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  "Date": "2026-05-08",
  "Title": "Phylogenetic Tools for Comparative Biology (and Other Things)",
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  "Description": "A wide range of methods for phylogenetic analysis -\nconcentrated in phylogenetic comparative biology, but also\nincluding numerous techniques for visualizing, analyzing,\nmanipulating, reading or writing, and even inferring\nphylogenetic trees. Included among the functions in\nphylogenetic comparative biology are various for ancestral\nstate reconstruction, model-fitting, and simulation of\nphylogenies and trait data. A broad range of plotting methods\nfor phylogenies and comparative data include (but are not\nrestricted to) methods for mapping trait evolution on trees,\nfor projecting trees into phenotype space or a onto a\ngeographic map, and for visualizing correlated speciation\nbetween trees. Lastly, numerous functions are designed for\nreading, writing, analyzing, inferring, simulating, and\nmanipulating phylogenetic trees and comparative data. For\ninstance, there are functions for computing consensus\nphylogenies from a set, for simulating phylogenetic trees and\ndata under a range of models, for randomly or non-randomly\nattaching species or clades to a tree, as well as for a wide\nrange of other manipulations and analyses that phylogenetic\nbiologists might find useful in their research.",
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      "file": "anoletree.rda",
      "class": [
        "simmap",
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ant.geog",
      "title": "Phylogenetic datasets",
      "object": "ant.geog",
      "file": "ant.geog.rda",
      "class": [
        "factor"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "ant.tree",
      "title": "Phylogenetic datasets",
      "object": "ant.tree",
      "file": "ant.tree.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "bat_virus.data",
      "title": "Phylogenetic datasets",
      "object": "bat_virus.data",
      "file": "bat_virus.data.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Bats",
        "betaCoVs"
      ],
      "rows": 17,
      "table": true,
      "tojson": true
    },
    {
      "name": "bat.tree",
      "title": "Phylogenetic datasets",
      "object": "bat.tree",
      "file": "bat.tree.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "betaCoV.tree",
      "title": "Phylogenetic datasets",
      "object": "betaCoV.tree",
      "file": "betaCoV.tree.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "bonyfish.data",
      "title": "Phylogenetic datasets",
      "object": "bonyfish.data",
      "file": "bonyfish.data.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "spawning_mode",
        "paternal_care"
      ],
      "rows": 90,
      "table": true,
      "tojson": true
    },
    {
      "name": "bonyfish.tree",
      "title": "Phylogenetic datasets",
      "object": "bonyfish.tree",
      "file": "bonyfish.tree.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "butterfly.data",
      "title": "Phylogenetic datasets",
      "object": "butterfly.data",
      "file": "butterfly.data.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "habitat"
      ],
      "rows": 287,
      "table": true,
      "tojson": true
    },
    {
      "name": "butterfly.tree",
      "title": "Phylogenetic datasets",
      "object": "butterfly.tree",
      "file": "butterfly.tree.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "cordylid.data",
      "title": "Phylogenetic datasets",
      "object": "cordylid.data",
      "file": "cordylid.data.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "pPC1",
        "pPC2",
        "pPC3"
      ],
      "rows": 28,
      "table": true,
      "tojson": true
    },
    {
      "name": "cordylid.tree",
      "title": "Phylogenetic datasets",
      "object": "cordylid.tree",
      "file": "cordylid.tree.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "darter.tree",
      "title": "Phylogenetic datasets",
      "object": "darter.tree",
      "file": "darter.tree.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "eel.data",
      "title": "Phylogenetic datasets",
      "object": "eel.data",
      "file": "eel.data.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "feed_mode",
        "Max_TL_cm"
      ],
      "rows": 61,
      "table": true,
      "tojson": true
    },
    {
      "name": "eel.tree",
      "title": "Phylogenetic datasets",
      "object": "eel.tree",
      "file": "eel.tree.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "elapidae.tree",
      "title": "Phylogenetic datasets",
      "object": "elapidae.tree",
      "file": "elapidae.tree.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "flatworm.data",
      "title": "Phylogenetic datasets",
      "object": "flatworm.data",
      "file": "flatworm.data.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Habitat"
      ],
      "rows": 28,
      "table": true,
      "tojson": true
    },
    {
      "name": "flatworm.tree",
      "title": "Phylogenetic datasets",
      "object": "flatworm.tree",
      "file": "flatworm.tree.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "liolaemid.data",
      "title": "Phylogenetic datasets",
      "object": "liolaemid.data",
