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  "Title": "Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies",
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  "Date": "2026-02-04",
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  "Description": "Fits and simulates multi-optima Ornstein-Uhlenbeck models\nto phylogenetic comparative data using Bayesian reversible-jump\nmethods. See Uyeda and Harmon (2014)\n<DOI:10.1093/sysbio/syu057>.",
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    "bayou.makeMCMC",
    "bayou2OUwie",
    "cdpois",
    "combine.chains",
    "dataSim",
    "dhalfcauchy",
    "dloc",
    "dsb",
    "gelman.R",
    "identifyBranches",
    "load.bayou",
    "Lposterior",
    "make.powerposteriorFn",
    "make.prior",
    "make.refFn",
    "makeBayouModel",
    "makeTransparent",
    "OU.lik",
    "OUphenogram",
    "OUwie2bayou",
    "parmap.W",
    "pars2simmap",
    "phalfcauchy",
    "phenogram.density",
    "plotBayoupars",
    "plotBranchHeatMap",
    "plotOUtreesim",
    "plotRegimes",
    "plotShiftSummaries",
    "plotSimmap.mcmc",
    "priorSim",
    "pull.pars",
    "qhalfcauchy",
    "rdpois",
    "rhalfcauchy",
    "rloc",
    "rsb",
    "set.burnin",
    "shiftSummaries",
    "simmapW"
  ],
  "_help": [
    {
      "page": "bayou-package",
      "title": "Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies",
      "topics": [
        "bayou-package",
        "bayou"
      ]
    },
    {
      "page": "bayou.checkModel",
      "title": "Function for checking parameter lists, prior and models are consistent and error-free",
      "topics": [
        "bayou.checkModel"
      ]
    },
    {
      "page": "bayou.lik",
      "title": "Function for calculating likelihood of an OU model in bayou using the threepoint algorithm",
      "topics": [
        "bayou.lik"
      ]
    },
    {
      "page": "bayou.makeMCMC",
      "title": "Builds a bayouMCMCFn object that can run MCMC and stepping stone analyses.",
      "topics": [
        "bayou.makeMCMC"
      ]
    },
    {
      "page": "bayou2OUwie",
      "title": "Converts bayou data into OUwie format",
      "topics": [
        "bayou2OUwie"
      ]
    },
    {
      "page": "cdpois",
      "title": "Conditional Poisson distribution",
      "topics": [
        "cdpois",
        "rdpois"
      ]
    },
    {
      "page": "combine.chains",
      "title": "Combine mcmc chains",
      "topics": [
        "combine.chains"
      ]
    },
    {
      "page": "dataSim",
      "title": "Simulates data from bayou models",
      "topics": [
        "dataSim"
      ]
    },
    {
      "page": "dhalfcauchy",
      "title": "Half cauchy distribution taken from the R package LaplacesDemon (Hall, 2012).",
      "topics": [
        "dhalfcauchy",
        "phalfcauchy",
        "qhalfcauchy",
        "rhalfcauchy"
      ]
    },
    {
      "page": "dloc",
      "title": "Probability density function for the location of the shift along the branch",
      "topics": [
        "dloc",
        "rloc"
      ]
    },
    {
      "page": "dsb",
      "title": "Probability density functions for bayou",
      "topics": [
        "dsb",
        "rsb"
      ]
    },
    {
      "page": "gelman.R",
      "title": "Calculate Gelman's R statistic",
      "topics": [
        "gelman.R"
      ]
    },
    {
      "page": "identifyBranches",
      "title": "Identify shifts on branches of a phylogenetic tree",
      "topics": [
        "identifyBranches"
      ]
    },
    {
      "page": "load.bayou",
      "title": "Loads a bayou object",
      "topics": [
        "load.bayou"
      ]
    },
    {
      "page": "Lposterior",
      "title": "Return a posterior of shift locations",
      "topics": [
        "Lposterior"
      ]
    },
    {
      "page": "make.powerposteriorFn",
      "title": "Makes a power posterior function in bayou",
      "topics": [
        "make.powerposteriorFn"
      ]
    },
    {
      "page": "make.prior",
      "title": "Make a prior function for bayou",
      "topics": [
        "make.prior"
      ]
    },
    {
      "page": "make.refFn",
      "title": "Make a reference function in bayou",
      "topics": [
        "make.refFn"
      ]
    },
    {
      "page": "makeBayouModel",
      "title": "This function makes a bayou model object that can be used for customized allometric regression models.",
      "topics": [
        "makeBayouModel"
      ]
    },
    {
      "page": "makeTransparent",
      "title": "Make a color transparent (Taken from an answer on StackOverflow by Nick Sabbe)",
      "topics": [
        "makeTransparent"
      ]
    },
    {
      "page": "model.OU",
      "title": "Bayou Models",
      "topics": [
        "model.OU"
      ]
    },
    {
      "page": "OU.lik",
      "title": "Function for calculating likelihood of an OU model in bayou using pruning algorithm or matrix inversion",
