{
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  "Title": "Solving Mixed Model Equations in R",
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  "Date": "2026-03-19",
  "Authors@R": "c(\nperson(\"Giovanny\",\"Covarrubias-Pazaran\", email=\"cova_ruber@live.com.mx\", role=c(\"aut\",\"cre\"),\ncomment=c(ORCID=\"0000-0002-7194-3837\"))\n)",
  "Maintainer": "Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>",
  "Description": "Structural multivariate-univariate linear mixed model\nsolver for estimation of multiple random effects with unknown\nvariance-covariance structures (e.g., heterogeneous and\nunstructured) and known covariance among levels of random\neffects (e.g., pedigree and genomic relationship matrices)\n(Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>;\nMaier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>; Jensen et\nal., 1997). REML estimates can be obtained using the\nDirect-Inversion Newton-Raphson and Direct-Inversion Average\nInformation algorithms for the problems r x r (r being the\nnumber of records) or using the Henderson-based average\ninformation algorithm for the problem c x c (c being the number\nof coefficients to estimate). Spatial models can also be fitted\nusing the two-dimensional spline functionality available.",
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  "License": "GPL (>= 2)",
  "BugReports": "https://github.com/covaruber/sommer/issues",
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  "Date/Publication": "2026-04-05 03:05:15 UTC",
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  "_exports": [
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    "ARMA",
    "atm",
    "atr",
    "coef.mmes",
    "corImputation",
    "covm",
    "CS",
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    "dsm",
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    "E.mat",
    "fitted.mmes",
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    "GWAS",
    "H.mat",
    "ism",
    "mmer",
    "mmes",
    "MNR",
    "plot.mmes",
    "pmonitor",
    "predict.mmes",
    "r2",
    "randef",
    "residuals.mmes",
    "spl2Dc",
    "spl2Dmats",
    "summary.mmes",
    "tpsmmbwrapper",
    "unsm",
    "unsm2",
    "usm",
    "usr",
    "vpredict",
    "vs",
    "vsm",
    "vsr"
  ],
  "_help": [
    {
      "page": "sommer-package",
      "title": "*So*lving *M*ixed *M*odel *E*quations in *R*",
      "topics": [
        "sommer"
      ]
    },
    {
      "page": "A.mat",
      "title": "Additive relationship matrix",
      "topics": [
        "A.mat"
      ]
    },
    {
      "page": "anova_mmes",
      "title": "anova form a GLMM fitted with mmes",
      "topics": [
        "anova.mmer",
        "anova.mmes"
      ]
    },
    {
      "page": "AR1mat",
      "title": "Autocorrelation matrix of order 1.",
      "topics": [
        "AR1"
      ]
    },
    {
      "page": "ARMAmat",
      "title": "Autocorrelation Moving average.",
      "topics": [
        "ARMA"
      ]
    },
    {
      "page": "atm",
      "title": "atm covariance structure",
      "topics": [
        "atm",
        "atr"
      ]
    },
    {
      "page": "coef_mmes",
      "title": "coef form a GLMM fitted with mmes",
      "topics": [
        "coef.mmer",
        "coef.mmes"
      ]
    },
    {
      "page": "corImputation",
      "title": "Imputing a matrix using correlations",
      "topics": [
        "corImputation"
      ]
    },
    {
      "page": "covm",
      "title": "covariance between random effects",
      "topics": [
        "covm"
      ]
    },
    {
      "page": "CSmat",
      "title": "Compound symmetry matrix",
      "topics": [
        "CS"
      ]
    },
    {
      "page": "csm",
      "title": "customized covariance structure",
      "topics": [
        "csm",
        "csr"
      ]
    },
    {
      "page": "D.mat",
      "title": "Dominance relationship matrix",
      "topics": [
        "D.mat"
      ]
    },
    {
      "page": "dfToMatrix",
      "title": "data frame to matrix",
      "topics": [
        "dfToMatrix"
      ]
    },
    {
      "page": "dsm",
      "title": "diagonal covariance structure",
      "topics": [
        "dsm",
        "dsr"
      ]
    },
    {
      "page": "E.mat",
      "title": "Epistatic relationship matrix",
      "topics": [
        "E.mat"
      ]
    },
    {
      "page": "fitted_mmes",
      "title": "fitted form a LMM fitted with mmes",
      "topics": [
        "fitted.mmer",
        "fitted.mmes"
      ]
    },
    {
      "page": "fixm",
      "title": "fixed indication matrix",
      "topics": [
        "fixm"
      ]
    },
    {
      "page": "DEPRECATED_GWAS",
      "title": "Genome wide association study analysis",
      "topics": [
        "GWAS"
      ]
    },
    {
      "page": "H.mat",
      "title": "Combined relationship matrix H",
      "topics": [
        "H.mat"
      ]
    },
    {
      "page": "ism",
      "title": "identity covariance structure",
      "topics": [
        "ism"
      ]
    },
    {
      "page": "mmer",
      "title": "*m*ixed *m*odel *e*quations for *r* records",
      "topics": [
        "mmer"
      ]
    },
    {
      "page": "mmes",
      "title": "*m*ixed *m*odel *e*quations *s*olver",
      "topics": [
        "mmes"
      ]
    },
    {
      "page": "MNR",
      "title": "Multivariate Newton-Raphson algorithm",
      "topics": [
        "MNR"
      ]
    },
    {
      "page": "plot_mmes",
      "title": "plot form a LMM plot with mmes",
      "topics": [
        "plot.mmer",
        "plot.mmes"
      ]
    },
    {
      "page": "plot.monitor",
      "title": "plot the change of VC across iterations",
      "topics": [
        "pmonitor"
      ]
    },
    {
      "page": "predict_mmes",
      "title": "Predict form of a LMM fitted with mmes",
      "topics": [
        "predict.mmer",
        "predict.mmes"
      ]
    },
    {
      "page": "r2",
      "title": "Reliability",
      "topics": [
        "r2"
      ]
    },
    {
      "page": "randef",
      "title": "extracting random effects",
      "topics": [
        "randef"
      ]
    },
    {
      "page": "residuals_mmes",
      "title": "Residuals form a GLMM fitted with mmes",
      "topics": [
        "residuals.mmer",
        "residuals.mmes"
      ]
    },
    {
      "page": "spl2Dc",
      "title": "Two-dimensional penalised tensor-product of marginal B-Spline basis.",
      "topics": [
        "spl2Da",
        "spl2Db",
        "spl2Dc"
      ]
    },
    {
      "page": "spl2Dmats",
      "title": "Get Tensor Product Spline Mixed Model Incidence Matrices",
      "topics": [
        "spl2Dmats"
      ]
    },
    {
      "page": "DEPRECATED_summary_mmer",
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