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  "Date": "2025-8-5",
  "Title": "Hidden State Speciation and Extinction",
  "Authors@R": "c(person(\"Jeremy\", \"Beaulieu\", role=c(\"aut\", \"cre\"),\nemail = \"jmbeauli@uark.edu\"),\nperson(\"Brian\", \"O'Meara\", role=c(\"aut\")),\nperson(\"Daniel\", \"Caetano\", role=c(\"aut\")),\nperson(\"James\", \"Boyko\", role=c(\"aut\")),\nperson(\"Thais\", \"Vasconcelos\", role=c(\"aut\")))",
  "Maintainer": "Jeremy Beaulieu <jmbeauli@uark.edu>",
  "Description": "Sets up and executes a HiSSE model (Hidden State\nSpeciation and Extinction) on a phylogeny and character sets to\ntest for hidden shifts in trait dependent rates of\ndiversification. Beaulieu and O'Meara (2016)\n<doi:10.1093/sysbio/syw022>.",
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  "Date/Publication": "2026-04-14 14:15:46 UTC",
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  "_exports": [
    "AddFossilPoints",
    "AddStratIntervals",
    "generateMiSSEGreedyCombinations",
    "GeoHiSSE",
    "GeoHiSSE.old",
    "GetAICWeights",
    "GetFossils",
    "GetModelAveRates",
    "hisse",
    "hisse.null4.old",
    "hisse.old",
    "makeGeoHiSSELikelihood",
    "makeHiSSELikelihood",
    "MarginRecon.old",
    "MarginReconGeoSSE",
    "MarginReconGeoSSE.old",
    "MarginReconHiSSE",
    "MarginReconMiSSE",
    "MarginReconMuHiSSE",
    "MiSSE",
    "MiSSEGreedy",
    "MiSSENet",
    "MuHiSSE",
    "ParDrop",
    "ParEqual",
    "plot.geohisse.states",
    "plot.hisse.states",
    "plot.misse.states",
    "plot.muhisse.states",
    "PlotMisseSpace",
    "ProcessSimSample",
    "ProcessSimStrat",
    "PruneRedundantModels",
    "SimToPhylo",
    "SimulateGeoHiSSE",
    "SimulateHisse",
    "SummarizeMiSSEGreedy",
    "SupportRegion.old",
    "SupportRegionGeoSSE",
    "SupportRegionGeoSSE.old",
    "SupportRegionHiSSE",
    "SupportRegionMiSSE",
    "SupportRegionMuHiSSE",
    "TipCorrelation",
    "TranslateParsMakerGeoHiSSE",
    "TransMatMaker.old",
    "TransMatMakerGeoHiSSE",
    "TransMatMakerGeoHiSSE.old",
    "TransMatMakerHiSSE",
    "TransMatMakerMuHiSSE"
  ],
  "_help": [
    {
      "page": "AddFossilPoints",
      "title": "Adds sampled fossils to a complete phylogeny",
      "topics": [
        "AddFossilPoints"
      ]
    },
    {
      "page": "AddStratIntervals",
      "title": "Adds sampled stratigraphic intervals to a complete phylogeny",
      "topics": [
        "AddStratIntervals"
      ]
    },
    {
      "page": "GetAICWeights",
      "title": "Compute model weights",
      "topics": [
        "GetAICWeights"
      ]
    },
    {
      "page": "generateMiSSEGreedyCombinations",
      "title": "Combinations for Character-free State Speciation and Extinction Searching Greedily",
      "topics": [
        "generateMiSSEGreedyCombinations"
      ]
    },
    {
      "page": "GeoHiSSE",
      "title": "Hidden Geographic State Speciation and Extinction",
      "topics": [
        "GeoHiSSE"
      ]
    },
    {
      "page": "GeoHiSSE.old",
      "title": "Original Hidden Geographic State Speciation and Extinction",
      "topics": [
        "GeoHiSSE.old"
      ]
    },
    {
      "page": "GetFossils",
      "title": "Get fossilized birth-death samples",
      "topics": [
        "GetFossils"
      ]
    },
    {
      "page": "hisse",
      "title": "Hidden State Speciation and Extinction",
      "topics": [
        "hisse"
      ]
    },
    {
      "page": "hisseNull4.old",
      "title": "Original Four state trait-independent Hidden State Speciation and Extinction",
