{
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  "Package": "RRPP",
  "Title": "Linear Model Evaluation with Randomized Residuals in a\nPermutation Procedure",
  "Version": "2.1.2.999",
  "Authors@R": "c(\nperson(\"Michael\", \"Collyer\", , \"mlcollyer@gmail.com\", c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-0238-2201\")),\nperson(\"Dean\", \"Adams\", , role = \"aut\",\ncomment = c(ORCID = \"0000-0001-9172-7894\"))\n)",
  "Description": "Linear model calculations are made for many random\nversions of data. Using residual randomization in a permutation\nprocedure, sums of squares are calculated over many\npermutations to generate empirical probability distributions\nfor evaluating model effects.  Additionally, coefficients,\nstatistics, fitted values, and residuals generated over many\npermutations can be used for various procedures including\npairwise tests, prediction, classification, and model\ncomparison.  This package should provide most tools one could\nneed for the analysis of high-dimensional data, especially in\necology and evolutionary biology, but certainly other fields,\nas well.",
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  "Author": "Michael Collyer [aut, cre]\n(<https://orcid.org/0000-0003-0238-2201>), Dean Adams [aut]\n(<https://orcid.org/0000-0001-9172-7894>)",
  "Maintainer": "Michael Collyer <mlcollyer@gmail.com>",
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  "_exports": [
    "add.trajectories",
    "add.tree",
    "anova.lm.rrpp",
    "anova.measurement.error",
    "betaTest",
    "classify",
    "convert2ggplot",
    "effect.size",
    "fixef.lmm.rrpp",
    "focusMEonSubjects",
    "getANOVAStats",
    "getModelCov",
    "getModels",
    "getPermInfo",
    "getResCov",
    "getTerms",
    "ICCstats",
    "interSubVar",
    "kcomp",
    "lm.rrpp",
    "lm.rrpp.ws",
    "lmm.rrpp",
    "looCV",
    "looCV_table",
    "lr_test",
    "mahal_dist",
    "manova.update",
    "measurement.error",
    "model.comparison",
    "ordinate",
    "pairwise",
    "pairwise.model.Z",
    "plot.kcomp",
    "plot.lm.rrpp",
    "plot.ordinate",
    "plot.predict.lm.rrpp",
    "prep.lda",
    "print.anova.lm.rrpp",
    "print.betaTest",
    "print.coef.lm.rrpp",
    "print.ICCstats",
    "print.lm.rrpp",
    "print.model.comparison",
    "print.pairwise",
    "print.pairwise.model.Z",
    "print.predict.lm.rrpp",
    "print.summary.betaTest",
    "print.summary.lm.rrpp",
    "print.summary.pairwise",
    "print.summary.trajectory.analysis",
    "print.trajectory.analysis",
    "pval",
    "QRforX",
    "ranef.lmm.rrpp",
    "reveal.model.designs",
    "rrpp.data.frame",
    "scaleCov",
    "summary.anova.lm.rrpp",
    "summary.betaTest",
    "summary.coef.lm.rrpp",
    "summary.ICCstats",
    "summary.lm.rrpp",
    "summary.model.comparison",
    "summary.pairwise",
    "summary.pairwise.model.Z",
    "summary.predict.lm.rrpp",
    "summary.trajectory.analysis",
    "trajectory.analysis",
    "vec.cor.matrix"
  ],
  "_datasets": [
    {
      "name": "fishy",
      "title": "Simulated Fish Data for Measurement Error Analysis",
      "object": "fishy",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "flower",
      "title": "Flower Production and Temperature",
      "object": "flower",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Year",
        "Temp",
        "FlowerProd"
      ],
      "rows": 24,
      "table": true,
      "tojson": true
    },
    {
      "name": "mammalHR",
      "title": "Mammal Home Range Data",
      "object": "mammalHR",
      "class": [
        "rrpp.data.frame"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "mammalHRphy",
      "title": "Phylogenetic Data for the Mammal Home Range Data",
      "object": "mammalHRphy",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "motionpaths",
      "title": "Simulated motion paths",
      "object": "motionpaths",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "phytoplankton",
      "title": "Phytoplankton Biomass and Eutrophication",
      "object": "phytoplankton",
      "class": [
        "data.frame"
      ],
      "fields": [
        "biomass",
        "status",
        "phos",
        "grid.lat",
        "grid.long"
      ],
      "rows": 70,
      "table": true,
      "tojson": true
    },
    {
      "name": "PlethCinHoff",
      "title": "Plethodon comparative SVL data",
      "object": "PlethCinHoff",
      "class": [
        "data.frame"
      ],
      "fields": [
        "SVL",
        "Group",
        "Species",
        "Local"
      ],
      "rows": 158,
      "table": true,
      "tojson": true
    },
    {
      "name": "PlethMorph",
      "title": "Plethodon comparative morphological data",
      "object": "PlethMorph",
      "class": [
        "rrpp.data.frame"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "podarcis",
      "title": "Podarcis Wall Lizards from the Mediterranean Basin",
      "object": "podarcis",
      "class": [
        "data.frame"
      ],
      "fields": [
        "X",
        "GROUP",
        "SEX",
        "SVL"
      ],
      "rows": 440,
      "table": true,
      "tojson": true
    },
    {
      "name": "Pupfish",
      "title": "Landmarks on pupfish",
      "object": "Pupfish",
      "class": [
        "rrpp.data.frame"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "PupfishHeads",
      "title": "Landmarks on pupfish heads",
      "object": "PupfishHeads",
      "class": [
        "rrpp.data.frame"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "PupfishMR",
      "title": "Experimental metabolic rate data from pupfish",