      "file": "liolaemid.data.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "parity_mode",
        "max_altitude",
        "temperature"
      ],
      "rows": 258,
      "table": true,
      "tojson": true
    },
    {
      "name": "liolaemid.tree",
      "title": "Phylogenetic datasets",
      "object": "liolaemid.tree",
      "file": "liolaemid.tree.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "mammal.data",
      "title": "Phylogenetic datasets",
      "object": "mammal.data",
      "file": "mammal.data.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "bodyMass",
        "homeRange"
      ],
      "rows": 49,
      "table": true,
      "tojson": true
    },
    {
      "name": "mammal.geog",
      "title": "Phylogenetic datasets",
      "object": "mammal.geog",
      "file": "mammal.geog.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "lat",
        "long"
      ],
      "rows": 72,
      "table": true,
      "tojson": true
    },
    {
      "name": "mammal.tree",
      "title": "Phylogenetic datasets",
      "object": "mammal.tree",
      "file": "mammal.tree.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "primate.data",
      "title": "Phylogenetic datasets",
      "object": "primate.data",
      "file": "primate.data.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Group",
        "Skull_length",
        "Optic_foramen_area",
        "Orbit_area",
        "Activity_pattern",
        "Activity_pattern_code"
      ],
      "rows": 90,
      "table": true,
      "tojson": true
    },
    {
      "name": "primate.tree",
      "title": "Phylogenetic datasets",
      "object": "primate.tree",
      "file": "primate.tree.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "salamanders",
      "title": "Phylogenetic datasets",
      "object": "salamanders",
      "file": "salamanders.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "sunfish.data",
      "title": "Phylogenetic datasets",
      "object": "sunfish.data",
      "file": "sunfish.data.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "feeding.mode",
        "gape.width",
        "buccal.length"
      ],
      "rows": 28,
      "table": true,
      "tojson": true
    },
    {
      "name": "sunfish.tree",
      "title": "Phylogenetic datasets",
      "object": "sunfish.tree",
      "file": "sunfish.tree.rda",
      "class": [
        "simmap",
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "tortoise.geog",
      "title": "Phylogenetic datasets",
      "object": "tortoise.geog",
      "file": "tortoise.geog.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "lat",
        "long"
      ],
      "rows": 15,
      "table": true,
      "tojson": true
    },
    {
      "name": "tortoise.tree",
      "title": "Phylogenetic datasets",
      "object": "tortoise.tree",
      "file": "tortoise.tree.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "tropidurid.data",
      "title": "Phylogenetic datasets",
      "object": "tropidurid.data",
      "file": "tropidurid.data.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "newsize",
        "body_height"
      ],
      "rows": 76,
      "table": true,
      "tojson": true
    },
    {
      "name": "tropidurid.tree",
      "title": "Phylogenetic datasets",
      "object": "tropidurid.tree",
      "file": "tropidurid.tree.rda",
      "class": [
        "simmap",
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "vertebrate.data",
      "title": "Phylogenetic datasets",
      "object": "vertebrate.data",
      "file": "vertebrate.data.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Mass",
        "Length",
        "Litter_size"
      ],
      "rows": 11,
      "table": true,
      "tojson": true
    },
    {
      "name": "vertebrate.tree",
      "title": "Phylogenetic datasets",
      "object": "vertebrate.tree",
      "file": "vertebrate.tree.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "wasp.data",
      "title": "Phylogenetic datasets",
      "object": "wasp.data",
      "file": "wasp.data.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Pleistodontes",
        "Sycoscapter"
      ],
      "rows": 15,
      "table": true,
      "tojson": true
    },
    {
      "name": "wasp.trees",
      "title": "Phylogenetic datasets",
      "object": "wasp.trees",
      "file": "wasp.trees.rda",
      "class": [
        "multiPhylo"
      ],
      "fields": [],
      "table": true,
      "tojson": false
    },
    {
      "name": "whale.tree",
      "title": "Phylogenetic datasets",
      "object": "whale.tree",
      "file": "whale.tree.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "phytools-package",
      "title": "phytools: Phylogenetic Tools for comparative biology (and other things)",
      "topics": [
        "phytools-package",
        "phytools"
      ]
    },
    {
      "page": "add.arrow",
      "title": "Add an arrow pointing to a tip or node on the tree",
      "topics": [
        "add.arrow"
      ]
    },
    {
      "page": "add.color.bar",
      "title": "Add color bar to a plot",
      "topics": [
        "add.color.bar"
      ]
    },
    {
      "page": "add.everywhere",
      "title": "Add tip to all edges in a tree",
      "topics": [
        "add.everywhere"
      ]
    },
    {
      "page": "add.random",
      "title": "Add tips at random to the tree",
