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  "Version": "2.7.0",
  "Date": "2026-02-23",
  "Title": "Phylogenetic Linear Regression",
  "Authors@R": "c(person(\"Lam Si Tung\", \"Ho\", role=c(\"aut\", \"cre\"), email=\"lamho86@gmail.com\"),\nperson(\"Cecile\", \"Ane\", role=\"aut\"),\nperson(\"Robert\", \"Lachlan\", role=\"ctb\"),\nperson(\"Kelsey\", \"Tarpinian\",role=\"ctb\"),\nperson(\"Rachel\", \"Feldman\",role=\"ctb\"),\nperson(\"Qing\", \"Yu\",role=\"ctb\"),\nperson(\"Wouter\", \"van der Bijl\",role=\"ctb\"),\nperson(\"Joan\", \"Maspons\",role=\"ctb\"),\nperson(\"Rutger\", \"Vos\",role=\"ctb\"),\nperson(\"Paul\", \"Bastide\",role=\"ctb\"),\nperson(\"Ana Marcia\", \"Barbosa\",role=\"ctb\"))",
  "Description": "Provides functions for fitting phylogenetic linear models\nand phylogenetic generalized linear models. The computation\nuses an algorithm that is linear in the number of tips in the\ntree. The package also provides functions for simulating\ncontinuous or binary traits along the tree. Other tools include\nfunctions to test the adequacy of a population tree.",
  "License": "GPL (>= 2) | file LICENSE",
  "URL": "https://github.com/lamho86/phylolm",
  "BugReports": "https://github.com/lamho86/phylolm/issues",
  "Encoding": "UTF-8",
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  "Author": "Lam Si Tung Ho [aut, cre],\nCecile Ane [aut],\nRobert Lachlan [ctb],\nKelsey Tarpinian [ctb],\nRachel Feldman [ctb],\nQing Yu [ctb],\nWouter van der Bijl [ctb],\nJoan Maspons [ctb],\nRutger Vos [ctb],\nPaul Bastide [ctb],\nAna Marcia Barbosa [ctb]",
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    "AIC.logLik.phylolm",
    "AIC.phyloglm",
    "AIC.phylolm",
    "confint.phylolm",
    "extractAIC.phylolm",
    "logLik.phyloglm",
    "logLik.phylolm",
    "mace",
    "model.frame.phylolm",
    "nobs.phyloglm",
    "nobs.phylolm",
    "OU1d.loglik",
    "OUshifts",
    "phyloglm",
    "phyloglmstep",
    "phylolm",
    "phylostep",
    "plot.OUshifts",
    "plot.phyloglm",
    "plot.phylolm",
    "predict.phyloglm",
    "predict.phylolm",
    "print.logLik.phyloglm",
    "print.logLik.phylolm",
    "print.phyloglm",
    "print.phylolm",
    "print.summary.phyloglm",
    "print.summary.phylolm",
    "pruningwise.branching.times",
    "pruningwise.distFromRoot",
    "rbinTrait",
    "residuals.phyloglm",
    "residuals.phylolm",
    "rTrait",
    "stepwise.test.tree",
    "summary.phyloglm",
    "summary.phylolm",
    "test.one.species.tree",
    "test.tree.preparation",
    "three.point.compute",
    "transf.branch.lengths",
    "vcov.phyloglm",
    "vcov.phylolm"
  ],
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      "name": "flowerSize",
      "title": "Flower size of 25 Euphorbiaceae species",
      "object": "flowerSize",
      "file": "flowerSize.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "flower_diameter_mm",
        "log_transformed_size"
      ],
      "rows": 25,
      "table": true,
      "tojson": true
    },
    {
      "name": "flowerTree",
      "title": "Phylogenetic tree of 25 Euphorbiaceae species",
      "object": "flowerTree",
      "file": "flowerTree.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "guidetree",
      "title": "Binary population tree within Arabidopsis thaliana",
      "object": "guidetree",
      "file": "guidetree.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "quartetCF",
      "title": "Quartet concordance factors across Arabidopsis thaliana",
      "object": "quartetCF",
      "file": "quartetCF.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
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        "taxon2",
        "taxon3",
        "taxon4",
        "CF12.34",
        "CF13.24",
        "CF14.23"
      ],
      "rows": 27405,
      "table": true,
      "tojson": true
    },
    {
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      "object": "tomato",
      "file": "tomato.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
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  "_help": [
    {
      "page": "phylolm-package",
