{
  "_id": "6a129ab2acfb0bcc41d0e498",
  "Package": "apTreeshape",
  "Date": "2018-03-22",
  "Version": "1.5-0.1",
  "Title": "Analyses of Phylogenetic Treeshape",
  "Author": "Nicolas Bortolussi, Michael Blum, Eric Durand, Olivier\nFrancois, Odile Maliet",
  "Maintainer": "Michael Blum <michael.blum@univ-grenoble-alpes.fr>",
  "Description": "Simulation and analysis of phylogenetic tree topologies\nusing statistical indices. It is a companion library of the\n'ape' package. It provides additional functions for reading,\nplotting, manipulating phylogenetic trees. It also offers\nconvenient web-access to public databases, and enables testing\nnull models of macroevolution using corrected test statistics.\nTrees of class \"phylo\" (from 'ape' package) can be converted\neasily. Implements methods described in Bortolussi et al.\n(2005) <doi:10.1093/bioinformatics/bti798> and Maliet et al.\n(2017) <doi:10.1101/224295>.",
  "License": "GPL (>= 2)",
  "Encoding": "latin1",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-24 06:25:20 UTC",
    "User": "root"
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  "Config/pak/sysreqs": "make",
  "Repository": "https://phylotastic.r-universe.dev",
  "Date/Publication": "2020-10-12 13:12:28 UTC",
  "RemoteUrl": "https://github.com/cran/apTreeshape",
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  "_created": "2026-05-24T06:25:20.000Z",
  "_published": "2026-05-24T06:29:06.747Z",
  "_distro": "noble",
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    "message": "version 1.5-0.1\n",
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    {
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    {
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    "aldous.test",
    "all.equal.treeshape",
    "ancestor",
    "as.phylo.treeshape",
    "as.treeshape",
    "as.treeshape.phylo",
    "as.treeshape.treebalance",
    "cladesize",
    "colless",
    "colless.test",
    "cutreeshape",
    "Delta",
    "get_PD_sample",
    "get_tree_beta",
    "is.binary.phylo",
    "likelihood.test",
    "logratio",
    "maxlik.betasplit",
    "mcmc_alpha",
    "mcmc_eta",
    "plot.treeshape",
    "raldous",
    "rbiased",
    "rpda",
    "rtreeshape",
    "ryule",
    "sackin",
    "sackin.test",
    "shape.statistic",
    "shift.test",
    "simulate_kingman",
    "simulate_tree",
    "simulate_yule",
    "smaller.clade.spectrum",
    "smaller.clade.spectrum2",
    "spectrum.treeshape",
    "subtree.test",
    "summary.treeshape",
    "tipsubtree",
    "treebalance",
    "treeshape"
  ],
  "_datasets": [
    {
      "name": "carnivora.treeshape",
      "title": "Phylogeny of carnivores.",
      "object": "carnivora.treeshape",
      "file": "carnivora.treeshape.rda",
      "class": [
        "treeshape"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "cytochromc",
      "title": "Phylogeny of the cytochrome C family.",
      "object": "cytochromc",
      "file": "cytochromc.rda",
      "class": [
        "treeshape"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "hivtree.treeshape",
      "title": "Phylogenetic Tree of 193 HIV-1 Sequences",
      "object": "hivtree.treeshape",
      "file": "hivtree.treeshape.rda",
      "class": [
        "treeshape"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "primates",
      "title": "Phylogeny of the primates.",
      "object": "primates",
      "file": "primates.rda",
      "class": [
        "treeshape"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "rhodopsin",
      "title": "Phylogeny of rhodopsin proteins.",
      "object": "rhodopsin",
      "file": "rhodopsin.rda",
      "class": [
        "treeshape"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "universal.treeshape",
      "title": "Universal phylogenetic tree of life",
      "object": "universal.treeshape",
      "file": "universal.treeshape.rda",
      "class": [
        "treeshape"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "a_N",
      "title": "Computes a_n",
      "topics": [
        "a_N"
      ]
    },
    {
      "page": "aldous.test",
      "title": "Visualizing balance via scatter diagrams",
      "topics": [
        "aldous.test"
      ]
    },
    {
