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  "Package": "MorphSim",
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  "Title": "Simulate Discrete Character Data along Phylogenetic Trees",
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  "Description": "Tools to simulate morphological traits along phylogenetic\ntrees with branch lengths representing evolutionary distance or\ntime. Includes functions for visualizing evolutionary processes\nalong trees and within morphological character matrices.",
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    "get.matrix",
    "get.reconstructed",
    "get.transitions",
    "is.morpho",
    "morpho",
    "plotMorphoGrid",
    "sim.missing.data",
    "sim.morpho",
    "stats.morpho",
    "symmetric.Q.matrix",
    "write.morpho",
    "write.recon.matrix",
    "write.recon.tree",
    "write.recon.tsv",
    "write.tsv"
  ],
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    {
      "name": "morpho_data",
      "title": "Example morpho dataset",
      "object": "morpho_data",
      "class": [
        "morpho",
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
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    {
      "page": "combine.morpho",
      "title": "Combine Two Morpho Objects",
      "topics": [
        "combine.morpho"
      ]
    },
    {
      "page": "convergent_evol",
      "title": "Determines the number of convergently evolved traits",
      "topics": [
        "convergent_evol"
      ]
    },
    {
      "page": "find_path_to_tip",
      "title": "Determines the route (nodes and branches) for a tip in a phylogenetic tree",
      "topics": [
        "find_path_to_tip"
      ]
    },
    {
      "page": "get_gamma_rates",
      "title": "Get discrete gamma rates",
      "topics": [
        "get_gamma_rates"
      ]
    },
    {
      "page": "get_lognormal_rates",
      "title": "Get discrete log-normal rates",
      "topics": [
        "get_lognormal_rates"
      ]
    },
    {
      "page": "get.convergent",
      "title": "Identify convergent traits",
      "topics": [
        "get.convergent"
      ]
    },
    {
      "page": "get.matrix",
      "title": "Get Specific Morphological Matrix",
      "topics": [
        "get.matrix"
      ]
    },
    {
      "page": "get.reconstructed",
      "title": "Add reconstructed tree and matrix to morpho object",
      "topics": [
        "get.reconstructed"
      ]
    },
    {
      "page": "get.transitions",
      "title": "Get Tranisition History",
      "topics": [
        "get.transitions"
      ]
    },
    {
      "page": "morpho",
      "title": "Morpho object",
      "topics": [
        "as.morpho",
        "is.morpho",
        "morpho"
      ]
    },
    {
      "page": "morpho_data",
      "title": "Example morpho dataset",
      "topics": [
        "morpho_data"
      ]
    },
    {
      "page": "morphsim_fossilsim",
      "title": "Match sampled ancestor labels",
      "topics": [
        "morphsim_fossilsim"
      ]
    },
    {
      "page": "plot.morpho",
      "title": "Plot full evolutionary history",
      "topics": [
        "plot.morpho"
      ]
    },
    {
      "page": "plotMorphoGrid",
      "title": "Plots morphological matrix",
      "topics": [
        "plotMorphoGrid"
      ]
    },
    {
      "page": "reconstruct.matrix",
      "title": "Get reconstructed matrix",
      "topics": [
        "reconstruct.matrix"
      ]
    },
    {
      "page": "reconstruct.tree",
      "title": "Color branches for plotting a reconstructed tree",
      "topics": [
        "reconstruct.tree"
      ]
    },
    {
      "page": "sim.missing.data",
      "title": "Remove morphological character data",
      "topics": [
        "sim.missing.data"
      ]
    },
    {
      "page": "sim.morpho",
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      "topics": [
        "sim.morpho"
      ]
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      ]
    },
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      ]
    },
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      "page": "write.morpho",
      "title": "Write morpho data to file",
      "topics": [
        "write.morpho"
      ]
    },
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      "title": "Write reconstructed character matrix to file",
      "topics": [
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      ]
    },
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      "page": "write.tsv",
      "title": "Write the taxa ages",
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      ]
    }
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