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  "Package": "motmot",
  "Title": "Models of Trait Macroevolution on Trees",
  "Version": "2.1.4",
  "Description": "Functions for fitting models of trait evolution on\nphylogenies for continuous traits. The majority of functions\nare described in Thomas and Freckleton (2012)\n<doi:10.1111/j.2041-210X.2011.00132.x> and allow tests of\nvariation in the rates of trait evolution.",
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  "URL": "https://puttickbiology.wordpress.com/motmot/",
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  "Author": "Mark Puttick [aut, cph] (ORCID:\n<https://orcid.org/0000-0002-1011-3442>),\nGavin Thomas [aut, cph],\nRob Freckleton [aut, cph],\nMagnus Clarke [ctb],\nTravis Ingram [ctb],\nDavid Orme [ctb],\nEmmanuel Paradis [ctb],\nMartin R. Smith [ctb, cre] (ORCID:\n<https://orcid.org/0000-0001-5660-1727>)",
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      "fields": [
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      "table": false,
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    {
      "page": "motmot-package",
      "title": "Models Of Trait Macroevolution On Trees",
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        "motmot-package",
        "motmot"
      ]
    },
    {
      "page": "addFossilToPhy",
      "title": "add a fossil to an interior branch of a time-scaled phylogeny",
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      "title": "Conversion among data and phylogeny objects",
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      "title": "Conversion among data and phylogeny objects",
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    },
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      "page": "blomberg.k",
      "title": "Blomberg's K Estimate Blomberg's K (Blomberg et al. 2003)",
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        "blomberg.k"
      ]
    },
    {
      "page": "calcCutOff",
      "title": "Calculate multiple-test cut-off",
      "topics": [
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    {
      "page": "chr.disp.lrt",
      "title": "Character displacement likelihood ratio test",
      "topics": [
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    },
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      "page": "chr.disp.param",
      "title": "Simulate character displacement data wrapper",
      "topics": [
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    },
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      "title": "Simulate character displacement data",
      "topics": [
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    {
      "page": "contemporaryPhy",
      "title": "prune tree and data to lineages present in a time bin in the past",
      "topics": [
        "contemporaryPhy"
      ]
    },
    {
      "page": "dropTipPartial",
      "title": "Drop tips from a phylogenetic tree while preserving deleted nodes",
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        "dropTipPartial"
      ]
    },
    {
      "page": "fairProportions",
      "title": "Calculate fair proportions phylogenetic diversity metric",
      "topics": [
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      ]
    },
    {
      "page": "finch.data",
      "title": "Finch phenotype data",
      "topics": [
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    },
    {
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      "title": "Log-likelihood estimation for traits and phylogenies",
      "topics": [
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    },
    {
      "page": "mcmc.plot",
      "title": "plot the output from transformPhylo.MCMC",
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    },
    {
      "page": "ML.RatePhylo",
      "title": "Maximum likelihood rate estimation for traits and phylogenies",
      "topics": [
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    },
    {
      "page": "node.descendents",
      "title": "Identify nodes and tips descended from a node",
      "topics": [
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      ]
    },
    {
      "page": "nodeTimes",
      "title": "Get times for nodes and tips",
      "topics": [
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    },
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      "page": "optim.likRatePhylo",
      "title": "Maximum likelihood rate estimation for traits and phylogenies",
      "topics": [
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    },
    {
      "page": "phyloCovar",
      "title": "Calculation of Brownian (co)variance using independent contrasts.",
      "topics": [
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    },
    {
      "page": "phyloMean",
      "title": "Calculation of phylogenetically corrected mean.",
      "topics": [
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    },
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      "title": "Calculation of Brownian variance.",
      "topics": [
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      "title": "Fast PLGS estimation based on contrasts",
      "topics": [
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      ]
    },
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      "page": "plot.timeSlice.ML",
      "title": "Identify shifts in the rate of trait diversification through time",
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      "page": "plot.traitMedusa.model",
      "title": "Tree plotting for rates",
      "topics": [
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    {
      "page": "RatePhylo.allCI",
      "title": "Confidence intervals for rate parameters",
      "topics": [
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    },
    {
      "page": "sampleShid",
      "title": "Sample hidden speciation events along branches of a tree",
      "topics": [
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    },
    {
      "page": "sortTraitData",
      "title": "Sort data and remove missing entries for tree and trait data",
      "topics": [
        "sortTraitData"
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    },
    {
      "page": "summary.traitMedusa",
      "title": "Identify shifts in the rate of trait diversification",
      "topics": [
        "summary.traitMedusa"
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    },
    {
      "page": "sympatric.data",
      "title": "Pairwise sympatry matrix for finch species",
      "topics": [
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    },
    {
      "page": "traitData.plot",
      "title": "plot a univariate continuous trait data on a phylogeny",
      "topics": [
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    },
    {
      "page": "transformPhylo",
      "title": "Phylogenetic tree transformations",
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      "page": "transformPhylo.ll",
      "title": "Log-likelhood for models of trait evolution.",
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      "source": "motmot.vignette.Rmd",
      "filename": "motmot.vignette.html",
      "title": "MOTMOT: Models Of Trait Macroevolution On Trees",
      "author": "Mark Puttick",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Models of trait evolution",
        "Brownian motion",
        "Pagel's lambda",
        "Delta",
        "Kappa",
        "Ornstein-Uhlenbeck",
        "ACDC and Early Burst",
        "psi and multispi",
        "Estimate Pagel's lambda alongside other modes",
        "Rate heterogeneous models of evolution",
        "rate heterogeneity selected a priori",
        "rate heterogeneity with no a priori information",
        "timeSlice model",
        "modeSlice model",
        "Nested models of evolution",
        "Bayesian estimation of tree transformation models",
        "Character displacement models",
        "Fast estimation of Phylogenetic Generalised Least Squares"
      ],
      "created": "2019-02-27 14:26:50",
      "modified": "2026-04-15 14:21:51",
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