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  "Title": "Analysis and Visualization of Macroevolutionary Dynamics on\nPhylogenetic Trees",
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  "Description": "Provides functions for analyzing and visualizing complex\nmacroevolutionary dynamics on phylogenetic trees. It is a\ncompanion package to the command line program BAMM (Bayesian\nAnalysis of Macroevolutionary Mixtures) and is entirely\noriented towards the analysis, interpretation, and\nvisualization of evolutionary rates. Functionality includes\nvisualization of rate shifts on phylogenies, estimating\nevolutionary rates through time, comparing posterior\ndistributions of evolutionary rates across clades, comparing\ndiversification models using Bayes factors, and more.",
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  "Maintainer": "Pascal Title <ptitle@umich.edu>",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2024-09-13 02:54:08 UTC",
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    "addBAMMshifts",
    "assignColorBreaks",
    "BAMMlikelihood",
    "cohorts",
    "computeBayesFactors",
    "credibleShiftSet",
    "cumulativeShiftProbsTree",
    "distinctShiftConfigurations",
    "dtRates",
    "generateControlFile",
    "getBestShiftConfiguration",
    "getBranchShiftPriors",
    "getCladeRates",
    "getCohortMatrix",
    "getEventData",
    "getJenksBreaks",
    "getMarginalBranchRateMatrix",
    "getMeanBranchLengthTree",
    "getmrca",
    "getRateThroughTimeMatrix",
    "getShiftNodesFromIndex",
    "getTipRates",
    "marginalOddsRatioBranches",
    "marginalShiftProbsTree",
    "maximumShiftCredibility",
    "plot.bammdata",
    "plot.bammshifts",
    "plot.credibleshiftset",
    "plotPrior",
    "plotRateThroughTime",
    "ratesHistogram",
    "richColors",
    "samplingProbs",
    "setBAMMpriors",
    "speciesByRatesMatrix",
    "stepBF",
    "subsetEventData",
    "subtreeBAMM",
    "testTimeVariableBranches",
    "traitDependentBAMM",
    "transparentColor",
    "writeEventData"
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      "page": "addBAMMlegend",
      "title": "Add a color legend to a phylo-rate plot",
      "topics": [
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      ]
    },
    {
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      "title": "Add 'BAMM'-inferred rate shifts to a phylogeny plot",
      "topics": [
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      "page": "assignColorBreaks",
      "title": "Map macroevolutionary rates to colors",
      "topics": [
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    {
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      "title": "Calculate 'BAMM' likelihood",
      "topics": [
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    {
      "page": "BAMMtools",
      "title": "BAMMtools",
      "topics": [
        "BAMMtools-package",
        "BAMMtools"
      ]
    },
    {
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      "title": "BAMMtools datasets",
      "topics": [
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        "events.fishes",
        "events.primates",
        "events.whales",
        "fishes",
        "mass.primates",
        "mcmc.primates",
        "mcmc.whales",
        "primates",
        "traits.fishes",
        "whales"
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    {
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      "title": "Visualize macroevolutionary cohorts",
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      "title": "Identify distinct rate shift configurations",
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      "title": "Calculate macroevolutionary rate changes on a phylogeny from 'BAMM' output",
      "topics": [
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      "title": "Generate control file for 'BAMM'",
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      "page": "getBestShiftConfiguration",
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      "title": "Compute prior odds of a rate shift on each branch of a phylogeny from BAMM output",
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    {
      "page": "getCladeRates",
      "title": "Compute clade-specific mean rates",
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      "title": "Compute the pairwise correlation in rate regimes between all tips in a 'bammdata' object",
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      "title": "Create 'bammdata' object from MCMC output",
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      "topics": [
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    {
      "page": "getMeanBranchLengthTree",
      "title": "Compute phylogeny with branch lengths equal to corresponding macroevolutionary rate estimates",
      "topics": [
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      "page": "getmrca",
      "title": "Find most recent common ancestors",
      "topics": [
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    {
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      "title": "Generate rate-through-time matrix from 'bammdata' object",
      "topics": [
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    {
      "page": "getShiftNodesFromIndex",
      "title": "Identify nodes associated with rate shifts from 'bammdata' object",
      "topics": [
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      "page": "getTipRates",
      "title": "Compute tip-specific macroevolutionary rates from 'bammdata' object",
      "topics": [
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    {
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    {
      "page": "maximumShiftCredibility",
      "title": "Estimate maximum shift credibility configuration",
      "topics": [
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    },
    {
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    {
      "page": "plot.bammshifts",
      "title": "Plot distinct rate shift configurations on a phylogeny",
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    {
      "page": "plot.credibleshiftset",
      "title": "Plot credible set of rate shift configurations from 'BAMM' analysis",
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    {
      "page": "plotPrior",
      "title": "Plot the prior and posterior distribution of shifts",
      "topics": [
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    {
      "page": "plotRateThroughTime",
      "title": "Plot rates through time",
      "topics": [
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    },
    {
      "page": "ratesHistogram",
      "title": "Histogram of 'BAMM' rate frequencies",
      "topics": [
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      "page": "richColors",
      "title": "Rich color palette",
      "topics": [
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      "title": "Creates clade-specific sampling fractions",
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    {
      "page": "setBAMMpriors",
      "title": "Set BAMM Priors",
      "topics": [
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    {
      "page": "speciesByRatesMatrix",
      "title": "Compute species-specific rate through time trajectories",
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    },
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      "page": "stepBF",
      "title": "Identify the optimal number of shifts using Bayes factors",
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      "page": "subsetEventData",
      "title": "Subset a 'bammdata' object",
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      "page": "subtreeBAMM",
      "title": "Pulls out a subtree from 'bammdata' object",
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        "summary.credibleshiftset"
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