      "topics": [
        "add.random"
      ]
    },
    {
      "page": "add.simmap.legend",
      "title": "Add legend to stochastically mapped tree",
      "topics": [
        "add.simmap.legend"
      ]
    },
    {
      "page": "add.species.to.genus",
      "title": "Add species to genus on a phylogeny or bind simulated species subtrees to a backbone genus tree",
      "topics": [
        "add.species.to.genus",
        "genus.to.species.tree"
      ]
    },
    {
      "page": "aic.w",
      "title": "Computes Akaike weights",
      "topics": [
        "aic.w"
      ]
    },
    {
      "page": "allFurcTrees",
      "title": "Generate all bi- and multifurcating unrooted trees",
      "topics": [
        "allFurcTrees"
      ]
    },
    {
      "page": "anc.Bayes",
      "title": "Bayesian ancestral character estimation",
      "topics": [
        "anc.Bayes",
        "density.anc.Bayes",
        "plot.anc.Bayes"
      ]
    },
    {
      "page": "anc.ML",
      "title": "Ancestral character estimation using likelihood",
      "topics": [
        "anc.ML"
      ]
    },
    {
      "page": "anc.trend",
      "title": "Ancestral character estimation with a trend",
      "topics": [
        "anc.trend"
      ]
    },
    {
      "page": "ancr",
      "title": "Compute marginal or joint ancestral state estimates",
      "topics": [
        "ancr",
        "hide.hidden",
        "plot.ancr"
      ]
    },
    {
      "page": "ancThresh",
      "title": "Ancestral character estimation under the threshold model using Bayesian MCMC",
      "topics": [
        "ancThresh"
      ]
    },
    {
      "page": "anoletree",
      "title": "Phylogenetic datasets",
      "topics": [
        "anole.data",
        "anoletree",
        "ant.geog",
        "ant.tree",
        "bat.tree",
        "bat_virus.data",
        "betaCoV.tree",
        "bonyfish.data",
        "bonyfish.tree",
        "butterfly.data",
        "butterfly.tree",
        "cordylid.data",
        "cordylid.tree",
        "darter.tree",
        "eel.data",
        "eel.tree",
        "elapidae.tree",
        "flatworm.data",
        "flatworm.tree",
        "liolaemid.data",
        "liolaemid.tree",
        "mammal.data",
        "mammal.geog",
        "mammal.tree",
        "primate.data",
        "primate.tree",
        "salamanders",
        "sunfish.data",
        "sunfish.tree",
        "tortoise.geog",
        "tortoise.tree",
        "tropidurid.data",
        "tropidurid.tree",
        "vertebrate.data",
        "vertebrate.tree",
        "wasp.data",
        "wasp.trees",
        "whale.tree"
      ]
    },
    {
      "page": "ansi_phylo",
      "title": "Graph a phylogeny using only ANSI characters",
      "topics": [
        "ansi_phylo"
      ]
    },
    {
      "page": "applyBranchLengths",
      "title": "Applies the branch lengths of a reference tree to a target",
      "topics": [
        "applyBranchLengths"
      ]
    },
    {
      "page": "as.multiPhylo",
      "title": "Conversion to object of class '\"multiPhylo\"'",
      "topics": [
        "as.multiPhylo",
        "as.multiPhylo.multiSimmap",
        "as.multiPhylo.phylo"
      ]
    },
    {
      "page": "as.Qmatrix",
      "title": "Convert a fitted M_k_ model to a Q-matrix",
      "topics": [
        "as.Qmatrix",
        "as.Qmatrix.fitMk",
        "plot.Qmatrix",
        "print.Qmatrix"
      ]
    },
    {
      "page": "ave.rates",
      "title": "Average the posterior rates",
      "topics": [
        "ave.rates"
      ]
    },
    {
      "page": "averageTree",
      "title": "Compute an average tree from a set of trees and related operations",
      "topics": [
        "averageTree",
        "ls.consensus",
        "minTreeDist"
      ]
    },
    {
      "page": "bd",
      "title": "Convert object of class '\"birthdeath\"' to raw birth & death rates",
      "topics": [
        "bd"
      ]
    },
    {
      "page": "bind.tip",
      "title": "Attaches a new tip to a tree",
      "topics": [
        "bind.tip"
      ]
    },
    {
      "page": "bind.tree.simmap",
      "title": "Binds two trees of class '\"simmap\"'",
      "topics": [
        "bind.tree.simmap"
      ]
    },
    {
      "page": "bmPlot",
      "title": "Simulates and visualizes continuous trait evolution on a phylogeny",
      "topics": [
        "bmPlot",
        "sim.absorbing",
        "sim.multiTrend",
        "sim.reflective"
      ]
    },
    {
      "page": "bounded_bm",
      "title": "Fits bounded and wrapped Brownian motion models",
      "topics": [
        "bounded_bm"
      ]
    },
    {
      "page": "branching.diffusion",
      "title": "Animation of branching random diffusion",
      "topics": [
        "branching.diffusion"
      ]
    },
    {
      "page": "brownie.lite",
      "title": "Likelihood test for rate variation in a continuous trait",
      "topics": [
        "brownie.lite"
      ]
    },
    {
      "page": "brownieREML",
      "title": "REML version of 'brownie.lite'",
      "topics": [
        "brownieREML"
      ]
    },
    {
      "page": "cladelabels",
      "title": "Add labels to subtrees of a plotted phylogeny",
      "topics": [
        "arc.cladelabels",
        "cladebox",
        "cladelabels"
      ]
    },
    {
      "page": "collapse.to.star",
