{
  "_id": "6ae2fd493d0f299392dd060b",
  "Package": "treestartr",
  "Type": "Package",
  "Title": "Generate Starting Trees For Combined Molecular, Morphological\nand Stratigraphic Data",
  "Version": "0.1.0",
  "Authors@R": "person(\"April\", \"Wright\", role = c(\"aut\", \"cre\"),\nemail = \"april.wright@selu.edu\")",
  "Description": "Combine a list of taxa with a phylogeny to generate a\nstarting tree for use in total evidence dating analyses.",
  "URL": "https://docs.ropensci.org/treestartr/",
  "BugReports": "https://github.com/ropensci/treeStartR/issues",
  "License": "MIT + file LICENSE",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "6.1.0",
  "Config/pak/sysreqs": "libglpk-dev libxml2-dev",
  "Repository": "https://ropensci.r-universe.dev",
  "Date/Publication": "2019-12-05 19:03:31 UTC",
  "RemoteUrl": "https://github.com/ropensci/treestartr",
  "RemoteRef": "HEAD",
  "RemoteSha": "b0535afdd7490ff7e8efd5714c14d6aa00dbde7b",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-29 07:58:00 UTC",
    "User": "root"
  },
  "Author": "April Wright [aut, cre]",
  "Maintainer": "April Wright <april.wright@selu.edu>",
  "_user": "ropensci",
  "_type": "src",
  "_file": "treestartr_0.1.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/7e955a62dd656a3767e3d1f52b8a1f78e052a7e1c8fe1c0e561d27396ea93f73",
  "_filesize": 131442,
  "_sha256": "7e955a62dd656a3767e3d1f52b8a1f78e052a7e1c8fe1c0e561d27396ea93f73",
  "_expires": "2027-02-06T08:01:11.000Z",
  "_created": "2026-10-29T07:58:00.000Z",
  "_published": "2026-10-29T08:01:13.243Z",
  "_upstream": "https://github.com/ropensci/treestartr",
  "_status": "success",
  "_maintainer": {
    "name": "April Wright",
    "email": "april.wright@selu.edu",
    "login": "wrightaprilm",
    "description": "",
    "uuid": 1715446
  },
  "_jobs": [
    {
      "job": 123330091744,
      "time": 137,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12880984548"
    },
    {
      "job": 123330091704,
      "time": 139,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12881927295"
    },
    {
      "job": 123330091814,
      "time": 121,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12882500013"
    },
    {
      "job": 123330091726,
      "time": 126,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12881748994"
    },
    {
      "job": 123327883401,
      "time": 121,
      "config": "pkgdown",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12882115482"
    },
    {
      "job": 123327883533,
      "time": 372,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12882086240"
    },
    {
      "job": 123330091765,
      "time": 102,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12881284709"
    },
    {
      "job": 123330091966,
      "time": 72,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12881987005"
    },
    {
      "job": 123330091967,
      "time": 97,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12882395305"
    },
    {
      "job": 123330091810,
      "time": 87,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12882300510"
    }
  ],
  "_buildurl": "https://github.com/r-universe/ropensci/actions/runs/40838147546",
  "_commit": {
    "id": "b0535afdd7490ff7e8efd5714c14d6aa00dbde7b",
    "author": "Jeroen Ooms <jeroenooms@gmail.com>",
    "committer": "Jeroen Ooms <jeroenooms@gmail.com>",
    "message": "Update docs url\n",
    "time": 1575572611
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.0.0",
      "role": "Depends"
    },
    {
      "package": "phytools",
      "version": ">= 0.6-4",
      "role": "Depends"
    },
    {
      "package": "ape",
      "version": ">= 5.0",
      "role": "Depends"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    }
  ],
  "_owner": "ropensci",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 9,
  "_contributors": [
    {
      "user": "wrightaprilm",
      "count": 89,
      "uuid": 1715446
    },
    {
      "user": "jeroen",
      "count": 1,
      "uuid": 216319
    }
