{
  "_id": "6ad930a0992ad85420b5f5ea",
  "Package": "treeplyr",
  "Type": "Package",
  "Title": "'dplyr' Functionality for Matched Tree and Data Objects",
  "Version": "0.1.11",
  "Date": "2025-02-19",
  "Authors@R": "c(\nperson(given = \"Josef\",\nfamily = \"Uyeda\",\nrole=c(\"cre\"),\nemail=\"juyeda@vt.edu\",\ncomment = c(ORCID=\"0000-0003-4624-9680\")\n),\nperson(given = \"Luke\",\nfamily = \"Harmon\",\nrole = c(\"aut\"),\nemail = \"lukeh@uidaho.edu\",\ncomment = c(ORCID=\"0000-0002-4985-5750\")\n)\n)",
  "Maintainer": "Josef Uyeda <juyeda@vt.edu>",
  "Description": "Matches phylogenetic trees and trait data, and allows\nsimultaneous manipulation of the tree and data using 'dplyr'.",
  "License": "GPL-2 | GPL-3",
  "URL": "https://github.com/uyedaj/treeplyr",
  "BugReports": "https://github.com/uyedaj/treeplyr/issues",
  "RoxygenNote": "7.1.1",
  "Encoding": "UTF-8",
  "Config/pak/sysreqs": "libglpk-dev make libxml2-dev",
  "Repository": "https://phylotastic.r-universe.dev",
  "Date/Publication": "2025-02-19 16:00:28 UTC",
  "RemoteUrl": "https://github.com/uyedaj/treeplyr",
  "RemoteRef": "HEAD",
  "RemoteSha": "bfbaf93bf50a98ce9a928324c61110e4a8128da4",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-21 21:13:25 UTC",
    "User": "root"
  },
  "Author": "Josef Uyeda [cre] (ORCID: <https://orcid.org/0000-0003-4624-9680>),\nLuke Harmon [aut] (ORCID: <https://orcid.org/0000-0002-4985-5750>)",
  "_user": "phylotastic",
  "_type": "src",
  "_file": "treeplyr_0.1.11.tar.gz",
  "_fileid": "https://r2.ropensci.org/5d829b7933edff90d48eae64648d4d220d9ba7703f35e0324ddf5bdda6af2576",
  "_filesize": 163004,
  "_sha256": "5d829b7933edff90d48eae64648d4d220d9ba7703f35e0324ddf5bdda6af2576",
  "_expires": "2027-01-29T21:37:34.000Z",
  "_created": "2026-10-21T21:13:25.000Z",
  "_published": "2026-10-21T21:37:36.109Z",
  "_upstream": "https://github.com/uyedaj/treeplyr",
  "_status": "success",
  "_maintainer": {
    "name": "Josef Uyeda",
    "email": "juyeda@vt.edu",
    "login": "uyedaj",
    "description": "",
    "uuid": 2087512,
    "orcid": "0000-0003-4624-9680"
  },
  "_jobs": [
    {
      "job": 119489576706,
      "time": 121,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "12382931180"
    },
    {
      "job": 119489576732,
      "time": 140,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "12381852577"
    },
    {
      "job": 119489576772,
      "time": 124,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12382718319"
    },
    {
      "job": 119489576814,
      "time": 150,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12381318035"
    },
    {
      "job": 119489576840,
      "time": 130,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "12383830087"
    },
    {
      "job": 119489576948,
      "time": 314,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "12382204976"
    },
    {
      "job": 119489576663,
      "time": 143,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12382838854"
    },
    {
      "job": 119489577124,
      "time": 438,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12383104225"
    },
    {
      "job": 119486637079,
      "time": 368,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12382776874"
    },
    {
      "job": 119489576710,
      "time": 119,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12382338654"
    },
    {
      "job": 119489576826,
      "time": 259,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "12382648740"
    },
    {
      "job": 119489576812,
      "time": 174,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "12381599234"
    },
    {
      "job": 119489576933,
      "time": 96,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "12382052582"
    },
    {
      "job": 119489577116,
      "time": 399,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12383006776"
    },
    {
      "job": 119489576919,
      "time": 114,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12382412636"
    }
  ],
  "_buildurl": "https://github.com/r-universe/phylotastic/actions/runs/39676172706",
  "_commit": {
    "id": "bfbaf93bf50a98ce9a928324c61110e4a8128da4",
    "author": "Britney Pereda <britneypereda@Britneys-MacBook-Pro.local>",
    "committer": "Britney Pereda <britneypereda@Britneys-MacBook-Pro.local>",
    "message": "test commit\n",
