{
  "_id": "6acb45bbfe5cc25786e8d39d",
  "Package": "windex",
  "Type": "Package",
  "Title": "Analysing Convergent Evolution using the Wheatsheaf Index",
  "Version": "2.1.0",
  "Date": "2025-02-05",
  "Author": "Kevin Arbuckle and Amanda Minter",
  "Maintainer": "Kevin Arbuckle <kevin.arbuckle@swansea.ac.uk>",
  "Description": "Analysing convergent evolution using the Wheatsheaf index,\ndescribed in Arbuckle et al. (2014) <doi:\n10.1111/2041-210X.12195>, and some other unrelated but perhaps\nuseful functions.",
  "License": "GPL-2",
  "Packaged": {
    "Date": "2026-10-11 07:53:34 UTC",
    "User": "root"
  },
  "Config/pak/sysreqs": "libglpk-dev libxml2-dev",
  "Repository": "https://kevinarbuckle.r-universe.dev",
  "Date/Publication": "2025-02-05 16:42:02 UTC",
  "RemoteUrl": "https://github.com/kevinarbuckle/windex",
  "RemoteRef": "HEAD",
  "RemoteSha": "c3fd537795b5e9326a4bf43cbaa8901495643f59",
  "NeedsCompilation": "no",
  "_user": "kevinarbuckle",
  "_type": "src",
  "_file": "windex_2.1.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/e547e33023f89f7f463e733995dd03810d484decf31ebcc51252a89c3990dbd6",
  "_filesize": 186251,
  "_sha256": "e547e33023f89f7f463e733995dd03810d484decf31ebcc51252a89c3990dbd6",
  "_expires": "2027-01-19T08:15:53.000Z",
  "_created": "2026-10-11T07:53:34.000Z",
  "_published": "2026-10-11T08:15:55.105Z",
  "_buildurl": "https://github.com/r-universe/kevinarbuckle/actions/runs/38122696555",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 114421203409,
      "time": 135,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "11695208888"
    },
    {
      "job": 114421203351,
      "time": 123,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11696146234"
    },
    {
      "job": 114421203410,
      "time": 194,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "11696547615"
    },
    {
      "job": 114421203369,
      "time": 144,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11696407803"
    },
    {
      "job": 114420582801,
      "time": 222,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11696575250"
    },
    {
      "job": 114421203381,
      "time": 93,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11696236034"
    },
    {
      "job": 114421203431,
      "time": 106,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "11696201084"
    },
    {
      "job": 114421203427,
      "time": 96,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "11695283834"
    },
    {
      "job": 114421203440,
      "time": 81,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11696151097"
    }
  ],
  "_upstream": "https://github.com/kevinarbuckle/windex",
  "_commit": {
    "id": "c3fd537795b5e9326a4bf43cbaa8901495643f59",
    "author": "kevinarbuckle <72972690+kevinarbuckle@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Add files via upload",
    "time": 1738773722
  },
  "_maintainer": {
    "name": "Kevin Arbuckle",
    "email": "kevin.arbuckle@swansea.ac.uk",
    "login": "kevinarbuckle",
    "description": "",
    "uuid": 72972690
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "phytools",
      "role": "Depends"
    },
    {
      "package": "geiger",
      "version": ">= 2.0",
      "role": "Depends"
    },
    {
      "package": "ape",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "phangorn",
      "role": "Depends"
    },
    {
      "package": "scatterplot3d",
      "role": "Depends"
    },
    {
      "package": "utils",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "R",
      "version": ">= 3.0.0",
      "role": "Depends"
    }
  ],
  "_owner": "kevinarbuckle",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "kevinarbuckle",
      "count": 105,
      "uuid": 72972690
    }
  ],
  "_userbio": {
    "uuid": 72972690,
    "type": "user",
    "name": "kevinarbuckle",
    "followers": 0
  },
  "_downloads": {
    "count": 269,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/windex"
  },
  "_mentions": 4,
  "_devurl": "https://github.com/kevinarbuckle/windex",
  "_searchresults": 9,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/windex.html",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/kevinarbuckle/windex",
  "_realowner": "kevinarbuckle",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0",
      "date": "2014-10-15"
    },
    {
      "version": "2.0",
      "date": "2020-10-19"
    },
    {
      "version": "2.0.1",
      "date": "2021-01-13"
    },
    {
      "version": "2.0.2",
      "date": "2021-04-14"
    },
    {
      "version": "2.0.3",
      "date": "2021-10-21"
    },
    {
      "version": "2.0.4",
      "date": "2023-02-28"
    },
    {
      "version": "2.0.4.1",
      "date": "2023-03-07"
