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  "Title": "Selection Models for Amino Acid and/or Codon Evolution",
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  "Date": "2020-06-15",
  "Authors@R": "c(person(\"Jeremy\", \"Beaulieu\", role=c(\"aut\", \"cre\"),\nemail = \"jmbeauli@uark.edu\"),\nperson(\"JJ\", \"Chai\", role=c(\"aut\")),\nperson(\"Mike\", \"Gilchrist\", role=c(\"aut\")),\nperson(\"Cedric\", \"Landerer\", role=c(\"aut\")),\nperson(\"Graham\", \"Derryberry\", role=c(\"aut\")),\nperson(\"Brian\", \"O'Meara\", role=c(\"aut\")))",
  "Maintainer": "Jeremy Beaulieu <jmbeauli@uark.edu>",
  "Description": "Sets up and executes a SelAC model (Selection on Amino\nacids and codons) for testing the presence of selection in\namino acid or codon among a set of genes on a fixed phylogeny.\nBeaulieu et al (2019) <doi:10.1093/molbev/msy222>.",
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    "GetAdequateSelac",
    "GetFunctionality",
    "GetMarginalAllGenes",
    "GetPartitionOrder",
    "GetSelacSiteLikelihoods",
    "NucSimulator",
    "SelacOptimize",
    "SelacSimulator",
    "SelacSimulatorEvolvingRates",
    "SelonOptimize",
    "SelonSimulator"
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      "name": "model.fit",
      "title": "Example yeast dataset",
      "object": "archosaurs",
      "file": "archosaurs.rda",
      "class": [
        "selon"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "model.fit",
      "title": "Example yeast dataset",
      "object": "yeast",
      "file": "yeast.rda",
      "class": [
        "selac"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "non_zero_pos",
      "title": "Example datasets",
      "object": "non_zero_pos",
      "file": "non_zero_pos.rda",
      "class": [
        "integer"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "phy",
      "title": "Example yeast dataset",
      "object": "archosaurs",
      "file": "archosaurs.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "phy",
      "title": "Example yeast dataset",
      "object": "yeast",
      "file": "yeast.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "yeast.gene",
      "title": "Example yeast dataset",
      "object": "yeast",
      "file": "yeast.rda",
      "class": [
        "DNAbin"
      ],
      "fields": [],
      "rows": 8,
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "GetAdequateManyReps",
      "title": "Parallel model adequacy test",
      "topics": [
        "GetAdequateManyReps"
      ]
    },
    {
      "page": "GetAdequateSelac",
      "title": "Model adequacy simulation",
      "topics": [
        "GetAdequateSelac"
      ]
    },
    {
      "page": "GetFunctionality",
      "title": "Calculate functionality",
      "topics": [
        "GetFunctionality"
      ]
    },
    {
      "page": "GetMarginalAllGenes",
      "title": "Get marginal reconstruction all genes",
      "topics": [
        "GetMarginalAllGenes"
      ]
    },
    {
      "page": "GetPartitionOrder",
      "title": "Get data partiion order",
      "topics": [
        "GetPartitionOrder"
      ]
    },
    {
      "page": "GetSelacPhiCat",
      "title": "Phi rate category information under SELAC+gamma",
      "topics": [
        "GetSelacPhiCat"
      ]
    },
    {
      "page": "GetSelacSiteLikelihoods",
      "title": "Calculate site likelihoods under SelAC",
      "topics": [
        "GetSelacSiteLikelihoods"
      ]
    },
    {
      "page": "non_zero_pos",
      "title": "Example datasets",
      "topics": [
        "non_zero_pos"
      ]
    },
    {
      "page": "NucSimulator",
      "title": "Simulate DNA under General-Time Reversible model",
      "topics": [
        "NucSimulator"
      ]
    },
    {
      "page": "PlotEquilbriumCodonDistribution",
      "title": "Function to plot a distribution of frequencies of codons given a 3d array of equilibrium frequency matrices",
      "topics": [
        "PlotEquilbriumCodonDistribution"
      ]
    },
    {
      "page": "PlotExpectedFitness",
      "title": "Function to plot a distribution of fitnesses based on codon equilibrium freqs",
      "topics": [
        "PlotExpectedFitness"
      ]
    },
    {
      "page": "PlotGeneSiteInfo",
      "title": "Function to plot info by site in a gene",
      "topics": [
        "PlotGeneSiteInfo"
      ]
    },
    {
      "page": "PlotMutationFitnessSpectra",
      "title": "Plot fitness of mutations, weighted by frequency of those mutations",
      "topics": [
        "PlotMutationFitnessSpectra"
      ]
    },
    {
      "page": "PlotPerAAFitness",
      "title": "Function to plot a distribution of fitnesses W or selection coefficients S for a given optimal aa and other terms.",
      "topics": [
        "PlotPerAAFitness"
      ]
    },
    {
      "page": "yeast",
      "title": "Example yeast dataset",
      "topics": [
        "model.fit",
        "phy",
        "yeast",
        "yeast.gene"
      ]
    },
    {
      "page": "SelacHMMOptimize",
      "title": "Efficient optimization of a Hidden Markov SELAC model",
      "topics": [
        "SelacHMMOptimize"
      ]
    },
    {
      "page": "SelacHMMSimulator",
      "title": "Simulate DNA under the SELAC model",
      "topics": [
        "SelacHMMSimulator"
      ]
    },
    {
      "page": "SelacOptimize",
      "title": "Efficient optimization of the SELAC model",
      "topics": [
        "selac",
        "SelacOptimize"
      ]
    },
    {
      "page": "SelacSimulator",
      "title": "Simulate DNA under the SELAC model",
      "topics": [
        "SelacSimulator"
      ]
    },
    {
      "page": "SelacSimulatorEvolvingRates",
      "title": "Simulate DNA under the SELAC model and evolving rates",
      "topics": [
        "SelacSimulatorEvolvingRates"
      ]
    },
    {
      "page": "archosaur",
      "title": "Example archosaur dataset",
      "topics": [
        "archosaur",
        "archosaur.phy",
        "uce.model.fit"
      ]
    },
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      "page": "SelonHMMOptimize",
      "title": "Optimize parameters under the HMM SELON model",
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      "title": "Optimize parameters under the SELON model",
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        "SelonOptimize"
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    },
    {
      "page": "SelonSimulator",
      "title": "Simulate DNA under the SELON model",
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