      "title": "Collapse a subtree to a star phylogeny",
      "topics": [
        "collapse.to.star"
      ]
    },
    {
      "page": "collapseTree",
      "title": "Interactive tree visualizer",
      "topics": [
        "collapseTree"
      ]
    },
    {
      "page": "compare.chronograms",
      "title": "Compares two chronograms with precisely matching nodes in a visual manner",
      "topics": [
        "compare.chronograms"
      ]
    },
    {
      "page": "consensus.edges",
      "title": "Compute consensus edges for a tree under some criterion",
      "topics": [
        "consensus.edges"
      ]
    },
    {
      "page": "contMap",
      "title": "Map continuous trait evolution on the tree",
      "topics": [
        "contMap",
        "errorbar.contMap",
        "plot.contMap"
      ]
    },
    {
      "page": "cophylo",
      "title": "Creates a co-phylogenetic plot",
      "topics": [
        "cophylo",
        "cotangleplot",
        "plot.cophylo"
      ]
    },
    {
      "page": "cospeciation",
      "title": "Conducts a statistical test of cospeciation between two trees",
      "topics": [
        "cospeciation",
        "plot.cospeciation",
        "print.cospeciation"
      ]
    },
    {
      "page": "countSimmap",
      "title": "Counts the number of character changes on a object of class '\"simmap\"' or '\"multiSimmap\"'",
      "topics": [
        "countSimmap"
      ]
    },
    {
      "page": "ctt",
      "title": "Generates (or simulates) a 'changes through time' plot from a set of stochastic map character histories",
      "topics": [
        "ctt",
        "sim.ctt",
        "sim.multiCtt"
      ]
    },
    {
      "page": "density.multiSimmap",
      "title": "Computes a posterior distribution for the number and types of changes on the tree",
      "topics": [
        "density.multiSimmap",
        "plot.changesMap"
      ]
    },
    {
      "page": "densityMap",
      "title": "Plot posterior density of stochastic mapping on a tree",
      "topics": [
        "densityMap",
        "plot.densityMap"
      ]
    },
    {
      "page": "densityTree",
      "title": "Plots a posterior sample of trees",
      "topics": [
        "densityTree",
        "make.transparent"
      ]
    },
    {
      "page": "describe.simmap",
      "title": "Summarizes a stochastic mapped tree or set of trees",
      "topics": [
        "describe.simmap",
        "plot.describe.simmap",
        "summary.multiSimmap",
        "summary.simmap"
      ]
    },
    {
      "page": "di2multi.simmap",
      "title": "Collapse or resolve polytomies in a tree with a character painted on the edges",
      "topics": [
        "di2multi.contMap",
        "di2multi.densityMap",
        "di2multi.multiSimmap",
        "di2multi.simmap",
        "multi2di.contMap",
        "multi2di.densityMap",
        "multi2di.multiSimmap",
        "multi2di.simmap"
      ]
    },
    {
      "page": "dotTree",
      "title": "Creates a phylogenetic dot plot",
      "topics": [
        "dot.legend",
        "dotTree"
      ]
    },
    {
      "page": "drop.clade",
      "title": "Drop a clade from a tree",
      "topics": [
        "drop.clade"
      ]
    },
    {
      "page": "drop.leaves",
      "title": "Drop all the leaves (tips) from a tree",
      "topics": [
        "drop.leaves"
      ]
    },
    {
      "page": "drop.tip.contMap",
      "title": "Drop tip or tips from an object of class '\"contMap\"' or '\"densityMap\"'",
      "topics": [
        "drop.tip.contMap",
        "drop.tip.densityMap",
        "keep.tip.contMap",
        "keep.tip.densityMap"
      ]
    },
    {
      "page": "drop.tip.multiSimmap",
      "title": "Drop or keep tip or tips from an object of class '\"multiSimmap\"'",
      "topics": [
        "drop.tip.multiSimmap",
        "keep.tip.multiSimmap"
      ]
    },
    {
      "page": "drop.tip.simmap",
      "title": "Drop tips or extract clade from tree with mapped discrete character",
      "topics": [
        "drop.tip.simmap",
        "extract.clade.simmap",
        "keep.tip.simmap"
      ]
    },
    {
      "page": "Dtest",
      "title": "Conducts correlational D-test from stochastic mapping",
      "topics": [
        "Dtest"
      ]
    },
    {
      "page": "edge.widthMap",
      "title": "Map continuous trait evolution on the tree",
      "topics": [
        "edge.widthMap",
        "plot.edge.widthMap"
      ]
    },
    {
      "page": "edgeProbs",
      "title": "Compute the relative frequencies of state changes along edges",
      "topics": [
        "edgeProbs"
      ]
    },
    {
      "page": "estDiversity",
      "title": "Estimate diversity at each node of the tree",
      "topics": [
        "estDiversity"
      ]
    },
    {
      "page": "evol.rate.mcmc",
      "title": "Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny",
      "topics": [
        "evol.rate.mcmc",
        "plot.summary.evol.rate.mcmc",
        "print.evol.rate.mcmc",
        "print.summary.evol.rate.mcmc",
        "summary.evol.rate.mcmc"
      ]
    },
    {
      "page": "evol.vcv",
      "title": "Likelihood test for variation in the evolutionary variance-covariance matrix",
      "topics": [
        "evol.vcv"
      ]
    },
    {
      "page": "evolvcv.lite",
