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  "Version": "5.2",
  "Date": "2026-09-29",
  "Title": "Fitting Mixed Models with Known Covariance Structures and GWAS",
  "Author": "Deniz Akdemir, Okeke Uche Godfrey",
  "Maintainer": "Deniz Akdemir <deniz.akdemir.work@gmail.com>",
  "Description": "An improved mixed model solver that handles a variety of\ncovariance structures. The main functions are 'emmreml',\n'emmremlMultiKernel', and 'emmremlMultivariate'. The 'emmreml'\nfunction solves mixed models with known covariance structure\nusing the 'EMMA' algorithm. 'emmremlMultiKernel' allows for\nfitting models with multiple random components with known\ncovariance structures. The 'emmremlMultivariate' function\nsolves multivariate Gaussian mixed models with known covariance\nstructures using the 'ECM' algorithm. The package now offers\nboth the original matrix interface (fully backward compatible\nwith v3.1) and a modern formula interface. The\n'emmremlMultivariate' function restores 'Gpred' and all test\noutputs from v3.1 while fixing ECM convergence. The new 'gwas'\nfunction provides genome-wide association studies with mixed\nmodels, including an accelerated algorithm and visualization\noptions.",
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  "BugReports": "https://github.com/dakdemir/EMMREML/issues",
  "Repository": "https://denizakdemir.r-universe.dev",
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      "date": "2015-03-31"
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    "calculate_allele_frequencies",
    "calculate_kinship",
    "compare_kinship",
    "convert_marker_coding",
    "demo_gwas",
    "demo_K_optimization",
    "demo_kinship",
    "demo_multivariate",
    "emmreml",
    "emmremlMultiKernel",
    "emmremlMultiKernel_core",
    "emmremlMultivariate",
    "emmremlMultivariate_core",
    "filter_markers",
    "generate_example_data",
    "gwas",
    "identify_marker_coding",
    "impute_markers",
    "is_diagonal_matrix",
    "is_identity_matrix",
    "marker_statistics",
    "plot_marker_stats",
    "plot.emmreml_gwas",
    "predict.emmreml",
    "print.emmreml",
    "print.emmreml_gwas",
    "print.emmreml_multi",
    "print.summary.emmreml",
    "print.summary.emmreml_gwas",
    "print.summary.emmreml_multi",
    "subset_markers_by_maf",
    "summarize_marker_data",
    "summary.emmreml",
    "summary.emmreml_gwas",
    "summary.emmreml_multi",
    "visualize_kinship"
  ],
  "_help": [
    {
      "page": "calculate_allele_frequencies",
      "title": "Calculate allele frequencies from marker data",
      "topics": [
        "calculate_allele_frequencies"
      ]
    },
    {
      "page": "calculate_kinship",
      "title": "Calculate a genomic relationship matrix (GRM/kinship matrix)",
      "topics": [
        "calculate_kinship"
      ]
    },
    {
      "page": "compare_kinship",
      "title": "Compare different kinship matrices",
      "topics": [
        "compare_kinship"
      ]
    },
    {
      "page": "convert_marker_coding",
      "title": "Convert marker coding between different types",
      "topics": [
        "convert_marker_coding"
      ]
    },
    {
      "page": "demo_gwas",
      "title": "Example of using GWAS functionality",
      "topics": [
        "demo_gwas"
      ]
    },
    {
      "page": "demo_K_optimization",
      "title": "Example of using EMMREML with K optimization",
      "topics": [
        "demo_K_optimization"
      ]
    },
    {
      "page": "demo_kinship",
      "title": "Demonstrate the kinship matrix calculation functionality",
      "topics": [
        "demo_kinship"
      ]
    },
    {
      "page": "demo_multivariate",
      "title": "Example of using the multivariate EMMREML",
      "topics": [
        "demo_multivariate"
      ]
    },
    {
      "page": "emmreml",
      "title": "Solver for Gaussian mixed model with known covariance structure.",
      "topics": [
        "emmreml"
      ]
    },
    {
      "page": "EMMREML-package",
      "title": "Fitting mixed models with known covariance structures.",
      "topics": [
        "EMMREML"
      ]
    },
    {
      "page": "emmremlMultiKernel",
      "title": "Function to fit Gaussian mixed model with multiple mixed effects with known covariances.",
      "topics": [
        "emmremlMultiKernel"
      ]
    },
    {
      "page": "emmremlMultivariate",
      "title": "Fit a Multivariate Gaussian Mixed Model with Known Covariance Structure",
      "topics": [
        "emmremlMultivariate"
      ]
    },
    {
      "page": "emmremlMultivariate_core",
      "title": "Fit a Multivariate Gaussian Mixed Model with Known Covariance Structure",
      "topics": [
        "emmremlMultivariate_core"
      ]
    },
    {
      "page": "filter_markers",
      "title": "Filter markers based on various criteria",
      "topics": [
        "filter_markers"
      ]
    },
    {
      "page": "generate_example_data",
      "title": "Generate example data for EMMREML demonstrations",
      "topics": [
        "generate_example_data"
      ]
    },
    {
      "page": "gwas",
      "title": "Genome-Wide Association Study Analysis",
      "topics": [
        "gwas"
      ]
    },
    {
      "page": "identify_marker_coding",
      "title": "Kinship Matrix Calculation and Marker Data Processing",
      "topics": [
        "identify_marker_coding"
      ]
    },
    {
      "page": "impute_markers",
      "title": "Impute missing marker data",
      "topics": [
        "impute_markers"
      ]
    },
    {
      "page": "kinship",
      "title": "Kinship Matrix Calculation and Marker Data Functions",
      "topics": [
        "kinship"
      ]
    },
    {
      "page": "marker_statistics",
      "title": "Calculate minor allele frequencies and return marker statistics",
      "topics": [
        "marker_statistics"
      ]
    },
    {
      "page": "plot_marker_stats",
      "title": "Plot marker data summary statistics",
      "topics": [
        "plot_marker_stats"
      ]
    },
    {
      "page": "plot.emmreml_gwas",
      "title": "Plot Method for emmreml_gwas Objects",
      "topics": [
        "plot.emmreml_gwas"
      ]
    },
    {
      "page": "predict.emmreml",
      "title": "Predict Method for emmreml Objects",
      "topics": [
        "predict.emmreml"
      ]
    },
    {
      "page": "print.emmreml",
      "title": "Print Method for emmreml Objects",
      "topics": [
        "print.emmreml"
      ]
    },
    {
      "page": "print.emmreml_gwas",
      "title": "Print Method for emmreml_gwas Objects",
      "topics": [
        "print.emmreml_gwas"
      ]
    },
    {
      "page": "print.emmreml_multi",
      "title": "Print Method for emmreml_multi Objects",
      "topics": [
        "print.emmreml_multi"
      ]
    },
    {
      "page": "print.summary.emmreml",
      "title": "Print Method for summary.emmreml Objects",
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      "title": "Print Method for summary.emmreml_gwas Objects",
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