{
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  "Package": "PHYLOGR",
  "Version": "1.0.12",
  "Date": "2026-01-30",
  "Title": "Functions for Phylogenetically Based Statistical Analyses",
  "Authors@R": "c(person(given = \"Ramon\",\nfamily = \"Diaz-Uriarte\",\nrole = c(\"aut\", \"cre\"),\nemail = \"rdiaz02@gmail.com\"),\nperson(given = \"Theodore\",\nfamily = \"Garland, Jr\",\nrole = \"aut\",\nemail = \"theodore.garland@ucr.edu\"))",
  "Maintainer": "Ramon Diaz-Uriarte <rdiaz02@gmail.com>",
  "Description": "Manipulation and analysis of phylogenetically simulated\ndata sets and phylogenetically based analyses using GLS.",
  "License": "GPL (>= 2)",
  "URL": "http://ligarto.org/rdiaz",
  "LazyData": "true",
  "Repository": "https://phylotastic.r-universe.dev",
  "Date/Publication": "2026-01-31 09:44:26 UTC",
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  "Author": "Ramon Diaz-Uriarte [aut, cre],\nTheodore Garland, Jr [aut]",
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    "lm.phylog",
    "matrix.D",
    "phylog.gls.fit",
    "prcomp.phylog",
    "read.inp.data",
    "read.pdi.data",
    "read.phylip.data",
    "read.phylog.matrix",
    "read.sim.data"
  ],
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      "title": "Independet contrasts for Garland & Janis data set",
      "object": "GarlandJanis.IC",
      "class": [
        "data.frame"
      ],
      "fields": [
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        "running.speed",
        "hind.l.length",
        "mtf.ratio",
        "branch.lengths",
        "names.contr",
        "clade.contr"
      ],
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      "table": true,
      "tojson": true
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    {
      "name": "GarlandJanis.Original",
      "title": "Garland & Janis's 1993 data on mammalian running speed and limb length",
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      "class": [
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      ],
      "fields": [
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        "body.mass",
        "running.speed",
        "hind.l.length",
        "mtf.ratio",
        "clade"
      ],
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      "table": true,
      "tojson": true
    },
    {
      "name": "GarlandJanis.varcov",
      "title": "Phylogenetic variance-covariance matrix for Garland & Janis (1993).",
      "object": "GarlandJanis.varcov",
      "class": [
        "data.frame"
      ],
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        "Ur",
        "Um",
        "Nn",
        "pl",
        "Mp",
        "Ml",
        "Cp",
        "Ct",
        "Lp",
        "Ca",
        "Uc",
        "Vf",
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        "Cc",
        "Aj",
        "Pp",
        "Pt",
        "Pl",
        "Tb",
        "Cs",
        "Db",
        "Eh",
        "Ec",
        "Eb",
        "Lg",
        "Cd",
        "Gc",
        "Sc",
        "Bb",
        "To",
        "Gg",
        "Gt",
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        "Mk",
        "Oa",
        "Oc",
        "He",
        "Am",
        "Cu",
        "Dl",
        "Ab",
        "Aa",
        "cc",
        "Dd",
        "Al",
        "Rt",
        "Ov",
        "Oh"
      ],
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      "table": true,
      "tojson": true
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      "title": "Independet contrasts for Bauwens and Diaz-Uriarte (1997) lacertid data set",
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      ],
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        "clutch.size",
        "age.mat",
        "cl.freq",
        "contr"
      ],
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      "table": true,
      "tojson": true
    },
    {
      "name": "Lacertid.Original",
      "title": "Bauwens and Diaz-Uriarte (1997) lacertid data",
      "object": "Lacertid.Original",
      "class": [
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        "clutch.size",
        "age.mat",
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      ],
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      "table": true,
      "tojson": true
    },
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      "name": "Lacertid.varcov",
      "title": "Variance-covariance matrix for lacertids from Bauwens and Diaz-uriarte (1997)",
      "object": "Lacertid.varcov",
      "class": [
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      ],
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        "My",
        "Pb",
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        "Ae",
        "Zv",
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        "La",
        "Ls",
        "Lv"
      ],
      "rows": 18,
      "table": true,
      "tojson": true
    },
    {
      "name": "SimulExample",
      "title": "A simulated data set",