      "title": "Likelihood test for a shift in the evolutionary correlation between traits",
      "topics": [
        "evolvcv.lite"
      ]
    },
    {
      "page": "exhaustiveMP",
      "title": "Exhaustive and branch & bound MP optimization",
      "topics": [
        "exhaustiveMP"
      ]
    },
    {
      "page": "expand.clade",
      "title": "Expands (or contracts) the tip-spacing of a given clade or clades",
      "topics": [
        "expand.clade",
        "plot.expand.clade"
      ]
    },
    {
      "page": "export.as.xml",
      "title": "Export trees & data in XML format",
      "topics": [
        "export.as.xml"
      ]
    },
    {
      "page": "fancyTree",
      "title": "Plots special types of phylogenetic trees",
      "topics": [
        "fancyTree",
        "phenogram95",
        "phyloScattergram"
      ]
    },
    {
      "page": "fastAnc",
      "title": "(Reasonably) fast estimation of ML ancestral states",
      "topics": [
        "fastAnc"
      ]
    },
    {
      "page": "fastBM",
      "title": "(Reasonably) fast quantitative trait simulation on phylogenies",
      "topics": [
        "fastBM"
      ]
    },
    {
      "page": "fastMRCA",
      "title": "Get the MRCA (or height above the root of the MRCA) of a pair of tip taxa",
      "topics": [
        "fastDist",
        "fastHeight",
        "fastMRCA"
      ]
    },
    {
      "page": "findMRCA",
      "title": "Get the MRCA of a set of taxa",
      "topics": [
        "findMRCA"
      ]
    },
    {
      "page": "fit.bd",
      "title": "Fits birth-death (speciation/extinction) model to reconstructed phylogeny",
      "topics": [
        "fit.bd",
        "fit.yule",
        "lik.bd",
        "print.fit.bd"
      ]
    },
    {
      "page": "fitBayes",
      "title": "Evolutionary model fitting with intraspecific variability using Bayesian MCMC",
      "topics": [
        "fitBayes"
      ]
    },
    {
      "page": "fitcontMk",
      "title": "Fits binary discrete character evolution model where the transition rate varies as a function of a continuous trait",
      "topics": [
        "fitcontMk"
      ]
    },
    {
      "page": "fitDiversityModel",
      "title": "Fit diversity-dependent phenotypic evolution model",
      "topics": [
        "fitDiversityModel",
        "logLik.fitDiversityModel",
        "print.fitDiversityModel"
      ]
    },
    {
      "page": "fitMk",
      "title": "Fits extended M_k_ model for discrete character evolution",
      "topics": [
        "density.mcmcMk",
        "fitfnMk",
        "fitgammaMk",
        "fitHRM",
        "fitMk",
        "fitMk.parallel",
        "fitmultiMk",
        "fitpolyMk",
        "graph.polyMk",
        "mcmcMk",
        "plot.density.mcmcMk",
        "plot.fitHRM",
        "plot.fitMk",
        "plot.fitpolyMk",
        "plot.gfit",
        "plot.mcmcMk"
      ]
    },
    {
      "page": "fitmultiBM",
      "title": "Fits multi-rate (or multi-trend) discrete character dependent continuous trait evolution",
      "topics": [
        "fitmultiBM",
        "fitmultiTrend"
      ]
    },
    {
      "page": "fitPagel",
      "title": "Function to test for correlated evolution of binary traits",
      "topics": [
        "fitPagel",
        "plot.fitPagel"
      ]
    },
    {
      "page": "fitThresh",
      "title": "Fits binary, multi-state, and semi-threshold models using the discretized diffusion approximation",
      "topics": [
        "fitsemiThresh",
        "fitThresh"
      ]
    },
    {
      "page": "force.ultrametric",
      "title": "Coerces a phylogenetic tree to be ultrametric",
      "topics": [
        "force.ultrametric"
      ]
    },
    {
      "page": "gamma_pruning",
      "title": "Internally used function",
      "topics": [
        "gamma_pruning"
      ]
    },
    {
      "page": "gammatest",
      "title": "gamma test of Pybus & Harvey (2000)",
      "topics": [
        "gammatest"
      ]
    },
    {
      "page": "genSeq",
      "title": "Simulate a DNA alignment on the tree under a model",
      "topics": [
        "genSeq"
      ]
    },
    {
      "page": "geo.legend",
      "title": "Adds a geological (or other temporal) legend to a plotted tree",
      "topics": [
        "geo.legend",
        "geo.palette"
      ]
    },
    {
      "page": "get.treepos",
      "title": "Get position or node of a plotted tree interactively",
      "topics": [
        "get.treepos",
        "getnode"
      ]
    },
    {
      "page": "getCladesofSize",
      "title": "Get all subtrees larger than or equal to a specified size",
      "topics": [
        "getCladesofSize"
      ]
    },
    {
      "page": "getDescendants",
      "title": "Get descendant node numbers",
      "topics": [
        "getDescendants",
        "getParent"
      ]
    },
    {
      "page": "getExtant",
      "title": "Returns a list of the extant or extinct lineages in a tree containing non-contemporaneous tips",
      "topics": [
        "getExtant",
        "getExtinct"
      ]
    },
    {
      "page": "getSisters",
      "title": "Get the sister node number, label, or set of nodes for a node or tip",
      "topics": [
        "getSisters"
      ]
    },
    {
      "page": "getStates",
      "title": "Get the states at nodes or tips from a mapped tree",
      "topics": [
        "getStates"
      ]
    },
    {
