{
  "_id": "6ae20bc23d0f299392dcfa2b",
  "Package": "diversitree",
  "Version": "0.10-1",
  "Title": "Comparative 'Phylogenetic' Analyses of Diversification",
  "Authors@R": "c(person(\"Richard G.\", \"FitzJohn\", role = c(\"aut\", \"cre\"),\nemail = \"rich.fitzjohn@gmail.com\"),\nperson(\"Emma\", \"Goldberg\", role = \"aut\"),\nperson(\"Karen\", \"Magnuson-Ford\", role = \"aut\"),\nperson(\"Roger\", \"Sidje\", role = \"aut\"))",
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  "SystemRequirements": "fftw3 (>= 3.1.2), gsl (>= 1.15)",
  "Description": "Contains a number of comparative 'phylogenetic' methods,\nmostly focusing on analysing diversification and character\nevolution.  Contains implementations of 'BiSSE' (Binary State\n'Speciation' and Extinction) and its unresolved tree\nextensions, 'MuSSE' (Multiple State 'Speciation' and\nExtinction), 'QuaSSE', 'GeoSSE', and 'BiSSE-ness' Other\nincluded methods include Markov models of discrete and\ncontinuous trait evolution and constant rate 'speciation' and\nextinction.",
  "License": "GPL (>= 2)",
  "URL": "https://www.zoology.ubc.ca/prog/diversitree/",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-28 09:49:43 UTC",
    "User": "root"
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  "Author": "Richard G. FitzJohn [aut, cre], Emma Goldberg [aut], Karen\nMagnuson-Ford [aut], Roger Sidje [aut]",
  "Maintainer": "Richard G. FitzJohn <rich.fitzjohn@gmail.com>",
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  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2024-10-03 03:00:50 UTC",
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  "_created": "2026-10-28T09:49:43.000Z",
  "_published": "2026-10-28T14:50:42.758Z",
  "_upstream": "https://github.com/cran/diversitree",
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    "expand.parameters",
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    "history.from.sim.discrete",
    "invert",
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    "make.asr.marginal",
    "make.asr.stoch",
    "make.bd",
    "make.bd.split",
    "make.bd.t",
    "make.bisse",
    "make.bisse.split",
    "make.bisse.t",
    "make.bisse.td",
    "make.bisse.uneven",
    "make.bisseness",
    "make.bm",
    "make.brownian.with.drift",
    "make.clade.tree",
    "make.classe",
    "make.eb",
    "make.geosse",
    "make.geosse.split",
    "make.geosse.t",
    "make.geosse.uneven",
    "make.lambda",
    "make.linear.x",
    "make.mk2",
    "make.mkn",
    "make.mkn.meristic",
    "make.mkn.multitrait",
    "make.musse",
    "make.musse.multitrait",
    "make.musse.split",
    "make.musse.t",
    "make.musse.td",
    "make.ou",
    "make.pgls",
    "make.prior.exponential",
    "make.prior.uniform",
    "make.quasse",
    "make.quasse.split",
    "make.sim.character",
    "make.yule",
    "mcmc",
    "mkn.multitrait.translate",
    "musse.multitrait.translate",
    "noroptimal.x",
    "polytomies.to.clades",
    "profiles.plot",
    "protect",
    "prune",
    "ROOT.ALL",
    "ROOT.BOTH",
    "ROOT.EQUI",
    "ROOT.FLAT",
    "ROOT.GIVEN",
    "ROOT.MAX",
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    "sigmoid.x",
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    "starting.point.bisse",
    "starting.point.classe",
    "starting.point.geosse",
    "starting.point.musse",
    "starting.point.musse.multitrait",
    "starting.point.quasse",
    "stepf.x",
    "trait.plot",
    "tree.bd",
    "tree.bisse",
    "tree.bisseness",
    "tree.classe",
    "tree.geosse",
    "tree.musse",
    "tree.musse.multitrait",
    "tree.quasse",
    "tree.yule",
    "trees"
  ],
  "_help": [
    {
      "page": "diversitree-package",
      "title": "Comparative 'Phylogenetic' Analyses of Diversification",
      "topics": [
        "diversitree-package",
        "diversitree"
      ]
    },
    {
      "page": "argnames",
      "title": "Argument Names for Vector-Argument Functions",
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        "argnames.constrained",
        "argnames<-",
        "argnames<-.constrained"
      ]
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      "title": "Ancestral State Reconstruction",
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        "make.asr.joint",
        "make.asr.marginal",
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    },
    {
      "page": "asr-bisse",
      "title": "Ancestral State Reconstruction Under BiSSE",
      "topics": [
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        "asr.marginal.bisse",
        "asr.marginal.musse",
        "asr.musse",
        "make.asr.marginal.bisse",
        "make.asr.marginal.musse"
      ]
    },
    {
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      "title": "Ancestral State Reconstruction Under Mk2/Mkn",
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        "make.asr.joint.mkn",
        "make.asr.marginal.mk2",
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        "make.asr.stoch.mkn"
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      "title": "Check Capabilities of the Diversitree Install",
      "topics": [
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    },
    {
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      "title": "Combine Several Likelihood Functions Multiplicatively",
      "topics": [
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        "constrain.i"
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      "title": "Maximimum Likelihood Inference",
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        "find.mle",
        "logLik.fit.mle"
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      "title": "Extract Character Histories From Simulations",
      "topics": [
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      ]
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    {
      "page": "make.bd",
      "title": "Constant Rate Birth-Death Models",
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    {
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      "title": "Constant Rate Birth-Death Models: Split Models",
