aff7d54",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/36693231811"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.0",
      "date": "2026-09-30T09:06:30.000Z",
      "commit": "1beb4a721edb00887d2fbcd05c7995bb35dc6c30",
      "fileid": "https://r2.ropensci.org/dd6ec5d0faa2729a89973be4fa00225a27bd19a79d10dea4ffb643caccb09390",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/36693231811"
    }
  ]
}