      "topics": [
        "hisse.null4.old"
      ]
    },
    {
      "page": "hisse.old",
      "title": "Original Hidden State Speciation and Extinction",
      "topics": [
        "hisse.old"
      ]
    },
    {
      "page": "makeGeoHiSSELikelihood",
      "title": "Export likelihood function for the GeoHiSSE model",
      "topics": [
        "makeGeoHiSSELikelihood"
      ]
    },
    {
      "page": "makeHiSSELikelihood",
      "title": "Export likelihood function for the HiSSE model",
      "topics": [
        "makeHiSSELikelihood"
      ]
    },
    {
      "page": "marginRecon.old",
      "title": "Original Ancestral State Estimation based on Marginal Reconstruction",
      "topics": [
        "MarginRecon.old"
      ]
    },
    {
      "page": "marginReconGeoSSE",
      "title": "Ancestral State Estimation based on Marginal Reconstruction for the GeoSSE and GeoHiSSE models.",
      "topics": [
        "MarginReconGeoSSE"
      ]
    },
    {
      "page": "marginReconGeoSSE.old",
      "title": "Original Ancestral State Estimation based on Marginal Reconstruction for the GeoSSE and GeoHiSSE models.",
      "topics": [
        "MarginReconGeoSSE.old"
      ]
    },
    {
      "page": "marginReconHiSSE",
      "title": "Ancestral State Estimation based on Marginal Reconstruction for the HiSSE model.",
      "topics": [
        "MarginReconHiSSE"
      ]
    },
    {
      "page": "marginReconMiSSE",
      "title": "Ancestral State Estimation based on Marginal Reconstruction for the MiSSE models.",
      "topics": [
        "MarginReconMiSSE"
      ]
    },
    {
      "page": "marginReconMuHiSSE",
      "title": "Ancestral State Estimation based on Marginal Reconstruction for the MuSSE and MuHiSSE models.",
      "topics": [
        "MarginReconMuHiSSE"
      ]
    },
    {
      "page": "MiSSE",
      "title": "Character-free State Speciation and Extinction",
      "topics": [
        "MiSSE"
      ]
    },
    {
      "page": "MiSSEGreedy",
      "title": "Character-free State Speciation and Extinction Searching Greedily",
      "topics": [
        "MiSSEGreedy"
      ]
    },
    {
      "page": "MiSSENet",
      "title": "A function for catching bad model fits from MiSSEGreedy",
      "topics": [
        "MiSSENet"
      ]
    },
    {
      "page": "modelAveRates",
      "title": "Model average rates at tips and nodes",
      "topics": [
        "GetModelAveRates"
      ]
    },
    {
      "page": "MuHiSSE",
      "title": "Multicharacter Hidden State Speciation and Extinction",
      "topics": [
        "MuHiSSE"
      ]
    },
    {
      "page": "plotGeoHiSSE",
      "title": "Plotting function geohisse.states objects",
      "topics": [
        "plot.geohisse.states"
      ]
    },
    {
      "page": "plotHisse",
      "title": "Plotting function hisse.states objects",
      "topics": [
        "plot.hisse.states"
      ]
    },
    {
      "page": "plotMiSSE",
      "title": "Plotting function misse.states objects",
      "topics": [
        "plot.misse.states"
      ]
    },
    {
      "page": "plotMuHiSSE",
      "title": "Plotting function muhisse.states objects",
      "topics": [
        "plot.muhisse.states"
      ]
    },
    {
      "page": "PlotMisseSpace",
      "title": "Plotting function for MiSSEGreedy",
      "topics": [
        "PlotMisseSpace"
      ]
    },
    {
      "page": "ProcessSimSample",
      "title": "Process fossilized birth-death sample of lineages",
      "topics": [
