{
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  "Title": "Phylogenetic Ridge Regression Methods for Comparative Studies",
  "Date": "2026-01-09",
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  "Authors@R": "c(person(given = \"Pasquale\",\nfamily = \"Raia\",\nrole = \"aut\"),\nperson(given = \"Silvia\",\nfamily = \"Castiglione\",\nrole = c(\"aut\",\"cre\"),\nemail = \"silvia.castiglione@unina.it\"),\nperson(given = \"Carmela\",\nfamily = \"Serio\",\nrole = \"aut\"),\nperson(given = \"Giorgia\",\nfamily = \"Girardi\",\nrole = \"aut\"),\nperson(given = \"Alessandro\",\nfamily = \"Mondanaro\",\nrole = \"aut\"),\nperson(given = \"Marina\",\nfamily = \"Melchionna\",\nrole = \"aut\"),\nperson(given = \"Mirko\",\nfamily = \"Di Febbraro\",\nrole = \"aut\"),\nperson(given = \"Antonio\",\nfamily = \"Profico\",\nrole = \"aut\"),\nperson(given = \"Francesco\",\nfamily = \"Carotenuto\",\nrole = \"aut\"))",
  "Maintainer": "Silvia Castiglione <silvia.castiglione@unina.it>",
  "Description": "Functions for phylogenetic analysis (Castiglione et al.,\n2018 <doi:10.1111/2041-210X.12954>). The functions perform the\nestimation of phenotypic evolutionary rates, identification of\nphenotypic evolutionary rate shifts, quantification of\ndirection and size of evolutionary change in multivariate\ntraits, the computation of ontogenetic shape vectors and test\nfor morphological convergence.",
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    "fix.poly",
    "getGenus",
    "getMommy",
    "getSis",
    "lollipoPlot",
    "makeFossil",
    "makeL",
    "makeL1",
    "move.lineage",
    "namesCompare",
    "node.paths",
    "overfitPGLS",
    "overfitRR",
    "overfitSC",
    "overfitSS",
    "overfitST",
    "PGLS_fossil",
    "phyloclust",
    "plotConv",
    "plotRates",
    "plotRR",
    "plotShift",
    "plotTrend",
    "random.evolvability.test",
    "rate.map",
    "rateHistory",
    "resampleTree",
    "rescaleRR",
    "retrieve.angles",
    "RRphylo",
    "scaleTree",
    "search.conv",
    "search.shift",
    "search.trend",
    "setBM",
    "sig2BM",
    "sizedsubtree",
    "StableTraitsR",
    "swap.phylo",
    "swapONE",
    "tips",
    "tree.merger",
    "treeCompare",
    "treedataMatch"
  ],
  "_datasets": [
    {
      "name": "DataApes",
      "title": "Example dataset",
      "object": "DataApes",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "DataCetaceans",
      "title": "Example dataset",
      "object": "DataCetaceans",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "DataFelids",
      "title": "Example dataset",
      "object": "DataFelids",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "DataOrnithodirans",
      "title": "Example dataset",
      "object": "DataOrnithodirans",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "DataSimians",
      "title": "Example dataset",
      "object": "DataSimians",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "DataUng",
      "title": "Example dataset",
      "object": "DataUng",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "RRphylo-package",
      "title": "Phylogenetic Ridge Regression Methods for Comparative Studies",
      "topics": [
        "RRphylo-package"
      ]
    },
    {
      "page": "angle.matrix",
      "title": "Ontogenetic shape vectors analysis",
      "topics": [
        "angle.matrix"
      ]
    },
    {
      "page": "colorbar",
      "title": "Draw colorbar on a plot",
      "topics": [
        "colorbar"
      ]
    },
    {
      "page": "compRates",
      "title": "Comparing average absolute rates between clades",
      "topics": [
        "compRates"
      ]
    },
    {
      "page": "conv.map",
      "title": "Mapping morphological convergence on 3D surfaces",
      "topics": [
        "conv.map"
      ]
    },
    {
      "page": "cutPhylo",
      "title": "Cut the phylogeny at a given age or node",
      "topics": [
        "cutPhylo"
      ]
    },
    {
      "page": "DataApes",
      "title": "Example dataset",
      "topics": [
        "DataApes"
      ]
    },
    {
      "page": "DataCetaceans",
      "title": "Example dataset",
      "topics": [
        "DataCetaceans"
      ]
    },
    {
      "page": "DataFelids",
      "title": "Example dataset",
      "topics": [
        "DataFelids"
      ]
    },
    {
      "page": "DataOrnithodirans",
      "title": "Example dataset",
      "topics": [
        "DataOrnithodirans"
      ]
    },
    {
      "page": "DataSimians",
      "title": "Example dataset",
      "topics": [
        "DataSimians"
      ]
    },
    {
      "page": "DataUng",
      "title": "Example dataset",
      "topics": [
        "DataUng"
      ]
    },
    {
      "page": "distNodes",
      "title": "Finding distance between nodes and tips",
      "topics": [
        "distNodes"
      ]
    },
    {
      "page": "evo.dir",
      "title": "Phylogenetic vector analysis of phenotypic change",
      "topics": [
        "evo.dir"
      ]
    },
    {
      "page": "fix.poly",
      "title": "Resolving polytomies to non-zero length branches",
      "topics": [
        "fix.poly"
      ]
    },
    {
      "page": "getGenus",
      "title": "Taxonomic inspection of the tree at the genus level",
      "topics": [
        "getGenus"
      ]
    },
    {
      "page": "getMommy",
      "title": "Upward tip or node to root path",
      "topics": [
        "getMommy"
      ]
    },
    {
      "page": "getSis",