      "topics": [
        "OU.lik"
      ]
    },
    {
      "page": "OU.repar",
      "title": "Calculates the alpha and sigma^2 from a parameter list with supplied phylogenetic half-life and stationary variance",
      "topics": [
        "OU.repar"
      ]
    },
    {
      "page": "OUphenogram",
      "title": "Experimental phenogram plotting function for set of model of model parameters",
      "topics": [
        "OUphenogram"
      ]
    },
    {
      "page": "OUwie2bayou",
      "title": "Converts OUwie data into bayou format",
      "topics": [
        "OUwie2bayou"
      ]
    },
    {
      "page": "parmap.W",
      "title": "Calculate the weight matrix of a set of regimes on a phylogeny",
      "topics": [
        "parmap.W"
      ]
    },
    {
      "page": "pars2simmap",
      "title": "Convert a bayou parameter list into a simmap formatted phylogeny",
      "topics": [
        "pars2simmap"
      ]
    },
    {
      "page": "phenogram.density",
      "title": "Plot a pheongram with the posterior density for optima values",
      "topics": [
        "phenogram.density"
      ]
    },
    {
      "page": "plot.bayouMCMC",
      "title": "S3 method for plotting bayouMCMC objects",
      "topics": [
        "plot.bayouMCMC"
      ]
    },
    {
      "page": "plot.ssMCMC",
      "title": "S3 method for plotting ssMCMC objects",
      "topics": [
        "plot.ssMCMC"
      ]
    },
    {
      "page": "plotBayoupars",
      "title": "Plot parameter list as a simmap tree",
      "topics": [
        "plotBayoupars"
      ]
    },
    {
      "page": "plotBranchHeatMap",
      "title": "A function to plot a heatmap of reconstructed parameter values on the branches of the tree",
      "topics": [
        "plotBranchHeatMap"
      ]
    },
    {
      "page": "plotOUtreesim",
      "title": "A function to visualize a multi-optimum OU process evolving on a phylogeny",
      "topics": [
        "plotOUtreesim"
      ]
    },
    {
      "page": "plotRegimes",
      "title": "Function to plot the regimes from a simmap tree",
      "topics": [
        "plotRegimes"
      ]
    },
    {
      "page": "plotShiftSummaries",
      "title": "A function to plot a list produced by 'shiftSummaries'",
      "topics": [
        "plotShiftSummaries"
      ]
    },
    {
      "page": "plotSimmap.mcmc",
      "title": "Plot a phylogenetic tree with posterior probabilities from a bayouMCMC chain (function adapted from phytools' plotSimmap)",
      "topics": [
        "plotSimmap.mcmc"
      ]
    },
    {
      "page": "print.bayouFit",
      "title": "S3 method for printing bayouFit objects",
      "topics": [
        "print.bayouFit"
      ]
    },
    {
      "page": "print.bayouMCMC",
      "title": "S3 method for printing bayouMCMC objects",
      "topics": [
        "print.bayouMCMC"
      ]
    },
    {
      "page": "print.priorFn",
      "title": "S3 method for printing priorFn objects",
      "topics": [
        "print.priorFn"
      ]
    },
    {
      "page": "print.refFn",
      "title": "S3 method for printing refFn objects",
      "topics": [
        "print.refFn"
      ]
    },
    {
      "page": "print.ssMCMC",
      "title": "S3 method for printing ssMCMC objects",
      "topics": [
        "print.ssMCMC"
      ]
    },
    {
      "page": "priorSim",
      "title": "Simulates parameters from bayou models",
      "topics": [
        "priorSim"
      ]
    },
    {
      "page": "pull.pars",
      "title": "Utility function for retrieving parameters from an MCMC chain",
      "topics": [
        "pull.pars"
      ]
    },
    {
      "page": "QG.alpha",
      "title": "Calculates the alpha parameter from a QG model",
      "topics": [
        "QG.alpha"
      ]
    },
    {
      "page": "QG.sig2",
      "title": "Calculates the sigma^2 parameter from a QG model",
      "topics": [
        "QG.sig2"
      ]
    },
    {
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      "title": "Adds visualization of regimes to a plot",
      "topics": [
        "regime.plot"
      ]
    },
    {
      "page": "set.burnin",
      "title": "Set the burnin proportion for bayouMCMC objects",
      "topics": [
        "set.burnin"
      ]
    },
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      "title": "A function for summarizing the state of a model after a shift",
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        "shiftSummaries"
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    },
    {
      "page": "simmapW",
      "title": "Calculate the weight matrix of a set of regimes on a phylogeny",
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        "simmapW"
      ]
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    {
      "page": "summary.bayouMCMC",
      "title": "S3 method for summarizing bayouMCMC objects",
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