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  "Title": "Evolutionary Quantitative Genetics",
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  "Date": "2025-09-05",
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  "Description": "Provides functions for covariance matrix comparisons,\nestimation of repeatabilities in measurements and matrices, and\ngeneral evolutionary quantitative genetics tools. Melo D,\nGarcia G, Hubbe A, Assis A P, Marroig G. (2016)\n<doi:10.12688/f1000research.7082.3>.",
  "License": "MIT + file LICENSE",
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  "Maintainer": "Diogo Melo <diogro@gmail.com>",
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    "AlphaRep",
    "Autonomy",
    "BayesianCalculateMatrix",
    "BootstrapR2",
    "BootstrapRep",
    "BootstrapStat",
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    "CalcEigenVar",
    "CalcICV",
    "CalcR2",
    "CalcR2CvCorrected",
    "CalcRepeatability",
    "CalculateMatrix",
    "Center2MeanJacobianFast",
    "ConditionalEvolvability",
    "Constraints",
    "CreateHypotMatrix",
    "DeltaZCorr",
    "DriftTest",
    "EigenTensorDecomposition",
    "Evolvability",
    "ExtendMatrix",
    "Flexibility",
    "JackKnifeMINT",
    "JacobianArray",
    "KrzCor",
    "KrzProjection",
    "KrzSubspace",
    "KrzSubspaceBootstrap",
    "KrzSubspaceDataFrame",
    "LModularity",
    "LocalShapeVariables",
    "MantelCor",
    "MantelModTest",
    "MatrixCompare",
    "MatrixCor",
    "MatrixDistance",
    "MeanMatrix",
    "MeanMatrixStatistics",
    "MINT",
    "MonteCarloR2",
    "MonteCarloRep",
    "MonteCarloStat",
    "MultiMahalanobis",
    "MultivDriftTest",
    "Norm",
    "Normalize",
    "OverlapDist",
    "Partition2HypotMatrix",
    "Pc1Percent",
    "PCAsimilarity",
    "PCScoreCorrelation",
    "PhyloCompare",
    "PhyloMantel",
    "PhyloW",
    "PlotKrzSubspace",
    "PlotRarefaction",
    "PlotRSprojection",
    "PlotTreeDriftTest",
    "PrintMatrix",
    "ProjectMatrix",
    "RandomMatrix",
    "RandomSkewers",
    "Rarefaction",
    "RarefactionStat",
    "RelativeEigenanalysis",
    "RemoveSize",
    "Respondability",
    "RevertMatrix",
    "RiemannDist",
    "Rotate2MidlineMatrix",
    "RSProjection",
    "SRD",
    "TestModularity",
    "TPS",
    "TreeDriftTest"
  ],
  "_datasets": [
    {
      "name": "dentus",
      "title": "Example multivariate data set",
      "object": "dentus",
      "file": "dentus.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "humerus",
        "ulna",
        "femur",
        "tibia",
        "species"
      ],
      "rows": 300,
      "table": true,
      "tojson": true
    },
    {
      "name": "dentus.tree",
      "title": "Tree for dentus example species",
      "object": "dentus.tree",
      "file": "dentus.tree.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ratones",
      "title": "Linear distances for five mouse lines",
      "object": "ratones",
      "file": "ratones.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        ".id",
        "ID",
        "SEX",
        "GER",
        "LIN",
        "MADRE",
        "PADRE",
        "AGE",
        "P49",
        "line",
        "original_line",
        "selection",
        "IS_PM",
        "IS_NSL",
        "IS_PNS",
        "PM_ZS",
        "PM_ZI",
        "PM_MT",
        "NSL_NA",
        "NSL_ZS",
        "NSL_ZI",
        "NA_BR",
        "NA_PNS",
        "BR_PT",
        "BR_APET",
        "PT_APET",
        "PT_BA",
        "PT_EAM",
        "PT_ZYGO",
        "PT_TSP",
        "ZS_ZI",
        "ZI_MT",
        "ZI_ZYGO",
        "ZI_TSP",
        "MT_PNS",
        "PNS_APET",
        "APET_BA",
        "APET_TS",
        "BA_EAM",
        "EAM_ZYGO",
        "ZYGO_TSP",
        "LD_AS",
        "BR_LD",
        "OPI_LD",
        "PT_AS",
        "JP_AS",
        "BA_OPI"
      ],
      "rows": 329,
      "table": true,
      "tojson": true
    }
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  "_help": [
