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  "Package": "MonoPhy",
  "Type": "Package",
  "Title": "Explore Monophyly of Taxonomic Groups in a Phylogeny",
  "Version": "1.3.2",
  "Date": "2024-10-16",
  "Authors@R": "c(person(\"Orlando\", \"Schwery\", role=c(\"aut\", \"cre\"), email=\"schwery.macroevo@pm.me\"),\nperson(\"Brian C.\", \"O'Meara\", role=c(\"aut\", \"ctb\")),\nperson(\"Peter\", \"Cowman\", role=c(\"ctb\")))",
  "Description": "Requires rooted phylogeny as input and creates a table of\ngenera, their monophyly-status, which taxa cause problems in\nmonophyly etc. Different information can be extracted from the\noutput and a plot function allows visualization of the results\nin a number of ways. \"MonoPhy: a simple R package to find and\nvisualize monophyly issues.\" Schwery, O. & O'Meara, B.C. (2016)\n<doi:10.7717/peerj-cs.56>.",
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  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libglpk-dev make libxml2-dev",
  "Repository": "https://phylotastic.r-universe.dev",
  "Date/Publication": "2024-10-16 23:33:23 UTC",
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  "Maintainer": "Orlando Schwery <schwery.macroevo@pm.me>",
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    "bluesky": "@oschwery.bsky.social",
    "description": "Research Scientist with @roszenil at UKY. Phylogenetics, macroevolution, diversification, model adequacy, dung beetles and more.",
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  "_devurl": "https://github.com/oschwery/monophy",
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  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
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  "_realowner": "oschwery",
  "_cranurl": true,
  "_releases": [
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      "version": "1.0",
      "date": "2015-10-19"
    },
    {
      "version": "1.1",
      "date": "2016-03-11"
    },
    {
      "version": "1.2",
      "date": "2016-07-26"
    },
    {
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      "date": "2021-02-17"
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      "date": "2024-05-05"
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      "date": "2024-10-17"
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    "AssessMonophyly",
    "CollapseMonophyletics",
    "GetAncNodes",
    "GetIntruderTaxa",
    "GetIntruderTips",
    "GetOutlierTaxa",
    "GetOutlierTips",
    "GetResultMonophyly",
    "GetSummaryMonophyly",
    "PlotMonophyly"
  ],
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      "name": "Ericacsubfams",
      "title": "Example dataset for the package MonoPhy.",
      "object": "Ericacsubfams",
      "file": "Ericacsubfams.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "V1",
        "V2",
        "V3"
      ],
      "rows": 77,
      "table": true,
      "tojson": true
    },
    {
      "name": "Ericactree",
      "title": "Example dataset for the package MonoPhy.",
      "object": "Ericactree",
      "file": "Ericactree.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "Ericactribes",
      "title": "Example dataset for the package MonoPhy.",
      "object": "Ericactribes",
      "file": "Ericactribes.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "V1",
        "V2"
      ],
      "rows": 77,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "MonoPhy-package",
      "title": "Explore Monophyly of Taxonomic Groups in a Phylogeny.",
      "topics": [
        "MonoPhy-package",
        "MonoPhy"
      ]
    },
    {
      "page": "AssessMonophyly",
      "title": "Assesses monophyly (or lack of it) of taxonomic groups in a phylogeny.",
      "topics": [
        "AssessMonophyly"
      ]
    },
    {
      "page": "CollapseMonophyletics",
      "title": "Get tree with collapsed monophyletic groups",
      "topics": [
        "CollapseMonophyletics"
      ]
    },
    {
      "page": "GetAncNodes",
      "title": "Get MRCA nodes of taxonomic groups from 'AssessMonophyly' output",
      "topics": [
        "GetAncNodes"
      ]
    },
    {
      "page": "GetIntruderTaxa",
      "title": "Get taxa or tips which are intruders or outliers to a taxon from AssessMonophyly",
      "topics": [
        "GetIntruderTaxa",
        "GetIntruderTips",
        "GetOutlierTaxa",
        "GetOutlierTips"
      ]
    },
    {
      "page": "GetResultMonophyly",
      "title": "Get main result table from 'AssessMonophyly' output",
      "topics": [
        "GetResultMonophyly",
        "GetSummaryMonophyly"
      ]
    },
    {
      "page": "MonophylyData",
      "title": "Example dataset for the package MonoPhy.",
      "topics": [
        "Ericacsubfams",
        "Ericactree",
        "Ericactribes",
        "MonophylyData"
      ]
    },
    {
      "page": "PlotMonophyly",
      "title": "Plot output of AssessMonophyly",
      "topics": [
        "PlotMonophyly"
      ]
    }
  ],
  "_pkglogo": "https://github.com/oschwery/MonoPhy/raw/HEAD/man/figures/logo.png",
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      "source": "MonoPhyVignette.Rmd",
      "filename": "MonoPhyVignette.html",
      "title": "MonoPhy Tutorial",
      "author": "Orlando Schwery",
      "engine": "knitr::rmarkdown",
      "headings": [
        "1 Introduction",
        "2 Installation",
        "2.1 CRAN",
        "2.2 Development Version from GitHub",
        "3 Use",
        "3.1 Load Data",
        "3.1.1 Example Files",
        "3.1.2 Own Files",
        "3.2 Run Main Analysis",
        "3.2.1 Taxonomy Based on Tip Labels",
        "3.2.2 Taxonomy Based on File",
        "3.2.3 Taxonomy Downloaded from Web",
        "3.2.4 Other Options",
        "3.3 Accessing the Results",
        "3.3.1 First Impression - Summary and Results Tables",
        "3.3.2 Further Look - Customized Access to Detailed Results",
        "3.4 Plotting",
        "3.4.1 Monophyly Plot",
        "3.4.2 Taxonomy Plot",
        "3.4.3 Monophyly-Taxonomy Mirror Plot",
        "3.4.4 Intruder Plot",
        "3.4.5 Solutions for Large Trees",
        "4 Final Notes"
      ],
      "created": "2015-09-05 01:24:16",
      "modified": "2024-05-05 00:29:43",
      "commits": 16
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