    "time": 1739980828
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "ape",
      "version": ">= 3.0-6",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "version": ">= 0.8.0",
      "role": "Depends"
    },
    {
      "package": "R",
      "version": ">= 3.1.2",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.10.3",
      "role": "Imports"
    },
    {
      "package": "lazyeval",
      "role": "Imports"
    },
    {
      "package": "phytools",
      "role": "Imports"
    },
    {
      "package": "geiger",
      "role": "Imports"
    }
  ],
  "_owner": "uyedaj",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 33,
  "_contributors": [
    {
      "user": "uyedaj",
      "count": 22,
      "uuid": 2087512
    },
    {
      "user": "macroevolab",
      "count": 19,
      "uuid": 43342043
    },
    {
      "user": "lukejharmon",
      "count": 11,
      "uuid": 1669734
    },
    {
      "user": "lionel-",
      "count": 1,
      "uuid": 4465050
    },
    {
      "user": "romainfrancois",
      "count": 1,
      "uuid": 2625526
    }
  ],
  "_userbio": {
    "uuid": 1652822,
    "type": "organization",
    "name": "phylotastic",
    "followers": 5
  },
  "_downloads": {
    "count": 46,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/treeplyr"
  },
  "_devurl": "https://github.com/uyedaj/treeplyr",
  "_searchresults": 132,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/readme.html",
    "extra/readme.md",
    "extra/treeplyr.html"
  ],
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.1",
      "date": "2016-03-02"
    },
    {
      "version": "0.1.1",
      "date": "2016-03-31"
    },
    {
      "version": "0.1.2",
      "date": "2016-06-24"
    },
    {
      "version": "0.1.3",
      "date": "2017-07-05"
    },
    {
      "version": "0.1.4",
      "date": "2018-06-07"
    },
    {
      "version": "0.1.6",
      "date": "2019-06-18"
    },
    {
      "version": "0.1.7",
      "date": "2019-07-26"
    },
    {
      "version": "0.1.10",
      "date": "2020-09-17"
    }
  ],
  "_exports": [
    "detectAllCharacters",
    "detectCharacterType",
    "filterMatrix",
    "forceFactor",
    "forceNames",
    "forceNumeric",
    "getVector",
    "hasNames",
    "make.treedata",
    "paint_clades",
    "reorder",
    "tdapply",
    "treedply",
    "treeply"
  ],
  "_datasets": [
    {
      "name": "anolis",
      "title": "Anole data",
      "object": "anolis",
      "file": "anolis.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "anolis",
      "title": "Anole data",
      "topics": [
        "anolis"
      ]
    },
    {
      "page": "detectAllCharacters",
      "title": "Apply detectCharacterType over an entire matrix",
      "topics": [
        "detectAllCharacters"
      ]
    },
    {
      "page": "detectCharacterType",
      "title": "Function to detect whether a character is continuous or discrete",
      "topics": [
        "detectCharacterType"
      ]
    },
    {
      "page": "filter.treedata",
      "title": "Function for filtering rows from an object of class 'treedata'",
      "topics": [
        "filter.grouped_treedata",
        "filter.treedata"
      ]
    },
    {
      "page": "filterMatrix",
      "title": "Filter a matrix, returning either all continuous or all discrete characters",
      "topics": [
        "filterMatrix"
      ]
    },
    {
      "page": "forceFactor",
      "title": "Function for checking whether a treedata object contains only factors and for forcing data columns into factor format",
      "topics": [
        "forceFactor"
      ]
    },
    {
      "page": "forceNames",
      "title": "Force names for rows, columns, or both",
      "topics": [
        "forceNames"
      ]
    },
    {
      "page": "forceNumeric",
      "title": "Function for checking whether a treedata object contains only numeric columns and for forcing data columns into numeric format",
      "topics": [
        "forceNumeric"
      ]
    },
    {
      "page": "getVector",
      "title": "A function for returning a named vector from a data frame or matrix with row names",
      "topics": [
        "getVector"
      ]
    },
    {
      "page": "group_by.treedata",
      "title": "Function for grouping an object of class 'treedata'",
      "topics": [
        "group_by.treedata",
        "ungroup.grouped_treedata"
