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  "Author": "R Hackathon et al. (alphabetically: Ben Bolker, Marguerite\nButler, Peter Cowan, Damien de Vienne, Dirk Eddelbuettel, Mark\nHolder, Thibaut Jombart, Steve Kembel, Francois Michonneau,\nDavid Orme, Brian O'Meara, Emmanuel Paradis, Jim Regetz,\nDerrick Zwickl)",
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  "Description": "Provides a base S4 class for comparative methods,\nincorporating one or more trees and trait data.",
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    "ancestors",
    "checkPhylo4",
    "children",
    "depthTips",
    "descendants",
    "edgeId",
    "edgeLabels",
    "edgeLabels<-",
    "edgeLength",
    "edgeLength<-",
    "edgeOrder",
    "edges",
    "extractTree",
    "getEdge",
    "getNode",
    "hasDuplicatedLabels",
    "hasEdgeLabels",
    "hasEdgeLength",
    "hasNodeData",
    "hasNodeLabels",
    "hasPoly",
    "hasRetic",
    "hasSingle",
    "hasTipData",
    "head",
    "internalEdges",
    "isRooted",
    "isUltrametric",
    "labels",
    "labels<-",
    "MRCA",
    "names",
    "nData",
    "nEdges",
    "nNodes",
    "nodeData",
    "nodeData<-",
    "nodeDepth",
    "nodeHeight",
    "nodeId",
    "nodeLabels",
    "nodeLabels<-",
    "nodeType",
    "nTips",
    "phylo4",
    "phylo4d",
    "phylobase.options",
    "phylobubbles",
    "phyloXXYY",
    "plot",
    "plotOneTree",
    "print",
    "prune",
    "readNCL",
    "readNewick",
    "readNexus",
    "reorder",
    "rootNode",
    "rootNode<-",
    "shortestPath",
    "show",
    "siblings",
    "subset",
    "sumEdgeLength",
    "summary",
    "tail",
    "tdata",
    "tdata<-",
    "terminalEdges",
    "tip.data.plot",
    "tipData",
    "tipData<-",
    "tipLabels",
    "tipLabels<-",
    "treePlot"
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      "name": "geospiza",
      "title": "Data from Darwin's finches",
      "object": "geospiza",
      "class": [
        "phylo4d"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "geospiza_raw",
      "title": "Data from Darwin's finches",
      "object": "geospiza_raw",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "owls4",
      "title": "'Owls' data from ape",
      "object": "owls4",
      "class": [
        "phylo4"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "phylobase-package",
      "title": "Utilities and Tools for Phylogenetics",
      "topics": [
        "phylobase-package",
        "phylobase"
      ]
    },
    {
      "page": "addData-methods",
      "title": "Adding data to a phylo4 or a phylo4d object",
      "topics": [
        "addData",
        "addData,phylo4-method",
        "addData,phylo4d-method",
        "addData-methods"
      ]
    },
    {
      "page": "ancestors",
      "title": "Tree traversal and utility functions",
      "topics": [
        "ancestor",
        "ancestors",
        "children",
        "descendants",
        "siblings"
      ]
    },
    {
      "page": "checkPhylo4",
      "title": "Validity checking for phylo4 objects",
      "topics": [
        "checkPhylo4",
        "checkPhylo4Data",
        "checkTree"
      ]
    },
    {
      "page": "edges-accessors",
      "title": "Edges accessors",
      "topics": [
        "edgeOrder",
        "edgeOrder,phylo4-method",
        "edges",
        "edges,phylo4-method",
        "internalEdges",
        "internalEdges,phylo4-method",
        "terminalEdges",
        "terminalEdges,phylo4-method"
      ]
    },
    {
      "page": "extractTree",
      "title": "Get tree from tree+data object",
      "topics": [
        "extractTree"
      ]
    },
    {
      "page": "formatData",
      "title": "Format data for use in phylo4d objects",
      "topics": [
        "formatData"
      ]
    },
    {
      "page": "geospiza",
      "title": "Data from Darwin's finches",
      "topics": [
        "geospiza",
        "geospiza_raw"
      ]
    },
    {
      "page": "getNode-methods",
      "title": "Node and Edge look-up functions",
      "topics": [
        "getEdge",
        "getEdge,phylo4-method",
        "getEdge-methods",
        "getNode",
        "getNode,phylo4-method"
      ]
    },
    {
      "page": "edgeLength-methods",
      "title": "edgeLength methods",
      "topics": [
        "depthTips",
        "depthTips,phylo4-method",
        "depthTips,phylo4-methods",
        "edgeLength",
        "edgeLength,phylo4-method",
        "edgeLength<-",
        "edgeLength<-,phylo4,ANY-method",
        "edgeLength<-,phylo4-method",
        "hasEdgeLength",
        "hasEdgeLength,phylo4-method",
        "isUltrametric",
        "isUltrametric,phylo4-method",
        "nodeDepth",
        "nodeDepth,phylo4-method",
        "nodeHeight",