    {
      "page": "AlphaRep",
      "title": "Alpha repeatability",
      "topics": [
        "AlphaRep"
      ]
    },
    {
      "page": "BayesianCalculateMatrix",
      "title": "Calculate Covariance Matrix from a linear model fitted with lm() using different estimators",
      "topics": [
        "BayesianCalculateMatrix"
      ]
    },
    {
      "page": "BootstrapR2",
      "title": "R2 confidence intervals by bootstrap resampling",
      "topics": [
        "BootstrapR2"
      ]
    },
    {
      "page": "BootstrapRep",
      "title": "Bootstrap analysis via resampling",
      "topics": [
        "BootstrapRep"
      ]
    },
    {
      "page": "BootstrapStat",
      "title": "Non-Parametric population samples and statistic comparison",
      "topics": [
        "BootstrapStat"
      ]
    },
    {
      "page": "CalcAVG",
      "title": "Calculates mean correlations within- and between-modules",
      "topics": [
        "CalcAVG"
      ]
    },
    {
      "page": "CalcEigenVar",
      "title": "Integration measure based on eigenvalue dispersion",
      "topics": [
        "CalcEigenVar"
      ]
    },
    {
      "page": "CalcICV",
      "title": "Calculates the ICV of a covariance matrix.",
      "topics": [
        "CalcICV"
      ]
    },
    {
      "page": "CalcR2",
      "title": "Mean Squared Correlations",
      "topics": [
        "CalcR2"
      ]
    },
    {
      "page": "CalcR2CvCorrected",
      "title": "Corrected integration value",
      "topics": [
        "CalcR2CvCorrected",
        "CalcR2CvCorrected.default",
        "CalcR2CvCorrected.lm"
      ]
    },
    {
      "page": "CalcRepeatability",
      "title": "Parametric per trait repeatabilities",
      "topics": [
        "CalcRepeatability"
      ]
    },
    {
      "page": "CalculateMatrix",
      "title": "Calculate Covariance Matrix from a linear model fitted with lm()",
      "topics": [
        "CalculateMatrix"
      ]
    },
    {
      "page": "Center2MeanJacobianFast",
      "title": "Centered jacobian residuals",
      "topics": [
        "Center2MeanJacobianFast"
      ]
    },
    {
      "page": "ComparisonMap",
      "title": "Generic Comparison Map functions for creating parallel list methods Internal functions for making eficient comparisons.",
      "topics": [
        "ComparisonMap"
      ]
    },
    {
      "page": "CreateHypotMatrix",
      "title": "Creates binary correlation matrices",
      "topics": [
        "CreateHypotMatrix"
      ]
    },
    {
      "page": "DeltaZCorr",
      "title": "Compare matrices via the correlation between response vectors",
      "topics": [
        "DeltaZCorr",
        "DeltaZCorr.default",
        "DeltaZCorr.list"
      ]
    },
    {
      "page": "dentus",
      "title": "Example multivariate data set",
      "topics": [
        "dentus"
      ]
    },
    {
      "page": "dentus.tree",
      "title": "Tree for dentus example species",
      "topics": [
        "dentus.tree"
      ]
    },
    {
      "page": "DriftTest",
      "title": "Test drift hypothesis",
      "topics": [
        "DriftTest"
      ]
    },
    {
      "page": "EigenTensorDecomposition",
      "title": "Eigentensor Decomposition",
      "topics": [
        "EigenTensorDecomposition",
        "EigenTensorDecomposition.default",
        "EigenTensorDecomposition.list"
      ]
    },
    {
      "page": "evolqg",
      "title": "EvolQG",
      "topics": [
        "evolqg-package",
        "evolqg"
      ]
    },
    {
      "page": "ExtendMatrix",
      "title": "Control Inverse matrix noise with Extension",
      "topics": [
        "ExtendMatrix"
      ]
    },
    {
      "page": "JacobianArray",
      "title": "Local Jacobian calculation",
      "topics": [
        "JacobianArray"
      ]
    },
    {
      "page": "KrzCor",
      "title": "Compare matrices via Krzanowski Correlation",
      "topics": [
        "KrzCor",
        "KrzCor.default",
        "KrzCor.list",
        "KrzCor.mcmc_sample"