    },
    {
      "version": "2.0.5",
      "date": "2023-08-24"
    },
    {
      "version": "2.0.6",
      "date": "2023-10-11"
    },
    {
      "version": "2.0.7",
      "date": "2023-12-14"
    },
    {
      "version": "2.0.8",
      "date": "2024-04-26"
    },
    {
      "version": "2.1.0",
      "date": "2025-02-06"
    }
  ],
  "_exports": [
    "backLog",
    "barplot.logreg",
    "error.bars",
    "lrTest",
    "mark.dist",
    "modSel.fitMk",
    "modSel.geiger",
    "modSel.phylolm",
    "modSel.rayDISC",
    "modSelTab",
    "nodeDist",
    "pir",
    "plotTrait",
    "prune2data",
    "richYuleInputs",
    "se",
    "test.windex",
    "treecheck",
    "treedatacheck",
    "windex",
    "windex.sim.test"
  ],
  "_datasets": [
    {
      "name": "sample.data",
      "title": "Sample data for windex",
      "object": "sample.data",
      "file": "sample.data.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "species",
        "focals",
        "bm1",
        "bm2",
        "bm3",
        "ou1",
        "ou2",
        "ou3",
        "bin"
      ],
      "rows": 100,
      "table": true,
      "tojson": true
    },
    {
      "name": "sample.tree",
      "title": "Phylogenetic tree to accompany sample.data",
      "object": "sample.tree",
      "file": "sample.tree.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "backLog",
      "title": "Backtransforms coefficient estimates from logistic regression",
      "topics": [
        "backLog"
      ]
    },
    {
      "page": "barplot.logreg",
      "title": "Plots a barplot from logistic regression parameter estimates",
      "topics": [
        "barplot.logreg"
      ]
    },
    {
      "page": "error.bars",
      "title": "Plots error bars on a barplot",
      "topics": [
        "error.bars"
      ]
    },
    {
      "page": "lrTest",
      "title": "Calculates likelihood ratio test",
      "topics": [
        "lrTest"
      ]
    },
    {
      "page": "mark.dist",
      "title": "Summarising distributions of (exam/coursework/etc.) marks for (UK) university teaching",
      "topics": [
        "mark.dist"
      ]
    },
    {
      "page": "modSel.fitMk",
      "title": "Model selection table for categorical trait evolution models fit in the fitMk function in the package phytools, based on information theoretical measures.",
      "topics": [
        "modSel.fitMk"
      ]
    },
    {
      "page": "modSel.geiger",
      "title": "Model selection table for phenotypic evolution models fit in the package geiger, based on information theoretical measures.",
      "topics": [
        "modSel.geiger"
      ]
    },
    {
      "page": "modSel.phylolm",
      "title": "Model selection table for phylogenetic (logistic) regressions fit in the phylolm and phyloglm functions in the package phylolm, based on information theoretical measures.",
      "topics": [
        "modSel.phylolm"
      ]
    },
    {
      "page": "modSel.rayDISC",
      "title": "Model selection table for evolutionary pathway models fit in the package corHMM, based on information theoretical measures.",
      "topics": [
        "modSel.rayDISC"
      ]
    },
    {
      "page": "modSelTab",
      "title": "Model selection table based on information theoretical measures.",
      "topics": [
        "modSelTab"
      ]
    },
    {
      "page": "nodeDist",
      "title": "Plotting and/or retrieving distribution of divergence times of a pair of species from a set of phylogenetic trees.",
      "topics": [
        "nodeDist"
      ]
    },
    {
      "page": "pir",
      "title": "Calculates phylogenetic imbalance ratio (PIR)",
      "topics": [
        "pir"
      ]
    },
    {
      "page": "plotTrait",
      "title": "Provides a visualisation of up to three-dimensional trait space (not accounting for phylogeny) for data exploration",
      "topics": [
        "plotTrait"
      ]
    },
    {
      "page": "prune2data",
      "title": "Prunes a phylogenetic tree to match a vector (e.g. of species names in a dataset)",
      "topics": [
        "prune2data"
      ]
    },
    {
      "page": "richYuleInputs",
      "title": "Generates the inputs necessary to run richness.yule.test() in ape",
      "topics": [
        "richYuleInputs"
      ]
    },
    {
      "page": "sample.data",
      "title": "Sample data for windex",
      "topics": [
        "sample.data"
      ]
    },
    {
      "page": "sample.tree",
      "title": "Phylogenetic tree to accompany sample.data",
      "topics": [
        "sample.tree"
      ]
    },
    {
      "page": "se",
      "title": "Calculates standard error",
      "topics": [
        "se"
      ]
    },
    {