      "page": "all.equal.treeshape",
      "title": "Compare two objects of class treeshape",
      "topics": [
        "all.equal.treeshape"
      ]
    },
    {
      "page": "as.phylo.treeshape",
      "title": "Conversion among tree objects",
      "topics": [
        "as.phylo.treeshape"
      ]
    },
    {
      "page": "as.treeshape",
      "title": "Conversion among tree objects",
      "topics": [
        "as.treeshape",
        "as.treeshape.phylo"
      ]
    },
    {
      "page": "aux_lik",
      "title": "Probability of the sampled node position",
      "topics": [
        "aux_lik"
      ]
    },
    {
      "page": "bind.trees",
      "title": "Binds two tree together",
      "topics": [
        "bind.trees"
      ]
    },
    {
      "page": "build_tree",
      "title": "Internal BetaAlphaEta function",
      "topics": [
        "build_tree"
      ]
    },
    {
      "page": "carnivora.treeshape",
      "title": "Phylogeny of carnivores.",
      "topics": [
        "carnivora.treeshape"
      ]
    },
    {
      "page": "change_int",
      "title": "Internal function",
      "topics": [
        "change_int"
      ]
    },
    {
      "page": "change_int_eta",
      "title": "Internal function",
      "topics": [
        "change_int_eta"
      ]
    },
    {
      "page": "cladesize",
      "title": "Compute the number of children of a randomly chosen node",
      "topics": [
        "cladesize"
      ]
    },
    {
      "page": "colless",
      "title": "Compute the Colless' shape statistic on tree data",
      "topics": [
        "colless"
      ]
    },
    {
      "page": "cutreeshape",
      "title": "Cut objects of class \"treeshape\"",
      "topics": [
        "cutreeshape"
      ]
    },
    {
      "page": "cytochromc",
      "title": "Phylogeny of the cytochrome C family.",
      "topics": [
        "cytochromc"
      ]
    },
    {
      "page": "depth",
      "title": "Gets the node depths of the tree",
      "topics": [
        "depth"
      ]
    },
    {
      "page": "enhance",
      "title": "Internal function",
      "topics": [
        "enhance"
      ]
    },
    {
      "page": "enhance_eta",
      "title": "Internal function",
      "topics": [
        "enhance_eta"
      ]
    },
    {
      "page": "get_extinction_list",
      "title": "Gives the tips of the phylogeny in their extinction order",
      "topics": [
        "get_extinction_list"
      ]
    },
    {
      "page": "get_PD_sample",
      "title": "Computes the proportion of conserved PD",
      "topics": [
        "get_PD_sample"
      ]
    },
    {
      "page": "get_tree_beta",
      "title": "Beta parameter as a function of the proportion of remaining tips",
      "topics": [
        "get_tree_beta"
      ]
    },
    {
      "page": "hivtree.treeshape",
      "title": "Phylogenetic Tree of 193 HIV-1 Sequences",
      "topics": [
        "hivtree.treeshape"
      ]
    },
    {
      "page": "index.test",
      "title": "Perform a test on the Yule or PDA hypothesis based on the Colless or the Sackin statistic",
      "topics": [
        "colless.test",
        "sackin.test"
      ]
    },
    {
      "page": "insert",
      "title": "Insert an element in a vector",
      "topics": [
        "insert"
      ]
    },
    {
      "page": "lambda_N",
      "title": "Computation of lambda_epsilon",
      "topics": [
        "lambda_N"
      ]
    },
    {
      "page": "lambda.epsilon",
      "title": "Computes lambda_epsilon",
      "topics": [
        "lambda.epsilon"
      ]
    },
    {
      "page": "likelihood.test",
      "title": "Test the Yule model vs PDA (uniform) model.",
      "topics": [
        "likelihood.test"
      ]
    },
    {
      "page": "maxlik.betasplit",
      "title": "Maximum likelihood of beta in the Beta-splitting model",
      "topics": [
        "maxlik.betasplit"
      ]
    },
    {
      "page": "mcmc_alpha",
      "title": "Inference of the alpha parameter",
      "topics": [
        "mcmc_alpha"
      ]
    },
    {
      "page": "mcmc_eta",
      "title": "Inference of the alpha and eta parameters",
      "topics": [
        "mcmc_eta"
      ]
    },
    {
      "page": "nodes_depths_ordonnes",