  ],
  "_userbio": {
    "uuid": 1200269,
    "type": "organization",
    "name": "rOpenSci",
    "followers": 1166,
    "description": "Tools and R Packages for Open Science"
  },
  "_downloads": {
    "count": 223,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/treestartr"
  },
  "_devurl": "https://github.com/ropensci/treestartr",
  "_pkgdown": "https://docs.ropensci.org/treestartr/",
  "_searchresults": 8,
  "_metadata": {
    "review": {
      "id": 239,
      "status": "reviewed",
      "version": "0.1.0",
      "organization": "rOpenSci Software Review",
      "url": "https://github.com/ropensci/software-review/issues/239"
    },
    "ropensci_category": "data-extraction"
  },
  "_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/treestartr.html",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/ropensci/treestartr",
  "_realowner": "ropensci",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2019-01-09"
    }
  ],
  "_exports": [
    "absent_tippr",
    "dataf_parsr",
    "echo_rb",
    "echo_subtree",
    "genera_strippr",
    "present_tippr",
    "rand_absent_tippr",
    "text_placr"
  ],
  "_datasets": [
    {
      "name": "absent_list",
      "title": "bears",
      "object": "bears",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "bears",
      "title": "bears",
      "object": "bears",
      "class": [
        "data.frame"
      ],
      "fields": [
        "taxon",
        "age"
      ],
      "rows": 22,
      "table": true,
      "tojson": true
    },
    {
      "name": "mrca_df",
      "title": "bears",
      "object": "bears",
      "class": [
        "data.frame"
      ],
      "fields": [
        "taxon",
        "clade"
      ],
      "rows": 5,
      "table": true,
      "tojson": true
    },
    {
      "name": "tax_frame",
      "title": "bears",
      "object": "bears",
      "class": [
        "data.frame"
      ],
      "fields": [
        "taxon",
        "age"
      ],
      "rows": 22,
      "table": true,
      "tojson": true
    },
    {
      "name": "tree",
      "title": "bears",
      "object": "bears",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "absent_tippR",
      "title": "Add tips to tree via user input",
      "topics": [
        "absent_tippr"
      ]
    },
    {
      "page": "bears",
      "title": "bears",
      "topics": [
        "absent_list",
        "bears",
        "mrca_df",
        "tax_frame",
        "tree"
      ]
    },
    {
      "page": "dataf_parsR",
      "title": "Detect file format of taxon file",
      "topics": [
        "dataf_parsr"
      ]
    },
    {
      "page": "echo_rb",
      "title": "Print RevBayes-formatted clade constriants.",
      "topics": [
        "echo_rb"
      ]
    },
    {
      "page": "echo_subtree",
      "title": "Print subtrees with tips added.",
      "topics": [
        "echo_subtree"
      ]
    },
    {
      "page": "fileFormat",
      "title": "Utility function to check if file is a csv or tsv.",
      "topics": [
        "fileformat"
      ]
    },
    {
      "page": "genera_strippR",
      "title": "Check if tip is on tree",
      "topics": [
        "genera_strippr"
      ]
    },
    {
      "page": "get_found",
      "title": "Get dataframe of tips that do not have congeners on tree.",
      "topics": [
        "get_found"
      ]
    },
    {
      "page": "get_lost",
      "title": "Determine if a tip is present on a tree",
      "topics": [
        "get_lost"
      ]
    },
    {
      "page": "make_absentdf",
      "title": "Determine which tips are not on the tree, and get their genera.",
      "topics": [
        "make_absentdf"
      ]
    },
    {
      "page": "make_treedf",
      "title": "Determine which tips are on the tree, and get their genera.",
      "topics": [
        "make_treedf"
      ]
    },
    {
      "page": "present_tippR",
      "title": "Add tips to the tree based on taxonomy.",
      "topics": [
        "present_tippr"
      ]
    },
    {