      "page": "test.windex",
      "title": "Tests for particularly strong convergent evolution given topological constraints",
      "topics": [
        "test.windex"
      ]
    },
    {
      "page": "treecheck",
      "title": "Checks a set of phylogenetic trees to confirm they are ultrametric and binary.",
      "topics": [
        "treecheck"
      ]
    },
    {
      "page": "treedatacheck",
      "title": "Checks a set of phylogenetic trees to confirm they are ultrametric and binary and that tip labels match a list of names.",
      "topics": [
        "treedatacheck"
      ]
    },
    {
      "page": "windex",
      "title": "Calculates Wheatsheaf index with 95% confidence intervals",
      "topics": [
        "windex"
      ]
    },
    {
      "page": "windex.sim.test",
      "title": "Tests for presence of convergent evolution (over and above that expected from Brownian motion)",
      "topics": [
        "windex.sim.test"
      ]
    }
  ],
  "_rundeps": [
    "ape",
    "cli",
    "clusterGeneration",
    "coda",
    "codetools",
    "colorspace",
    "combinat",
    "cpp11",
    "DEoptim",
    "deSolve",
    "digest",
    "doParallel",
    "expm",
    "fastmatch",
    "foreach",
    "geiger",
    "generics",
    "glue",
    "igraph",
    "iterators",
    "lattice",
    "lifecycle",
    "magrittr",
    "maps",
    "MASS",
    "Matrix",
    "mnormt",
    "mvtnorm",
    "ncbit",
    "nlme",
    "numDeriv",
    "optimParallel",
    "phangorn",
    "phytools",
    "pkgconfig",
    "quadprog",
    "Rcpp",
    "rlang",
    "scatterplot3d",
    "subplex",
    "vctrs"
  ],
  "_score": 2.6020599913279625,
  "_indexed": true,
  "_nocasepkg": "windex",
  "_universes": [
    "kevinarbuckle"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.1.0",
      "date": "2026-10-11T07:55:34.000Z",
      "distro": "resolute",
      "commit": "c3fd537795b5e9326a4bf43cbaa8901495643f59",
      "fileid": "https://r2.ropensci.org/6e42dac66003597cf882613faf0e372ed8bd02bf7bf38818025de61f3f8ec613",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/kevinarbuckle/actions/runs/38122696555"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2.1.0",
      "date": "2026-10-11T07:55:29.000Z",
      "distro": "resolute",
      "commit": "c3fd537795b5e9326a4bf43cbaa8901495643f59",
      "fileid": "https://r2.ropensci.org/1090ccf5fe963fdc49964de9ab11a8263c83325be4754d2c2627f4726eb5b827",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/kevinarbuckle/actions/runs/38122696555"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.1.0",
      "date": "2026-10-11T08:14:59.000Z",
      "commit": "c3fd537795b5e9326a4bf43cbaa8901495643f59",
      "fileid": "https://r2.ropensci.org/e47fa66da103996833aba309a4d6e372551a80ff7e417769d7fe456f3a2d3c2e",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/kevinarbuckle/actions/runs/38122696555"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2.1.0",
      "date": "2026-10-11T08:13:37.000Z",
      "commit": "c3fd537795b5e9326a4bf43cbaa8901495643f59",
      "fileid": "https://r2.ropensci.org/6e7b42e7de955fe6a81e43ac9281bd70abb5391cadae38d1d9274dfb80853ddc",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/kevinarbuckle/actions/runs/38122696555"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.1.0",
      "date": "2026-10-11T07:55:30.000Z",
      "commit": "c3fd537795b5e9326a4bf43cbaa8901495643f59",
      "fileid": "https://r2.ropensci.org/387968b33c2b78a60bc60b99091c2d63341f4257b18112499cdcffe1ff8a2a42",
      "status": "success",
      "buildurl": "https://github.com/r-universe/kevinarbuckle/actions/runs/38122696555"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.1.0",
      "date": "2026-10-11T07:55:00.000Z",
      "commit": "c3fd537795b5e9326a4bf43cbaa8901495643f59",
      "fileid": "https://r2.ropensci.org/43568621fc777555e1fee1844e2b245d108d1714090a1bf4d2f3d2aed730fe38",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/kevinarbuckle/actions/runs/38122696555"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.1.0",
      "date": "2026-10-11T07:54:52.000Z",
      "commit": "c3fd537795b5e9326a4bf43cbaa8901495643f59",
      "fileid": "https://r2.ropensci.org/ccde3aad8e88baae742b0f63eb28142668d5288aa44f57f903cd7b057c65139a",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/kevinarbuckle/actions/runs/38122696555"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "2.1.0",
      "date": "2026-10-11T07:54:39.000Z",
      "commit": "c3fd537795b5e9326a4bf43cbaa8901495643f59",
      "fileid": "https://r2.ropensci.org/89213d6d3ab596d55bca47b5190ed536ae8083628ba1f3291bce98d28a579c9d",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/kevinarbuckle/actions/runs/38122696555"
    }
  ]
}