      "object": "PupfishMR",
      "class": [
        "data.frame"
      ],
      "fields": [
        "MR",
        "Mass",
        "SL",
        "Treatment"
      ],
      "rows": 100,
      "table": true,
      "tojson": true
    },
    {
      "name": "ReptAbund",
      "title": "Reptile Abundance Data in Western Australia",
      "object": "ReptAbund",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Season",
        "Year",
        "Fire",
        "Session",
        "Site",
        "Aprasia_repens",
        "Christinus_marmoratus",
        "Cryptoblepharus_buchananii",
        "Ctenotus_australis",
        "Ctenotus_fallens",
        "Cyclodomorphus_celatus",
        "Hemiergis_quadrilineata",
        "Lerista_elegans",
        "Lerista_lineopunctulata",
        "Lerista_praepedita",
        "Lialis_burtonis",
        "Menetia_greyii",
        "Morethia_obscura",
        "Neelaps_bimaculatus",
        "Pogona_minor",
        "Pseudonaja_affinis",
        "Ramphotyphlops_australis",
        "Tiliqua_rugosa",
        "Varanus_tristis",
        "reptile_richness",
        "reptile_abundance",
        "Simpson",
        "Eveness"
      ],
      "rows": 50,
      "table": true,
      "tojson": true
    },
    {
      "name": "snakeHS",
      "title": "Snake Head Size and Regional Variation",
      "object": "snakeHS",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Site",
        "Region",
        "Sex",
        "SVL",
        "HS",
        "RW1",
        "RW2",
        "RW3",
        "RW4",
        "RW5",
        "RW6",
        "RW7",
        "RW8",
        "RW9",
        "RW10",
        "RW11",
        "RW12",
        "RW13",
        "RW14",
        "RW15"
      ],
      "rows": 107,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "add.trajectories",
      "title": "Plot Function for RRPP",
      "topics": [
        "add.trajectories"
      ]
    },
    {
      "page": "add.tree",
      "title": "Plot tool to add phylogenetic trees to ordination plots",
      "topics": [
        "add.tree"
      ]
    },
    {
      "page": "anova.lm.rrpp",
      "title": "ANOVA for lm.rrpp model fits",
      "topics": [
        "anova.lm.rrpp"
      ]
    },
    {
      "page": "anova.measurement.error",
      "title": "ANOVA for lm.rrpp model fits used in measurement.error",
      "topics": [
        "anova.measurement.error"
      ]
    },
    {
      "page": "betaTest",
      "title": "Test of beta parameters for lm.rrpp model fits",
      "topics": [
        "betaTest"
      ]
    },
    {
      "page": "classify",
      "title": "Deprecated functions in RRPP",
      "topics": [
        "classify"
      ]
    },
    {
      "page": "coef.lm.rrpp",
      "title": "coef for lm.rrpp model fits",
      "topics": [
        "coef.lm.rrpp"
      ]
    },
    {
      "page": "coef.lmm.rrpp",
      "title": "coef for lmm.rrpp model fits",
      "topics": [
        "coef.lmm.rrpp"
      ]
    },
    {
      "page": "convert2ggplot",
      "title": "Convert RRPP plots to ggplot objects",
      "topics": [
        "convert2ggplot"
      ]
    },
    {
      "page": "effect.size",
      "title": "Obtain Effect-size from a vector of values",
      "topics": [
        "effect.size"
      ]
    },
    {
      "page": "fishy",
      "title": "Simulated Fish Data for Measurement Error Analysis",
      "topics": [
        "fishy"
      ]
    },
    {
      "page": "fitted.lm.rrpp",
      "title": "Extract fitted values",
      "topics": [
        "fitted.lm.rrpp"
      ]
    },
    {
      "page": "fixef.lmm.rrpp",
      "title": "fixef for lmm.rrpp model fits",
      "topics": [
        "fixef.lmm.rrpp"
      ]
    },
    {
      "page": "flower",
      "title": "Flower Production and Temperature",
      "topics": [
        "flower"
      ]
    },
    {
      "page": "focusMEonSubjects",
      "title": "Plot Function for RRPP",
      "topics": [
        "focusMEonSubjects"
      ]
    },
    {
      "page": "getANOVAStats",
      "title": "Utility Function for RRPP",
      "topics": [
        "getANOVAStats"
      ]
    },
    {
      "page": "getModelCov",
      "title": "Utility Function for RRPP",
      "topics": [
        "getModelCov"
      ]
    },
    {
      "page": "getModels",
      "title": "Utility Function for RRPP",
      "topics": [
        "getModels"
      ]
    },
    {
      "page": "getPermInfo",
      "title": "Utility Function for RRPP",
      "topics": [
        "getPermInfo"
      ]
    },
    {
      "page": "getResCov",
      "title": "Utility Function for RRPP",
      "topics": [
        "getResCov"
      ]
    },
    {
      "page": "getTerms",
      "title": "Utility Function for RRPP",
      "topics": [
        "getTerms"
      ]
    },
    {
      "page": "ICCstats",
      "title": "Intraclass correlation statistics from an lm.rrpp model fits",
      "topics": [
        "ICCstats"
      ]
    },
    {
      "page": "interSubVar",
      "title": "Reveal the inter-subject variability from a measurement error analysis",
      "topics": [
        "interSubVar"
      ]
    },
    {
      "page": "kcomp",
      "title": "K-component analysis",
      "topics": [
        "kcomp"
      ]
    },
    {
      "page": "lm.rrpp",
      "title": "Linear Model Evaluation with a Randomized Residual Permutation Procedure",
      "topics": [
        "lm.rrpp"
      ]
    },
    {
      "page": "lm.rrpp.ws",
      "title": "Linear Model Evaluation with RRPP performed within subjects",
      "topics": [
        "lm.rrpp.ws"
      ]
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