      "title": "Get sister clade",
      "topics": [
        "getSis"
      ]
    },
    {
      "page": "lollipoPlot",
      "title": "Lollipop charts",
      "topics": [
        "lollipoPlot"
      ]
    },
    {
      "page": "makeFossil",
      "title": "Make fossil species on a phylogeny",
      "topics": [
        "makeFossil"
      ]
    },
    {
      "page": "makeL",
      "title": "Matrix of branch lengths along root-to-tip paths",
      "topics": [
        "makeL"
      ]
    },
    {
      "page": "makeL1",
      "title": "Matrix of branch lengths along a root-to-node path",
      "topics": [
        "makeL1"
      ]
    },
    {
      "page": "move.lineage",
      "title": "Move tips or clades",
      "topics": [
        "move.lineage"
      ]
    },
    {
      "page": "namesCompare",
      "title": "Checking species names for misspelling and synonyms",
      "topics": [
        "namesCompare"
      ]
    },
    {
      "page": "node.paths",
      "title": "Tracing nodes along paths",
      "topics": [
        "node.paths"
      ]
    },
    {
      "page": "overfitPGLS",
      "title": "Testing PGLS_fossil overfit",
      "topics": [
        "overfitPGLS"
      ]
    },
    {
      "page": "overfitRR",
      "title": "Testing RRphylo overfit",
      "topics": [
        "overfitRR"
      ]
    },
    {
      "page": "overfitSC",
      "title": "Testing search.conv overfit",
      "topics": [
        "overfitSC"
      ]
    },
    {
      "page": "overfitSS",
      "title": "Testing search.shift overfit",
      "topics": [
        "overfitSS"
      ]
    },
    {
      "page": "overfitST",
      "title": "Testing search.trend overfit",
      "topics": [
        "overfitST"
      ]
    },
    {
      "page": "PGLS_fossil",
      "title": "Phylogenetic Generalized Least Square with phylogenies including fossils",
      "topics": [
        "PGLS_fossil"
      ]
    },
    {
      "page": "phyloclust",
      "title": "Test for phylogenetic clustering",
      "topics": [
        "phyloclust"
      ]
    },
    {
      "page": "plotConv",
      "title": "Graphical representation of search.conv results",
      "topics": [
        "plotConv"
      ]
    },
    {
      "page": "plotRates",
      "title": "Plot RRphylo rates at a specified node",
      "topics": [
        "plotRates"
      ]
    },
    {
      "page": "plotRR",
      "title": "Plot the RRphylo output onto the phylogenetic tree",
      "topics": [
        "plotRR"
      ]
    },
    {
      "page": "plotShift",
      "title": "Graphical representation of search.shift results",
      "topics": [
        "addShift",
        "plotShift"
      ]
    },
    {
      "page": "plotTrend",
      "title": "Graphical representation of search.trend results",
      "topics": [
        "plotTrend"
      ]
    },
    {
      "page": "random.evolvability.test",
      "title": "Randomization test for phylogenetic structuring in evolvability",
      "topics": [
        "random.evolvability.test"
      ]
    },
    {
      "page": "rate.map",
      "title": "Mapping rate and direction of phenotypic change on 3D surfaces.",
      "topics": [
        "rate.map"
      ]
    },
    {
      "page": "rateHistory",
      "title": "Computing historical rates",
      "topics": [
        "rateHistory"
      ]
    },
    {
      "page": "resampleTree",
      "title": "Altering phylogenetic trees",
      "topics": [
        "resampleTree"
      ]
    },
    {
      "page": "rescaleRR",
      "title": "Rescaling phylogenetic trees",
      "topics": [
        "rescaleRR"
      ]
    },
    {
      "page": "retrieve.angles",
      "title": "Extracting a user-specified subset of the evo.dir results",
      "topics": [
        "retrieve.angles"
      ]
    },
    {
      "page": "RRphylo",
      "title": "Evolutionary rates computation along phylogenies",
      "topics": [
        "RRphylo"
      ]
    },
    {
      "page": "RRphylo-defunct",
      "title": "Defunct functions in Package RRphylo",
      "topics": [
        "RRphylo-defunct",
        "swap.phylo"
      ]
    },
    {
      "page": "RRphylo-deprecated",
      "title": "Deprecated functions in Package RRphylo",
      "topics": [
        "RRphylo-deprecated"
      ]
    },
    {
      "page": "scaleTree",
      "title": "Phylogenetic tree calibration",
      "topics": [
        "scaleTree"
      ]
    },
    {
      "page": "search.conv",
      "title": "Searching for morphological convergence among species and clades",
      "topics": [
        "search.conv"
      ]
    },
    {
      "page": "search.shift",
      "title": "Locating shifts in phenotypic evolutionary rates",
      "topics": [
        "search.shift"
      ]
    },
    {
      "page": "search.trend",
      "title": "Searching for evolutionary trends in phenotypes and rates",
      "topics": [
        "search.trend"
      ]
    },
    {
      "page": "setBM",
      "title": "Producing simulated phenotypes with trends",
      "topics": [
        "setBM"
      ]
    },
    {
      "page": "sig2BM",
      "title": "Brownian Motion rate computation",
      "topics": [
        "sig2BM"
      ]
    },
    {
      "page": "sizedsubtree",
      "title": "Find a node subtending to a clade of desired size",
      "topics": [
        "sizedsubtree"
      ]
    },
    {
      "page": "StableTraitsR",
      "title": "Run StableTraits from within R",
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