      "page": "labelnodes",
      "title": "Function to interactively label nodes of a plotted tree",
      "topics": [
        "labelnodes"
      ]
    },
    {
      "page": "ladderize.simmap",
      "title": "Ladderize a tree with a mapped discrete character",
      "topics": [
        "ladderize.simmap"
      ]
    },
    {
      "page": "lambda.transform",
      "title": "lambda transformation of matrix",
      "topics": [
        "lambda.transform"
      ]
    },
    {
      "page": "likMlambda",
      "title": "Likelihood for joint lambda",
      "topics": [
        "likMlambda"
      ]
    },
    {
      "page": "linklabels",
      "title": "Function to add tip labels to a plotted tree with linking lines",
      "topics": [
        "linklabels"
      ]
    },
    {
      "page": "locate.fossil",
      "title": "Locate a fossil lineage in a tree using continuous characters",
      "topics": [
        "locate.fossil"
      ]
    },
    {
      "page": "locate.yeti",
      "title": "Locate a cryptic, recently extinct, or missing taxon on a tree",
      "topics": [
        "locate.yeti"
      ]
    },
    {
      "page": "ls.tree",
      "title": "Least squares branch lengths for a given tree",
      "topics": [
        "ls.tree"
      ]
    },
    {
      "page": "ltt",
      "title": "Creates lineage-through-time plot (including extinct lineages)",
      "topics": [
        "gtt",
        "ltt",
        "ltt.multiPhylo",
        "ltt.multiSimmap",
        "ltt.phylo",
        "ltt.simmap",
        "mccr"
      ]
    },
    {
      "page": "ltt95",
      "title": "Creates a (1-alpha)% CI for a set of LTTs",
      "topics": [
        "ltt95",
        "plot.ltt95"
      ]
    },
    {
      "page": "make.era.map",
      "title": "Create \"era\" map on a phylogenetic tree",
      "topics": [
        "make.era.map"
      ]
    },
    {
      "page": "make.simmap",
      "title": "Simulate stochastic character maps on a phylogenetic tree or trees",
      "topics": [
        "make.simmap",
        "simmap"
      ]
    },
    {
      "page": "map.overlap",
      "title": "Proportional overlap between two mapped character histories on a tree",
      "topics": [
        "Map.Overlap",
        "map.overlap"
      ]
    },
    {
      "page": "map.to.singleton",
      "title": "Converts a tree without singletons to a tree with singleton nodes",
      "topics": [
        "drop.tip.singleton",
        "map.to.singleton",
        "plotTree.singletons",
        "rootedge.to.singleton"
      ]
    },
    {
      "page": "mapped.states",
      "title": "Returns a vector, matrix, or list of the mapped states on a tree or set of trees",
      "topics": [
        "mapped.states"
      ]
    },
    {
      "page": "markChanges",
      "title": "Add marked changes to a plotted tree with mapped discrete character",
      "topics": [
        "markChanges"
      ]
    },
    {
      "page": "matchNodes",
      "title": "Matches nodes between two trees",
      "topics": [
        "matchLabels",
        "matchNodes"
      ]
    },
    {
      "page": "mergeMappedStates",
      "title": "Merge two or more mapped states into one state",
      "topics": [
        "mergeMappedStates"
      ]
    },
    {
      "page": "midpoint.root",
      "title": "Midpoint root a phylogeny",
      "topics": [
        "midpoint.root",
        "midpoint_root"
      ]
    },
    {
      "page": "minRotate",
      "title": "Rotates all nodes of the tree to minimize the difference in order with a vector",
      "topics": [
        "minRotate",
        "tipRotate"
      ]
    },
    {
      "page": "minSplit",
      "title": "Finding the minimum (median) split in the posterior sample",
      "topics": [
        "minSplit"
      ]
    },
    {
      "page": "modified.Grafen",
      "title": "Computes modified Grafen edge lengths",
      "topics": [
        "modified.Grafen",
        "node.paths"
      ]
    },
    {
      "page": "mrp.supertree",
      "title": "Matrix representation parsimony supertree estimation",
      "topics": [
        "compute.mr",
        "mrp.supertree"
      ]
    },
    {
      "page": "multi.mantel",
      "title": "Multiple matrix regression (partial Mantel test)",
      "topics": [
        "multi.mantel"
      ]
    },
    {
      "page": "multiC",
      "title": "Returns a list with phylogenetic VCV matrix for each mapped state",
      "topics": [
        "multiC"
      ]
    },
    {
      "page": "multirateBM",
      "title": "Function to fit a multi-rate Brownian evolution model",
      "topics": [
        "multirateBM"
      ]
    },
    {
      "page": "multiRF",
      "title": "Computes Robinson-Foulds distance between a set of trees",
      "topics": [
        "multiRF"
      ]
    },
    {
      "page": "nodeHeights",
      "title": "Compute the heights above the root of each node",
      "topics": [
        "nodeheight",
        "nodeHeights"
      ]
    },
    {
      "page": "nodelabels.cophylo",
      "title": "Add labels to a plotted \"cophylo\" object",
      "topics": [
        "edgelabels.cophylo",
        "nodelabels.cophylo",
        "tiplabels.cophylo"
      ]
    },
    {
      "page": "optim.phylo.ls",
      "title": "Phylogeny inference using the least squares method",
      "topics": [
        "optim.phylo.ls"
      ]
    },