      "object": "SimulExample",
      "class": [
        "data.frame"
      ],
      "fields": [
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        "Tips",
        "y",
        "x1",
        "x2",
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        "x4",
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        "x6",
        "x7",
        "diet"
      ],
      "rows": 918,
      "table": true,
      "tojson": true
    }
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  "_help": [
    {
      "page": "cancor.phylog",
      "title": "Canonical Correlation Analysis from Simulated Data Sets",
      "topics": [
        "cancor.phylog"
      ]
    },
    {
      "page": "cor.origin",
      "title": "Correlation Through the Origin",
      "topics": [
        "cor.origin"
      ]
    },
    {
      "page": "GarlandJanis.IC",
      "title": "Independet contrasts for Garland & Janis data set",
      "topics": [
        "GarlandJanis.IC"
      ]
    },
    {
      "page": "GarlandJanis.Original",
      "title": "Garland & Janis's 1993 data on mammalian running speed and limb length",
      "topics": [
        "GarlandJanis.Original"
      ]
    },
    {
      "page": "GarlandJanis.varcov",
      "title": "Phylogenetic variance-covariance matrix for Garland & Janis (1993).",
      "topics": [
        "GarlandJanis.varcov"
      ]
    },
    {
      "page": "Helper.functions",
      "title": "Helper functions",
      "topics": [
        "num.sim.tips",
        "number.of.simulations",
        "number.of.tips.inp",
        "number.of.tips.pdi",
        "number.of.tips.sim",
        "scan.inp.file",
        "scan.pdi.file",
        "scan.simulation.file",
        "tips.names.inp",
        "tips.names.pdi"
      ]
    },
    {
      "page": "Lacertid.IC",
      "title": "Independet contrasts for Bauwens and Diaz-Uriarte (1997) lacertid data set",
      "topics": [
        "Lacertid.IC"
      ]
    },
    {
      "page": "Lacertid.Original",
      "title": "Bauwens and Diaz-Uriarte (1997) lacertid data",
      "topics": [
        "Lacertid.Original"
      ]
    },
    {
      "page": "Lacertid.varcov",
      "title": "Variance-covariance matrix for lacertids from Bauwens and Diaz-uriarte (1997)",
      "topics": [
        "Lacertid.varcov"
      ]
    },
    {
      "page": "lm.phylog",
      "title": "Linear Models from Simulated Data Sets",
      "topics": [
        "lm.phylog"
      ]
    },
    {
      "page": "matrix.D",
      "title": "Produce the Matrix D of Garland and Ives (2000) for GLS",
      "topics": [
        "matrix.D"
      ]
    },
    {
      "page": "phylog.gls.fit",
      "title": "Phylogenetically-Based GLS Model Fitting",
      "topics": [
        "phylog.gls.fit"
      ]
    },
    {
      "page": "plot.phylog.cancor",
      "title": "Plot a phylog.cancor object",
      "topics": [
        "plot.phylog.cancor"
      ]
    },
    {
      "page": "plot.phylog.lm",
      "title": "Plot a phylog.lm object",
      "topics": [
        "plot.phylog.lm"
      ]
    },
    {
      "page": "plot.phylog.prcomp",
      "title": "Plot a phylog.prcomp object",
      "topics": [
        "plot.phylog.prcomp"
      ]
    },
    {
      "page": "prcomp.phylog",
      "title": "Principal Components Analysis from Simulated Data Sets",
      "topics": [
        "prcomp.phylog"
      ]
    },
    {
      "page": "print.summary.phylog",
      "title": "Printing summaries of PHYLOGR statistical functions",
      "topics": [
        "print.summary.phylog.cancor",
        "print.summary.phylog.lm",
        "print.summary.phylog.prcomp"
      ]
    },
    {
      "page": "read.inp.data",
      "title": "Read Inp Data Files",
      "topics": [
        "read.inp.data"
      ]
    },
    {
      "page": "read.pdi.data",
      "title": "Read Pdi Data Files",
      "topics": [
        "read.pdi.data"
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    },
    {
      "page": "read.phylip.data",
      "title": "Read Phylip Infile Data Files",
      "topics": [
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      ]
    },
    {
      "page": "read.phylog.matrix",
      "title": "Read a Phylogenetic Covariance Matrix",
      "topics": [
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    },
    {
      "page": "read.sim.data",
      "title": "Read Sim Files From PDSIMUL",
      "topics": [
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    },
    {
      "page": "SimulExample",
      "title": "A simulated data set",
      "topics": [
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    {
      "page": "summary.phylog.cancor",
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      "page": "summary.phylog.lm",
      "title": "Summarize a phylog.lm object",
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    },
    {
      "page": "summary.phylog.prcomp",
      "title": "Summarize a phylog.prcomp object",
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      ]
    }
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