      "title": "Gets the node depths of the tree",
      "topics": [
        "nodes_depths_ordonnes"
      ]
    },
    {
      "page": "plot.treeshape",
      "title": "Plot phylogenetic treeshapes.",
      "topics": [
        "plot.treeshape"
      ]
    },
    {
      "page": "primates",
      "title": "Phylogeny of the primates.",
      "topics": [
        "primates"
      ]
    },
    {
      "page": "rbactrian",
      "title": "Proposal for the mcmc functions",
      "topics": [
        "rbactrian"
      ]
    },
    {
      "page": "rhodopsin",
      "title": "Phylogeny of rhodopsin proteins.",
      "topics": [
        "rhodopsin"
      ]
    },
    {
      "page": "rtreeshape",
      "title": "Generate a list of random binary trees according to a given model",
      "topics": [
        "rtreeshape"
      ]
    },
    {
      "page": "sackin",
      "title": "Compute the Sackin's index of a tree",
      "topics": [
        "sackin"
      ]
    },
    {
      "page": "shape.statistic",
      "title": "Computes the log of the likelihood ratio (yule/pda)",
      "topics": [
        "shape.statistic"
      ]
    },
    {
      "page": "shift.test",
      "title": "Testing diversification rate variation in phylogenetic trees",
      "topics": [
        "shift.test"
      ]
    },
    {
      "page": "simulate_kingman",
      "title": "Ranked topology with Kingman's coalescent depths",
      "topics": [
        "simulate_kingman"
      ]
    },
    {
      "page": "simulate_tree",
      "title": "Simulates ranked topology",
      "topics": [
        "simulate_tree"
      ]
    },
    {
      "page": "simulate_yule",
      "title": "Ranked topology with Birth-death process depths",
      "topics": [
        "simulate_yule"
      ]
    },
    {
      "page": "simulate.R",
      "title": "Simulate R knowing K=k",
      "topics": [
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      "page": "simulate.Tau.X",
      "title": "Simulate (Tau, X_Tau-)",
      "topics": [
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    {
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      "title": "Simulates the random variables Y_i",
      "topics": [
        "simulate.Yi"
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    },
    {
      "page": "smaller.clade.spectrum",
      "title": "Compute the smaller clade spectrum of a tree.",
      "topics": [
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      "page": "spectrum.treeshape",
      "title": "Compute the spectrum of a tree",
      "topics": [
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      "page": "split",
      "title": "Computes the splits at each node of a tree",
      "topics": [
        "split"
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      "title": "Test the Yule or PDA hypothesis",
      "topics": [
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    {
      "page": "summary.treeshape",
      "title": "Print a summary of an object of class \"treeshape\"",
      "topics": [
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      "page": "tipsubtree",
      "title": "Extract a subtree that contains pre-specified tip names or labels",
      "topics": [
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      "page": "transform",
      "title": "Internal function",
      "topics": [
        "transform"
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    },
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      "page": "transform_eta",
      "title": "Internal function",
      "topics": [
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    },
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      "page": "treeshape",
      "title": "Builds an object of class treeshape",
      "topics": [
        "treeshape"
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    },
    {
      "page": "universal.treeshape",
      "title": "Universal phylogenetic tree of life",
      "topics": [
        "universal.treeshape"
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    },
    {
      "page": "yule_lengths",
      "title": "Internal BetaAlphaEta function",
      "topics": [
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