      "title": "Phylogenetic Linear Regression",
      "topics": [
        "phylolm-package"
      ]
    },
    {
      "page": "add.individuals",
      "title": "Add individuals as tips of the tree",
      "topics": [
        "add.individuals"
      ]
    },
    {
      "page": "flowerSize",
      "title": "Flower size of 25 Euphorbiaceae species",
      "topics": [
        "flowerSize"
      ]
    },
    {
      "page": "flowerTree",
      "title": "Phylogenetic tree of 25 Euphorbiaceae species",
      "topics": [
        "flowerTree"
      ]
    },
    {
      "page": "guidetree",
      "title": "Binary population tree within Arabidopsis thaliana",
      "topics": [
        "guidetree"
      ]
    },
    {
      "page": "mace",
      "title": "Multi-task learning for ancestral state estimation.",
      "topics": [
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      ]
    },
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      "topics": [
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      ]
    },
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      "title": "Detections of shifts in the OU process along a phylogeny.",
      "topics": [
        "OUshifts"
      ]
    },
    {
      "page": "OUshifts-methods",
      "title": "Methods for class 'OUshifts'.",
      "topics": [
        "plot.OUshifts"
      ]
    },
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      "title": "Phylogenetic Generalized Linear Model",
      "topics": [
        "phyloglm"
      ]
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    {
      "page": "phyloglm-methods",
      "title": "Methods for class 'phyloglm'.",
      "topics": [
        "AIC.logLik.phyloglm",
        "AIC.phyloglm",
        "logLik.phyloglm",
        "nobs.phyloglm",
        "plot.phyloglm",
        "predict.phyloglm",
        "print.logLik.phyloglm",
        "print.phyloglm",
        "print.summary.phyloglm",
        "residuals.phyloglm",
        "summary.phyloglm",
        "vcov.phyloglm"
      ]
    },
    {
      "page": "phyloglmstep",
      "title": "Stepwise model selection for Phylogenetic Generalized Linear Model",
      "topics": [
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      ]
    },
    {
      "page": "phylolm",
      "title": "Phylogenetic Linear Model",
      "topics": [
        "phylolm"
      ]
    },
    {
      "page": "phylolm-methods",
      "title": "Methods for class 'phylolm'.",
      "topics": [
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        "AIC.phylolm",
        "confint.phylolm",
        "extractAIC.phylolm",
        "logLik.phylolm",
        "model.frame.phylolm",
        "nobs.phylolm",
        "plot.phylolm",
        "predict.phylolm",
        "print.logLik.phylolm",
        "print.phylolm",
        "print.summary.phylolm",
        "residuals.phylolm",
        "summary.phylolm",
        "vcov.phylolm"
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      "title": "Stepwise model selection for Phylogenetic Linear Model",
      "topics": [
        "phylostep"
      ]
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      ]
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      "title": "Quartet concordance factors across Arabidopsis thaliana",
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      ]
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      "title": "Binary trait simulation",
      "topics": [
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      ]
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      "title": "Fits a population tree to data from quartet concordance factors",
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      "page": "tomato",
      "title": "Phylogenetic tree and trait data for 12 wild tomato accessions.",
      "topics": [
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      ]
    },
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      "page": "transf.branch.lengths",
      "title": "Creates a tree with branch lengths to represent the 3-point structure of a covariance matrix",
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