    {
      "page": "orderMappedEdge",
      "title": "Order the columns of 'mapped.edge' to match across trees",
      "topics": [
        "orderMappedEdge"
      ]
    },
    {
      "page": "paintSubTree",
      "title": "Paint sub-trees with a discrete character",
      "topics": [
        "paintBranches",
        "paintSubTree"
      ]
    },
    {
      "page": "paste.tree",
      "title": "Paste two trees together",
      "topics": [
        "paste.tree"
      ]
    },
    {
      "page": "pbtree",
      "title": "Simulate pure-birth or birth-death stochastic tree or trees",
      "topics": [
        "pbtree"
      ]
    },
    {
      "page": "pgls.Ives",
      "title": "Phylogenetic regression with intraspecific sampling error",
      "topics": [
        "pgls.Ives",
        "pgls.SEy"
      ]
    },
    {
      "page": "phenogram",
      "title": "Plot traitgram (phenogram)",
      "topics": [
        "phenogram"
      ]
    },
    {
      "page": "phyl.cca",
      "title": "Phylogenetic canonical correlation analysis",
      "topics": [
        "phyl.cca"
      ]
    },
    {
      "page": "phyl.pairedttest",
      "title": "Phylogenetic paired _t_-test",
      "topics": [
        "phyl.pairedttest"
      ]
    },
    {
      "page": "phyl.pca",
      "title": "Phylogenetic principal components analysis",
      "topics": [
        "as.prcomp",
        "as.princomp",
        "biplot.phyl.pca",
        "phyl.pca",
        "scores",
        "scores.phyl.pca"
      ]
    },
    {
      "page": "phyl.resid",
      "title": "Phylogenetic size-correction via GLS regression",
      "topics": [
        "phyl.resid"
      ]
    },
    {
      "page": "phyl.RMA",
      "title": "Phylogenetic reduced major axis (RMA) regression",
      "topics": [
        "coef.phyl.RMA",
        "phyl.RMA",
        "plot.phyl.RMA"
      ]
    },
    {
      "page": "phyl.vcv",
      "title": "Compute evolutionary VCV matrix for a tree & dataset",
      "topics": [
        "phyl.vcv"
      ]
    },
    {
      "page": "phylANOVA",
      "title": "Phylogenetic ANOVA and post-hoc tests",
      "topics": [
        "phylANOVA"
      ]
    },
    {
      "page": "phylo.heatmap",
      "title": "Creates a phylogenetic heat map",
      "topics": [
        "phylo.heatmap"
      ]
    },
    {
      "page": "phylo.impute",
      "title": "Phylogenetic imputation for multivariate continuous character data",
      "topics": [
        "phylo.impute"
      ]
    },
    {
      "page": "phylo.to.map",
      "title": "Plot tree with tips linked to geographic coordinates",
      "topics": [
        "phylo.to.map",
        "plot.phylo.to.map"
      ]
    },
    {
      "page": "phylo.toBackbone",
      "title": "Converts tree to backbone or vice versa",
      "topics": [
        "backbone.toPhylo",
        "phylo.toBackbone"
      ]
    },
    {
      "page": "phyloDesign",
      "title": "Compute design matrix for least squares analyses",
      "topics": [
        "phyloDesign"
      ]
    },
    {
      "page": "phylomorphospace",
      "title": "Creates phylomorphospace plot",
      "topics": [
        "phylomorphospace",
        "project.phylomorphospace"
      ]
    },
    {
      "page": "phylomorphospace3d",
      "title": "Creates three-dimensional phylomorphospace plot",
      "topics": [
        "phylomorphospace3d"
      ]
    },
    {
      "page": "phylosig",
      "title": "Compute phylogenetic signal with two methods",
      "topics": [
        "phylosig",
        "plot.phylosig"
      ]
    },
    {
      "page": "plot.backbonePhylo",
      "title": "Plots backbone tree with triangles as clades",
      "topics": [
        "plot.backbonePhylo"
      ]
    },
    {
      "page": "plotBranchbyTrait",
      "title": "Plot branch colors by a quantitative trait or value",
      "topics": [
        "plotBranchbyTrait"
      ]
    },
    {
      "page": "plotSimmap",
      "title": "Plot stochastic character mapped tree",
      "topics": [
        "plot.multiSimmap",
        "plot.simmap",
        "plotSimmap"
      ]
    },
    {
      "page": "plotThresh",
      "title": "Tree plotting with posterior probabilities of ancestral states from the threshold model",
      "topics": [
        "plotThresh"
      ]
    },
    {
      "page": "plotTree",
      "title": "Plots rooted phylogenetic tree",
      "topics": [
        "plotTree"
      ]
    },
    {
      "page": "plotTree.datamatrix",
      "title": "Plot a tree with a discrete (or continuous) character data matrix at the tips",
      "topics": [
        "plotFanTree.wTraits",
        "plotTree.datamatrix"
      ]
    },
    {
      "page": "plotTree.errorbars",
      "title": "Plot a tree with error bars around divergence dates",
      "topics": [
        "plotTree.errorbars"
      ]
    },
    {
      "page": "plotTree.lollipop",
      "title": "Plot a tree with one or more matched lollipop plots",
      "topics": [
        "plotTree.lollipop"
      ]
    },
    {
      "page": "plotTree.wBars",
      "title": "Plot a tree with bars at the tips",
      "topics": [
        "plotTree.barplot",
        "plotTree.boxplot",
        "plotTree.wBars"
      ]
    },
    {
      "page": "posterior.evolrate",
      "title": "Analysis of the posterior sample from evol.rate.mcmc",
      "topics": [
        "posterior.evolrate"