      ]
    },
    {
      "page": "hasNames",
      "title": "Row and column name check",
      "topics": [
        "hasNames"
      ]
    },
    {
      "page": "make.treedata",
      "title": "Function for making an object of class 'treedata'",
      "topics": [
        "make.treedata"
      ]
    },
    {
      "page": "mutate.treedata",
      "title": "Function for mutating an object of class 'treedata'",
      "topics": [
        "mutate.grouped_treedata",
        "mutate.treedata"
      ]
    },
    {
      "page": "paint_clades",
      "title": "Add regimes to a treedata object",
      "topics": [
        "paint_clades"
      ]
    },
    {
      "page": "reorder.treedata",
      "title": "Reorder a 'treedata' object",
      "topics": [
        "reorder",
        "reorder.treedata"
      ]
    },
    {
      "page": "select.treedata",
      "title": "Function for selecting columns from an object of class 'treedata'",
      "topics": [
        "select.grouped_treedata",
        "select.treedata"
      ]
    },
    {
      "page": "slice.treedata",
      "title": "Choose rows by their ordinal position in the tbl for an object of class 'treedata'",
      "topics": [
        "slice.treedata"
      ]
    },
    {
      "page": "summarise.treedata",
      "title": "Function for summarizing an object of class 'treedata'",
      "topics": [
        "summarise.grouped_treedata",
        "summarise.treedata",
        "summarize.grouped_treedata",
        "summarize.treedata"
      ]
    },
    {
      "page": "tdapply",
      "title": "Apply a function over all treedata object columns and return a list of results, analogously to the normal apply function",
      "topics": [
        "tdapply"
      ]
    },
    {
      "page": "treedply.treedata",
      "title": "Run a function on a 'treedata' object",
      "topics": [
        "treedply",
        "treedply.treedata"
      ]
    },
    {
      "page": "treeply.treedata",
      "title": "Run a function on the phylogeny of a 'treedata' object",
      "topics": [
        "treeply",
        "treeply.treedata"
      ]
    },
    {
      "page": "treeplyr",
      "title": "treeplyr: 'dplyr' Functionality for Matched Tree and Data Objects",
      "topics": [
        "treeplyr"
      ]
    },
    {
      "page": "treeplyr-defunct",
      "title": "Defunct functions in treeplyr",
      "topics": [
        "treeplyr-defunct"
      ]
    }
  ],
  "_readme": "https://github.com/uyedaj/treeplyr/raw/HEAD/README.md",
  "_rundeps": [
    "ape",
    "backports",
    "checkmate",
    "cli",
    "clusterGeneration",
    "coda",
    "codetools",
    "colorspace",
    "combinat",
    "cpp11",
    "DEoptim",
    "deSolve",
    "digest",
    "doParallel",
    "dplyr",
    "expm",
    "foreach",
    "future",
    "future.apply",
    "geiger",
    "generics",
    "globals",
    "glue",
    "igraph",
    "iterators",
    "lattice",
    "lazyeval",
    "lifecycle",
    "listenv",
    "magrittr",
    "maps",
    "MASS",
    "Matrix",
    "mnormt",
    "mvtnorm",
    "ncbit",
    "nlme",
    "numDeriv",
    "optimParallel",
    "osqp",
    "parallelly",
    "phangorn",
    "phytools",
    "pillar",
    "pkgconfig",
    "progressr",
    "R6",
    "Rcpp",
    "RcppArmadillo",
    "rlang",
    "S7",
    "scatterplot3d",
    "subplex",
    "tibble",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr"
  ],
  "_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"
    }
  ],
  "_score": 4.940117866747719,
  "_indexed": false,
  "_nocasepkg": "treeplyr",
  "_universes": [
    "phylotastic"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.11",
      "date": "2026-10-21T21:15:17.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "bfbaf93bf50a98ce9a928324c61110e4a8128da4",
      "fileid": "https://r2.ropensci.org/1907774a00aee5d997f2f3efa9fa7c7d13005eee4b4c9ad8e9157415aaa49d5e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/39676172706"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.11",
      "date": "2026-10-21T21:15:32.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "bfbaf93bf50a98ce9a928324c61110e4a8128da4",
      "fileid": "https://r2.ropensci.org/52859f9bf110ef5a5f45b0e42bf3463bf57d7d1e961be7f863b4c25ac3886e4d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/39676172706"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.11",