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    {
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      "title": "Time-varing Birth-Death Models",
      "topics": [
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    },
    {
      "page": "make.bisse",
      "title": "Binary State Speciation and Extinction Model",
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        "starting.point.bisse"
      ]
    },
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      "title": "Binary State Speciation and Extinction Model: Time Dependant Models",
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      "page": "make.bm",
      "title": "Brownian Motion and Related Models of Character Evolution",
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        "make.eb",
        "make.lambda",
        "make.ou"
      ]
    },
    {
      "page": "make.clade.tree",
      "title": "Make a \"Clade Tree\"",
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        "clades.from.polytomies",
        "make.clade.tree"
      ]
    },
    {
      "page": "make.classe",
      "title": "Cladogenetic State change Speciation and Extinction Model",
      "topics": [
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        "starting.point.classe"
      ]
    },
    {
      "page": "make.geosse",
      "title": "Geographic State Speciation and Extinction Model",
      "topics": [
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        "starting.point.geosse"
      ]
    },
    {
      "page": "make.geosse.split",
      "title": "Geographic State Speciation and Extinction Model: Split Models",
      "topics": [
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        "make.geosse.uneven"
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    },
    {
      "page": "make.geosse.t",
      "title": "Geographic State Speciation and Extinction Model: Time Dependent Models",
      "topics": [
        "make.geosse.t"
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    },
    {
      "page": "make.mkn",
      "title": "Mk2 and Mk-n Models of character evolution",
      "topics": [
        "make.mk2",
        "make.mkn",
        "make.mkn.meristic"
      ]
    },
    {
      "page": "make.musse",
      "title": "MuSSE: Multi-State Speciation and Extinction",
      "topics": [
        "make.musse",
        "starting.point.musse"
      ]
    },
    {
      "page": "make.musse.multitrait",
      "title": "MuSSE: Multi-State Speciation and Extinction (Multiple Binary Traits Version)",
      "topics": [
        "make.mkn.multitrait",
        "make.musse.multitrait",
        "mkn.multitrait.translate",
        "musse.multitrait.translate",
        "starting.point.musse.multitrait"
      ]
    },
    {
      "page": "make.musse.split",
      "title": "Multiple State Speciation and Extinction Model: Split Models",
      "topics": [
        "make.musse.split"
      ]
    },
    {
      "page": "make.musse.td",
      "title": "Multiple State Speciation and Extinction Model: Time Dependent Models",
      "topics": [
        "make.musse.t",
        "make.musse.td"
      ]
    },
    {
      "page": "make.pgls",
      "title": "Phylogenetic Generalised Least Squares",
      "topics": [
        "make.pgls"
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    },
    {
      "page": "make.prior",
      "title": "Simple Prior Functions",
      "topics": [
        "make.prior",
        "make.prior.exponential",
        "make.prior.uniform"
      ]
    },
    {
      "page": "make.quasse",
      "title": "Quantitative State Speciation and Extinction Model",
      "topics": [
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        "starting.point.quasse"
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      "page": "make.quasse.split",
      "title": "Quantitative State Speciation and Extinction Model: Split Models",
      "topics": [
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    },
    {
      "page": "mcmc",
      "title": "Simple Markov Chain Monte Carlo with Slice Sampling",
      "topics": [
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        "sampler.norm",
        "sampler.slice"
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    },
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      "page": "plot.history",
      "title": "Plot Character History",
      "topics": [
        "plot.history"
      ]
    },
    {
      "page": "profiles.plot",
      "title": "Plot Marginal Distributions from MCMC",
      "topics": [
        "profiles.plot"
      ]
    },
    {
      "page": "quasse-common",
      "title": "Support Functions for QuaSSE Models",
      "topics": [
        "constant.x",
        "make.brownian.with.drift",
        "make.linear.x",
        "noroptimal.x",
        "sigmoid.x",
        "sigmoid2.x",
        "stepf.x"
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      "page": "set.defaults",
      "title": "Set Default Arguments of a Function",
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    {
      "page": "sim.character",
      "title": "Simulate a Character Distribution on a Tree",
      "topics": [
        "make.sim.character",
        "sim.character"
      ]
    },
    {
      "page": "simulate",
      "title": "Evolve Birth-Death Trees",
      "topics": [
        "prune",
        "tree.bd",
        "tree.bisse",
        "tree.bisseness",
        "tree.classe",
        "tree.geosse",
        "tree.musse",
        "tree.musse.multitrait",
        "tree.quasse",
        "tree.yule",
        "trees"
      ]
    },
    {
      "page": "trait.plot",
      "title": "Plot a Phylogeny and Traits",
      "topics": [
        "trait.plot"
      ]
    },
    {
      "page": "utils",
      "title": "Utility Functions",
      "topics": [
        "drop.likelihood",
        "expand.parameters",
        "get.descendants",
        "get.likelihood",
        "run.cached"
      ]
    }
  ],
  "_readme": "https://github.com/cran/diversitree/raw/HEAD/README.md",
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    "lattice",
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