        "nodeHeight,phylo4-method",
        "sumEdgeLength",
        "sumEdgeLength,phylo4-method"
      ]
    },
    {
      "page": "treeStructure-methods",
      "title": "Test trees for polytomies, inline nodes (singletons), or reticulation",
      "topics": [
        "hasPoly",
        "hasPoly,phylo4-method",
        "hasRetic",
        "hasRetic,phylo4-method",
        "hasSingle",
        "hasSingle,phylo4-method"
      ]
    },
    {
      "page": "phylo4d-accessors",
      "title": "Tests for presence of data associated with trees stored as phylo4d objects",
      "topics": [
        "hasNodeData",
        "hasNodeData,phylo4d-method",
        "hasNodeData-methods",
        "hasTipData",
        "hasTipData,phylo4d-method",
        "hasTipData-method,phylo4d-method",
        "nData",
        "nData,phylo4d-method"
      ]
    },
    {
      "page": "readNexus",
      "title": "Create a 'phylo4', 'phylo4d' or 'data.frame' object from a NEXUS or a Newick file",
      "topics": [
        "Import Nexus and Newick files",
        "readNCL",
        "readNewick",
        "readNexus"
      ]
    },
    {
      "page": "root-methods",
      "title": "Methods to test, access (and modify) the root of a phylo4 object.",
      "topics": [
        "isRooted",
        "isRooted,phylo4-method",
        "rootNode",
        "rootNode,phylo4-method",
        "rootNode<-",
        "rootNode<-,phylo4-method"
      ]
    },
    {
      "page": "MRCA",
      "title": "MRCA",
      "topics": [
        "MRCA",
        "MRCA,phylo-method",
        "MRCA,phylo4-method"
      ]
    },
    {
      "page": "multiPhylo-class",
      "title": "multiPhylo4 and extended classes",
      "topics": [
        "multiPhylo-class",
        "multiPhylo4-class",
        "multiPhylo4d-class",
        "tbind"
      ]
    },
    {
      "page": "nodeId-methods",
      "title": "nodeId methods",
      "topics": [
        "edgeId",
        "edgeId,phylo4-method",
        "nodeId",
        "nodeId,phylo4-method"
      ]
    },
    {
      "page": "nTips-methods",
      "title": "nTips, nNodes, nEdges",
      "topics": [
        "nEdges",
        "nEdges,phylo4-method",
        "nNodes",
        "nNodes,phylo4-method",
        "nTips",
        "nTips,phylo-method",
        "nTips,phylo4-method"
      ]
    },
    {
      "page": "owls4",
      "title": "'Owls' data from ape",
      "topics": [
        "owls4"
      ]
    },
    {
      "page": "pdata",
      "title": "Constructor for pdata (phylogenetic data) class",
      "topics": [
        "check_pdata",
        "pdata"
      ]
    },
    {
      "page": "pdata-class",
      "title": "Class \"pdata\"",
      "topics": [
        "pdata-class",
        "ptypes",
        "[,pdata,ANY,ANY,ANY-method",
        "[,pdata-method",
        "[<-,pdata-method",
        "[[,pdata,ANY,ANY-method",
        "[[,pdata,ANY,missing-method",
        "[[,pdata-method",
        "[[<-,pdata-method"
      ]
    },
    {
      "page": "phylo4-class",
      "title": "The phylo4 class",
      "topics": [
        "phylo4-class"
      ]
    },
    {
      "page": "labels-methods",
      "title": "Labels for phylo4/phylo4d objects",
      "topics": [
        "edgeLabels",
        "edgeLabels,phylo4-method",
        "edgeLabels<-",
        "edgeLabels<-,phylo4-method",
        "hasDuplicatedLabels",
        "hasDuplicatedLabels,phylo4,ANY-method",
        "hasDuplicatedLabels,phylo4-method",
        "hasEdgeLabels",
        "hasEdgeLabels,phylo4-method",
        "hasNodeLabels",
        "hasNodeLabels,phylo4-method",
        "labels",
        "labels,phylo4-method",
        "labels<-",
        "labels<-,phylo4-method",
        "nodeLabels",
        "nodeLabels,phylo4-method",
        "nodeLabels<-",
        "nodeLabels<-,phylo4-method",
        "phylo4-labels",
        "tipLabels",
        "tipLabels,phylo4-method",
        "tipLabels<-",
        "tipLabels<-,phylo4-method"
      ]
    },
    {
      "page": "phylo4-methods",
      "title": "Create a phylogenetic tree",
      "topics": [
        "nexml,phylo4-method",
        "phylo4",
        "phylo4,matrix-method",
        "phylo4,nexml-method",
        "phylo4,phylo-method",
        "phylo4-methods",
        "phylo4_orderings"
      ]
    },
    {
      "page": "phylo4d-class",
      "title": "phylo4d class",
      "topics": [
        "phylo4d-class"
      ]
    },
    {
      "page": "phylo4d-methods",
      "title": "Combine a phylogenetic tree with data",
      "topics": [
        "nexml,phylo4d-method",
        "phylo4d",
        "phylo4d,matrix,matrix-method",
        "phylo4d,matrix-method",
        "phylo4d,nexml-method",
        "phylo4d,phylo,phylo-method",
        "phylo4d,phylo-method",
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