        "ProcessSimSample"
      ]
    },
    {
      "page": "ProcessSimStrat",
      "title": "Process fossilized birth-death sample of lineages into stratigraphic intervals.",
      "topics": [
        "ProcessSimStrat"
      ]
    },
    {
      "page": "PruneRedundantModels",
      "title": "Prune Redundant Models",
      "topics": [
        "PruneRedundantModels"
      ]
    },
    {
      "page": "simToPhylo",
      "title": "Convert simulated result to a tree",
      "topics": [
        "SimToPhylo"
      ]
    },
    {
      "page": "SimulateGeoHiSSE",
      "title": "Simulate under a GeoHiSSE model",
      "concept": [
        "simulation",
        "GeoSSE",
        "GeoHiSSE"
      ],
      "topics": [
        "SimulateGeoHiSSE"
      ]
    },
    {
      "page": "simulateHisse",
      "title": "Simulate under a HiSSE model",
      "topics": [
        "SimulateHisse"
      ]
    },
    {
      "page": "SummarizeMiSSEGreedy",
      "title": "Summarize Results of the Greedy Algorithm",
      "topics": [
        "SummarizeMiSSEGreedy"
      ]
    },
    {
      "page": "supportRegion.old",
      "title": "Adaptive Sampling of the Likelihood Surface",
      "topics": [
        "SupportRegion.old"
      ]
    },
    {
      "page": "supportRegionGeoSSE",
      "title": "Adaptive Sampling of the Likelihood Surface under the new version of GeoHiSSE model",
      "topics": [
        "SupportRegionGeoSSE"
      ]
    },
    {
      "page": "supportRegionGeoSSE.old",
      "title": "Adaptive Sampling of the Likelihood Surface under the original GeoHiSSE model",
      "topics": [
        "SupportRegionGeoSSE.old"
      ]
    },
    {
      "page": "supportRegionHiSSE",
      "title": "Adaptive Sampling of the Likelihood Surface under the new version of HiSSE",
      "topics": [
        "SupportRegionHiSSE"
      ]
    },
    {
      "page": "supportRegionMiSSE",
      "title": "Adaptive Sampling of the Likelihood Surface under MiSSE",
      "topics": [
        "SupportRegionMiSSE"
      ]
    },
    {
      "page": "supportRegionMuHiSSE",
      "title": "Adaptive Sampling of the Likelihood Surface under MuHiSSE",
      "topics": [
        "SupportRegionMuHiSSE"
      ]
    },
    {
      "page": "TipCorrelation",
      "title": "Phylogenetic independent contrasts using tip rates",
      "topics": [
        "TipCorrelation"
      ]
    },
    {
      "page": "TranslateParsMakerGeoHiSSE",
      "title": "Key to translate GeoHiSSE into ClaSSE",
      "concept": [
        "simulation",
        "GeoSSE",
        "GeoHiSSE"
      ],
      "topics": [
        "TranslateParsMakerGeoHiSSE"
      ]
    },
    {
      "page": "transMat",
      "title": "Transition Rate matrix generator",
      "topics": [
        "ParDrop",
        "ParEqual",
        "TransMatMaker.old"
      ]
    },
    {
      "page": "transMatMakerGeoHiSSE",
      "title": "Transition Rate matrix generator for the GeoHiSSE model",
      "topics": [
        "TransMatMakerGeoHiSSE",
        "TransMatMakerGeoHiSSE.old"
      ]
    },
    {
      "page": "transMatMakerHiSSE",
      "title": "Transition Rate matrix generator for the HiSSE model",
      "topics": [
        "TransMatMakerHiSSE"
      ]
    },
    {
      "page": "transMatMakerMuHiSSE",
      "title": "Transition Rate matrix generator for the MuHiSSE model",
      "topics": [
        "TransMatMakerMuHiSSE"
      ]
    }
  ],
  "_readme": "https://github.com/thej022214/hisse/raw/HEAD/README.md",
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