      ]
    },
    {
      "page": "KrzProjection",
      "title": "Compare matrices via Modified Krzanowski Correlation",
      "topics": [
        "KrzProjection",
        "KrzProjection.default",
        "KrzProjection.list"
      ]
    },
    {
      "page": "KrzSubspace",
      "title": "Krzanowski common subspaces analysis",
      "topics": [
        "KrzSubspace"
      ]
    },
    {
      "page": "KrzSubspaceBootstrap",
      "title": "Quasi-Bayesian Krzanowski subspace comparison",
      "topics": [
        "KrzSubspaceBootstrap"
      ]
    },
    {
      "page": "KrzSubspaceDataFrame",
      "title": "Extract confidence intervals from KrzSubspaceBootstrap",
      "topics": [
        "KrzSubspaceDataFrame"
      ]
    },
    {
      "page": "LModularity",
      "title": "L Modularity",
      "topics": [
        "LModularity"
      ]
    },
    {
      "page": "LocalShapeVariables",
      "title": "Local Shape Variables",
      "topics": [
        "LocalShapeVariables"
      ]
    },
    {
      "page": "MantelCor",
      "title": "Compare matrices via Mantel Correlation",
      "topics": [
        "MantelCor",
        "MantelCor.default",
        "MantelCor.list",
        "MantelCor.mcmc_sample",
        "MatrixCor",
        "MatrixCor.default",
        "MatrixCor.list",
        "MatrixCor.mcmc_sample"
      ]
    },
    {
      "page": "MantelModTest",
      "title": "Test single modularity hypothesis using Mantel correlation",
      "topics": [
        "MantelModTest",
        "MantelModTest.default",
        "MantelModTest.list"
      ]
    },
    {
      "page": "MatrixCompare",
      "title": "Matrix Compare",
      "topics": [
        "MatrixCompare"
      ]
    },
    {
      "page": "MatrixDistance",
      "title": "Matrix distance",
      "topics": [
        "MatrixDistance",
        "MatrixDistance.default",
        "MatrixDistance.list"
      ]
    },
    {
      "page": "MeanMatrix",
      "title": "Mean Covariance Matrix",
      "topics": [
        "MeanMatrix"
      ]
    },
    {
      "page": "MeanMatrixStatistics",
      "title": "Calculate mean values for various matrix statistics",
      "topics": [
        "Autonomy",
        "ConditionalEvolvability",
        "Constraints",
        "Evolvability",
        "Flexibility",
        "MeanMatrixStatistics",
        "Pc1Percent",
        "Respondability"
      ]
    },
    {
      "page": "MINT",
      "title": "Modularity and integration analysis tool",
      "topics": [
        "JackKnifeMINT",
        "MINT"
      ]
    },
    {
      "page": "MonteCarloR2",
      "title": "R2 confidence intervals by parametric sampling",
      "topics": [
        "MonteCarloR2"
      ]
    },
    {
      "page": "MonteCarloRep",
      "title": "Parametric repeatabilities with covariance or correlation matrices",
      "topics": [
        "MonteCarloRep"
      ]
    },
    {
      "page": "MonteCarloStat",
      "title": "Parametric population samples with covariance or correlation matrices",
      "topics": [
        "MonteCarloStat"
      ]
    },
    {
      "page": "MultiMahalanobis",
      "title": "Calculate Mahalonabis distance for many vectors",
      "topics": [
        "MultiMahalanobis"
      ]
    },
    {
      "page": "MultivDriftTest",
      "title": "Multivariate genetic drift test for 2 populations",
      "topics": [
        "MultivDriftTest"
      ]
    },
    {
      "page": "Normalize",
      "title": "Normalize and Norm",
      "topics": [
        "Norm",
        "Normalize"
      ]
    },
    {
      "page": "OverlapDist",
      "title": "Distribution overlap distance",
      "topics": [
        "OverlapDist"
      ]
    },
    {
      "page": "Partition2HypotMatrix",
      "title": "Create binary hypothesis",
      "topics": [
        "Partition2HypotMatrix"
      ]
    },
    {
      "page": "PCAsimilarity",
      "title": "Compare matrices using PCA similarity factor",
      "topics": [
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