      "date": "2026-10-21T21:15:19.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "bfbaf93bf50a98ce9a928324c61110e4a8128da4",
      "fileid": "https://r2.ropensci.org/3031cbf65f6638a537c0d1ba77156006a78a0798f48df86c6c06312ecb3b6207",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/39676172706"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.11",
      "date": "2026-10-21T21:15:34.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "bfbaf93bf50a98ce9a928324c61110e4a8128da4",
      "fileid": "https://r2.ropensci.org/fb303feb3ccd2559ef85c8e810e99e93f42c2b9a8302285f4a7cbffc615ac2c5",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/39676172706"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.11",
      "date": "2026-10-21T21:31:26.000Z",
      "arch": "aarch64",
      "commit": "bfbaf93bf50a98ce9a928324c61110e4a8128da4",
      "fileid": "https://r2.ropensci.org/c6acc466880f913ad3d048a759e38e40208caa598c141588f60d0338388f2fc9",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/39676172706"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.11",
      "date": "2026-10-21T21:33:37.000Z",
      "arch": "x86_64",
      "commit": "bfbaf93bf50a98ce9a928324c61110e4a8128da4",
      "fileid": "https://r2.ropensci.org/41f2e85f8f4f3c3b6e0ff429a3923778f1ac76347d1cfc6459fa6167e6369d64",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/39676172706"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.11",
      "date": "2026-10-21T21:31:27.000Z",
      "arch": "aarch64",
      "commit": "bfbaf93bf50a98ce9a928324c61110e4a8128da4",
      "fileid": "https://r2.ropensci.org/0ed84d09390c6f2d2f5480d351aba2404e3c22843f7b61940a9a0b893e0f0356",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/39676172706"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.11",
      "date": "2026-10-21T21:34:46.000Z",
      "arch": "x86_64",
      "commit": "bfbaf93bf50a98ce9a928324c61110e4a8128da4",
      "fileid": "https://r2.ropensci.org/9f28805016069f73aff42132d63600ba7a7613693595cefd2971053e2abb338c",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/39676172706"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.11",
      "date": "2026-10-21T21:15:45.000Z",
      "arch": "emscripten",
      "commit": "bfbaf93bf50a98ce9a928324c61110e4a8128da4",
      "fileid": "https://r2.ropensci.org/a4313fd96b17b74c34bdb3d53564ea930fbb9e5ebea4cdda54e985ea4a7a9edb",
      "status": "success",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/39676172706"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.11",
      "date": "2026-10-21T21:17:09.000Z",
      "arch": "aarch64",
      "commit": "bfbaf93bf50a98ce9a928324c61110e4a8128da4",
      "fileid": "https://r2.ropensci.org/47fe135ff1cb31041ed1f980461bca8786338ef3e73f80b4c54256ab64066d2a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/39676172706"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.11",
      "date": "2026-10-21T21:14:53.000Z",
      "arch": "x86_64",
      "commit": "bfbaf93bf50a98ce9a928324c61110e4a8128da4",
      "fileid": "https://r2.ropensci.org/dfc97783d4aced93c5e11bb9f301aec9a5e23dee09803e058f100cc6a5acb598",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/39676172706"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.11",
      "date": "2026-10-21T21:14:36.000Z",
      "arch": "x86_64",
      "commit": "bfbaf93bf50a98ce9a928324c61110e4a8128da4",
      "fileid": "https://r2.ropensci.org/5755acb284f49517626962a3ed396ecf92e41d58591106b975241053c5aa6735",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/39676172706"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.11",
      "date": "2026-10-21T21:19:15.000Z",
      "arch": "aarch64",
      "commit": "bfbaf93bf50a98ce9a928324c61110e4a8128da4",
      "fileid": "https://r2.ropensci.org/842abba2c192b8acb09dd944f6512dea845b7d4332c8581c1d07761481711534",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/39676172706"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.11",
      "date": "2026-10-21T21:14:47.000Z",
      "arch": "x86_64",
      "commit": "bfbaf93bf50a98ce9a928324c61110e4a8128da4",
      "fileid": "https://r2.ropensci.org/1595d86cae1bb0551abc71cdab003cb876b970d18be1cf71136e7e915668cee4",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/39676172706"
    }
  ]
}