      "page": "rand_absent_tippR",
      "title": "Random addition of taxa",
      "topics": [
        "rand_absent_tippr"
      ]
    },
    {
      "page": "taxon_testr",
      "title": "Utility function to check taxon_names in parsed data file",
      "topics": [
        "taxon_testr"
      ]
    },
    {
      "page": "text_placR",
      "title": "Add tips to tree via taxon list",
      "topics": [
        "text_placr"
      ]
    },
    {
      "page": "treestartr",
      "title": "treestartr: A package for generating reasonable starting trees for phylogenetic analysis.",
      "topics": [
        "treestartr-package",
        "treestartr"
      ]
    }
  ],
  "_readme": "https://github.com/ropensci/treestartr/raw/HEAD/README.md",
  "_rundeps": [
    "ape",
    "cli",
    "clusterGeneration",
    "coda",
    "codetools",
    "combinat",
    "cpp11",
    "DEoptim",
    "digest",
    "doParallel",
    "expm",
    "fastmatch",
    "foreach",
    "generics",
    "glue",
    "igraph",
    "iterators",
    "lattice",
    "lifecycle",
    "magrittr",
    "maps",
    "MASS",
    "Matrix",
    "mnormt",
    "nlme",
    "numDeriv",
    "optimParallel",
    "phangorn",
    "phytools",
    "pkgconfig",
    "quadprog",
    "Rcpp",
    "rlang",
    "scatterplot3d",
    "vctrs"
  ],
  "_score": 3.6532125137753435,
  "_indexed": true,
  "_nocasepkg": "treestartr",
  "_universes": [
    "ropensci",
    "wrightaprilm"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-10-29T08:00:08.000Z",
      "distro": "resolute",
      "commit": "b0535afdd7490ff7e8efd5714c14d6aa00dbde7b",
      "fileid": "https://r2.ropensci.org/17a5d9a8e9b14e465c157169bc7ab307a87c006e84ffbc6a86219986a1ff24cc",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/40838147546"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-10-29T08:00:08.000Z",
      "distro": "resolute",
      "commit": "b0535afdd7490ff7e8efd5714c14d6aa00dbde7b",
      "fileid": "https://r2.ropensci.org/3313ef08a9e2cd417c1c83506bcf85235f4046f476092219cb4d2c8720f20f6d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/40838147546"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-10-29T07:59:50.000Z",
      "commit": "b0535afdd7490ff7e8efd5714c14d6aa00dbde7b",
      "fileid": "https://r2.ropensci.org/b9f913b20533f612ace6d63df9d2eb263ad6cb29ebd667256ed862b9b36addd9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/40838147546"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-10-29T07:59:53.000Z",
      "commit": "b0535afdd7490ff7e8efd5714c14d6aa00dbde7b",
      "fileid": "https://r2.ropensci.org/f37d7ef2070991da55d6564474782e6c39caaa5e4f0d2293e399adc9b45fb9aa",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/40838147546"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.0",
      "date": "2026-10-29T08:00:02.000Z",
      "commit": "b0535afdd7490ff7e8efd5714c14d6aa00dbde7b",
      "fileid": "https://r2.ropensci.org/22fc39e2a66ca930dadfa951ad7090edc0f2d3a29b8fcd75674bf6b64033f1ab",
      "status": "success",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/40838147546"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-10-29T07:59:03.000Z",
      "commit": "b0535afdd7490ff7e8efd5714c14d6aa00dbde7b",
      "fileid": "https://r2.ropensci.org/c5579e3a5d260a1568307d1898b590dfb4b14f997e14d21cd5d77667ac061dbe",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/40838147546"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-10-29T07:59:21.000Z",
      "commit": "b0535afdd7490ff7e8efd5714c14d6aa00dbde7b",
      "fileid": "https://r2.ropensci.org/997ab78ada85d423eb04a7fc237f18c0fb99e69ac2340a62fdeb5822627ed3eb",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/40838147546"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-10-29T07:59:11.000Z",
      "commit": "b0535afdd7490ff7e8efd5714c14d6aa00dbde7b",
      "fileid": "https://r2.ropensci.org/0038064eae41911dcef740054fd08ba212963cee72e6dce0b51c35d7b81cd0d9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/40838147546"
    }
  ]
}