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  "Version": "2.1.5",
  "Date": "2019-08-02",
  "Type": "Package",
  "Title": "Comparative Methods for Phylogenetic Networks",
  "Authors@R": "c(person(\"Dwueng-Chwuan\", \"Jhwueng\", role = c(\"aut\", \"cre\"),\nemail = \"djhwueng@umail.iu.edu\"),\nperson(\"Brian C.\", \"O'Meara\", role = c(\"aut\"),\nemail = \"omeara.brian@gmail.com\"))",
  "Description": "Analyze the phenotypic evolution of species of hybrid\norigin on a phylogenetic network. This can detect a burst of\nvariation at the formation of a hybrid as well as an increase\nor decrease in trait value at a hybridization event. Parameters\nare estimated by maximum likelihood, and model averaging can be\ndone automatically. Users need to enter a comparative data set\nand a phylogenetic network.",
  "License": "GPL (>=2)",
  "URL": "http://github.com/bomeara/BMhyb",
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  "Date/Publication": "2021-11-08 16:09:12 UTC",
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    "AddHybridization",
    "BMhyb",
    "BMhybExhaustive",
    "ComputeLikelihood",
    "ComputeVCV",
    "ConvertEvonetToIgraphWithNodeNumbers",
    "CreateHybridlessEvonet",
    "MergeExhaustiveForPlotting",
    "SimulateNetwork",
    "SimulateTips"
  ],
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    {
      "name": "cichlid",
      "title": "Cichlid dataset",
      "object": "cichlid",
      "file": "cichlid.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
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      "title": "Nicotiana dataset",
      "object": "nicotiana",
      "file": "nicotiana.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "AddHybridization",
      "title": "Add hybrid events to a phy.graph",
      "topics": [
        "AddHybridization"
      ]
    },
    {
      "page": "BMhyb",
      "title": "Optimize model",
      "topics": [
        "BMhyb"
      ]
    },
    {
      "page": "BMhybExhaustive",
      "title": "Exhaustively evaluate models",
      "topics": [
        "BMhybExhaustive"
      ]
    },
    {
      "page": "cichlid",
      "title": "Cichlid dataset",
      "topics": [
        "cichlid"
      ]
    },
    {
      "page": "ComputeLikelihood",
      "title": "Compute the likelihood for a set of parameters",
      "topics": [
        "ComputeLikelihood"
      ]
    },
    {
      "page": "ComputeVCV",
      "title": "Compute the variance-covariance matrix",
      "topics": [
        "ComputeVCV"
      ]
    },
    {
      "page": "ConvertEvonetToIgraphWithNodeNumbers",
      "title": "Convert an evonet object into igraph",
      "topics": [
        "ConvertEvonetToIgraphWithNodeNumbers"
      ]
    },
    {
      "page": "CreateHybridlessEvonet",
      "title": "Convert phylo object to evonet",
      "topics": [
        "CreateHybridlessEvonet"
      ]
    },
    {
      "page": "GetConvexHull",
      "title": "Get convex hull at a given threshold",
      "topics": [
        "GetConvexHull"
      ]
    },
    {
      "page": "MergeExhaustiveForPlotting",
      "title": "Function to merge adaptive sampling sims for plotting",
      "topics": [
        "MergeExhaustiveForPlotting"
      ]
    },
    {
      "page": "nicotiana",
      "title": "Nicotiana dataset",
      "topics": [
        "nicotiana"
      ]
    },
    {
      "page": "plot.BMhybExhaustiveResult",
      "title": "Plot BMhybExhaustive result",
      "topics": [
        "plot.BMhybExhaustiveResult"
      ]
    },
    {
      "page": "plot.BMhybResult",
      "title": "Plot BMhyb result",
      "topics": [
        "plot.BMhybResult"
      ]
    },
    {
      "page": "print.BMhybExhaustiveResult",
      "title": "Print BMhybExhaustive result",
      "topics": [
        "print.BMhybExhaustiveResult"
      ]
    },
    {
      "page": "print.BMhybResult",
      "title": "Print BMhyb result",
      "topics": [
        "print.BMhybResult"
      ]
    },
    {
      "page": "SimulateNetwork",
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        "SimulateNetwork"
      ]
    },
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      "page": "SimulateTips",
      "title": "Simulate trait data",
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      ]
    },
    {
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      "title": "Summarize BMhybExhaustive result",
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      ]
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      "title": "Summarize BMhyb result",
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