      ]
    },
    {
      "page": "posthoc",
      "title": "Generic post-hoc test",
      "topics": [
        "posthoc"
      ]
    },
    {
      "page": "print.backbonePhylo",
      "title": "Print method for backbone phylogeny",
      "topics": [
        "print.backbonePhylo"
      ]
    },
    {
      "page": "pscore",
      "title": "Compute the parsimony score",
      "topics": [
        "pscore"
      ]
    },
    {
      "page": "ratebystate",
      "title": "Method for investigating the rate of one trait as a function of the state of another",
      "topics": [
        "ratebystate"
      ]
    },
    {
      "page": "ratebytree",
      "title": "Likelihood test for rate variation among trees, clades, or traits",
      "topics": [
        "posthoc.ratebytree",
        "ratebytree"
      ]
    },
    {
      "page": "rateshift",
      "title": "Find the temporal position of one or more rate shifts",
      "topics": [
        "likSurface.rateshift",
        "plot.rateshift",
        "rateshift"
      ]
    },
    {
      "page": "read.newick",
      "title": "Newick or Nexus style tree reader",
      "topics": [
        "read.newick",
        "readNexus"
      ]
    },
    {
      "page": "read.simmap",
      "title": "Read SIMMAP style trees from file",
      "topics": [
        "read.simmap"
      ]
    },
    {
      "page": "reorder.backbonePhylo",
      "title": "Reorders a backbone phylogeny",
      "topics": [
        "reorder.backbonePhylo"
      ]
    },
    {
      "page": "reorderSimmap",
      "title": "Reorder edges of a '\"simmap\"' tree",
      "topics": [
        "reorderSimmap"
      ]
    },
    {
      "page": "rep.phylo",
      "title": "Replicate a tree or set of trees",
      "topics": [
        "rep.multiPhylo",
        "rep.phylo",
        "repPhylo"
      ]
    },
    {
      "page": "reroot",
      "title": "Re-root a tree along an edge",
      "topics": [
        "reroot"
      ]
    },
    {
      "page": "rerootingMethod",
      "title": "Get marginal ancestral state reconstructions by re-rooting",
      "topics": [
        "rerootingMethod"
      ]
    },
    {
      "page": "rescale",
      "title": "Rescale phylogenetic objects of different types",
      "topics": [
        "rescale"
      ]
    },
    {
      "page": "rescaleSimmap",
      "title": "Rescale object of class '\"simmap\"'",
      "topics": [
        "rescale.multiSimmap",
        "rescale.simmap",
        "rescaleSimmap"
      ]
    },
    {
      "page": "resolveNode",
      "title": "Compute all possible resolutions of a node or all nodes in a multifurcating tree",
      "topics": [
        "resolveAllNodes",
        "resolveNode"
      ]
    },
    {
      "page": "rotateNodes",
      "title": "Rotates a node or set of nodes in a phylogenetic tree",
      "topics": [
        "allRotations",
        "rotate.multi",
        "rotateNodes"
      ]
    },
    {
      "page": "roundBranches",
      "title": "Rounds the branch lengths of a tree",
      "topics": [
        "roundBranches"
      ]
    },
    {
      "page": "roundPhylogram",
      "title": "Plot a round, sigmoidal, or spline phylogram or cladogram",
      "topics": [
        "roundPhylogram",
        "sigmoidPhylogram",
        "splinePhylogram"
      ]
    },
    {
      "page": "rstate",
      "title": "Pick a random state according to a vector of probabilities",
      "topics": [
        "rstate"
      ]
    },
    {
      "page": "sampleFrom",
      "title": "Sample from a set of distributions",
      "topics": [
        "sampleFrom"
      ]
    },
    {
      "page": "setMap",
      "title": "Set color map for various phylogenetic objects of classes",
      "topics": [
        "setMap",
        "setMap.contMap",
        "setMap.densityMap",
        "setMap.multirateBM_plot",
        "setMap.phyloScattergram"
      ]
    },
    {
      "page": "sim.corrs",
      "title": "Multivariate Brownian simulation with multiple correlations and rates",
      "topics": [
        "sim.corrs"
      ]
    },
    {
      "page": "sim.history",
      "title": "Simulate character history or a discrete character at the tips of the tree under some model",
      "topics": [
        "sim.history",
        "sim.Mk",
        "sim.multiMk"
      ]
    },
    {
      "page": "sim.ratebystate",
      "title": "Conduct simulation of state dependent rate variation",
      "topics": [
        "sim.ratebystate"
      ]
    },
    {
      "page": "sim.rates",
      "title": "Brownian or OU simulation with multiple evolutionary regimes",
      "topics": [
        "multiOU",
        "sim.rates"
      ]
    },
    {
      "page": "simBMphylo",
      "title": "Creates a graphical illustration of Brownian motion evolution on a phylogeny",
      "topics": [
        "plot.simBMphylo",
        "simBMphylo"
      ]
    },
    {
      "page": "skewers",
      "title": "Matrix comparison using the method of random skewers",
      "topics": [
        "skewers"
      ]
    },
    {
      "page": "splitEdgeColor",
      "title": "Split edge colors when descendant edges have different mapped states",
      "topics": [
        "splitEdgeColor"
      ]
    },
    {
      "page": "splitplotTree",
      "title": "Plots a phylogeny in two columns",
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