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  "Title": "An Extension (for Package 'SigTree') of Some of the Classes in\nPackage 'phylobase'",
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  "Date": "2015-07-27",
  "Author": "J. Conrad Stack",
  "Maintainer": "John R. Stevens <john.r.stevens@usu.edu>",
  "Description": "Based on (but not identical to) the no-longer-maintained\npackage 'phyext', provides enhancements to 'phylobase' classes,\nspecifically for use by package 'SigTree'; provides classes and\nmethods which help users manipulate branch-annotated trees (as\nin 'SigTree'); also provides support for a few other extra\nfeatures.",
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    "User": "root"
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    "author": "John R. Stevens <john.r.stevens@usu.edu>",
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    "message": "version 0.0.4\n",
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    "extra/citation.json",
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      "date": "2015-07-17"
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    "read.nexus.simmap",
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    "tipdate.ci",
    "treeHeight",
    "validPhylo4d_ext",
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    "weight<-",
    "write.characters2",
    "write.nexus.simmap",
    "write.simmap",
    "write.simmap.new",
    "write.simmap.old"
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  "_help": [
    {
      "page": "phyext2",
      "title": "Misc. functions from phyext package",
      "topics": [
        "addSubNode",
        "collapse.singletons",
        "collapse.subnodes",
        "collapse.to.singles",
        "contData",
        "deep.phy.copy",
        "discData",
        "expand.singles",
        "get.nexus.comments",
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        "get.tree.weights",
        "getEmptyDataFrame",
        "getSubNodeData",
        "getSubNodeEdgeInds",
        "getSubNodePosish",
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        "has.characters2",
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        "validPhylo4d_ext",
        "write.characters2",
        "write.nexus.simmap",
        "write.simmap",
        "write.simmap.new",
        "write.simmap.old"
      ]
    },
    {
      "page": "phyext2class",
      "title": "Misc. functions from phyext package (class definitions)",
      "topics": [
        "as",
        "as,phylo,phylo4d_ext-method",
        "as,phylo4,phylo4d_ext-method",
        "as,phylo4d,phylo4d_ext-method",
        "as-method",
        "coerce,phylo,phylo4d_ext-method",
        "coerce,phylo4,phylo4d_ext-method",
        "coerce,phylo4d,phylo4d_ext-method",
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        "snposition,phylo4d_ext-method",
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        "weight<-",
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      ]
    },
    {
      "page": "phyext2methods",
      "title": "Misc. functions from phyext package (methods definitions)",
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        "hasData",
        "hasData,list-method",
        "hasData,phylo-method",
        "hasData,phylo4-method",
        "hasData,phylo4d-method",
        "hasData-methods",
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        "hasDataColumn,phylo4,ANY-method",
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    }
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