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  "Title": "(Non)Additive Genetic Relatedness Matrices",
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  "Description": "Constructs (non)additive genetic relationship matrices,\nand their inverses, from a pedigree to be used in linear mixed\neffect models (A.K.A. the 'animal model'). Also includes other\nfunctions to facilitate the use of animal models. Some\nfunctions have been created to be used in conjunction with the\nR package 'asreml' for the 'ASReml' software, which can be\nobtained upon purchase from 'VSN' international\n(<https://vsni.co.uk/software/asreml>).",
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  "Packaged": {
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    "makeSd",
    "makeSdsim",
    "makeT",
    "makeTinv",
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    "pcc",
    "pin",
    "prepPed",
    "prunePed",
    "ronPed",
    "simGG",
    "simPedDFC",
    "simPedHS",
    "simPedMCN",
    "sm2list",
    "varTrans"
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    }
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      "page": "nadiv-package",
      "title": "(Non)Additive Genetic Relatedness Matrices in Animal Model Analyses",
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        "nadiv-package",
        "nadiv"
      ]
    },
    {
      "page": "aic",
      "title": "Akaike Information Criterion",
      "topics": [
        "aic"
      ]
    },
    {
      "page": "aiCI",
      "title": "Confidence Intervals for Variance Components",
      "topics": [
        "aiCI"
      ]
    },
    {
      "page": "aiFun",
      "title": "Sampling (co)variances",
      "topics": [
        "aiFun"
      ]
    },
    {
      "page": "constrainFun",
      "title": "Fix a Model Parameter and Conduct Likelihood Ratio Test",
      "topics": [
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      ]
    },
    {
      "page": "drfx",
      "title": "Simulated design random effects",
      "topics": [
        "drfx"
      ]
    },
    {
      "page": "F2009",
      "title": "Pedigree adapted from Fikse 2009 with genetic groups and fuzzy classification",
      "topics": [
        "F2009"
      ]
    },
    {
      "page": "FG90",
      "title": "Pedigree, adapted from Table 1 in Fernando & Grossman (1990)",
      "topics": [
        "FG90"
      ]
    },
    {
      "page": "findDFC",
      "title": "Finds the double first cousins in a pedigree",
      "topics": [
        "findDFC"
      ]
    },
    {
      "page": "founderLine",
      "title": "Identifies the matriline or patriline to which each individual in a pedigree belongs",
      "topics": [
        "founderLine"
      ]
    },
    {
      "page": "genAssign",
      "title": "Generation assignment",
      "topics": [
        "genAssign",
        "genAssign.default",
        "genAssign.numPed"
      ]
    },
    {
      "page": "geneDrop",
      "title": "Functions to conduct gene dropping through a pedigree",
      "topics": [
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        "geneDrop.default",
        "geneDrop.numPed"
      ]
    },
    {
      "page": "ggcontrib",
      "title": "Genetic group contribution",
      "topics": [
        "ggcontrib"
      ]
    },
    {
      "page": "ggTutorial",
      "title": "Simulated dataset used to analyze data with genetic group animal models",
      "topics": [
        "ggTutorial"
      ]
    },
    {
      "page": "grfx",
      "title": "Simulated genetic random effects",
      "topics": [
        "grfx"
      ]
    },
    {
      "page": "LRTest",
      "title": "log-Likelihood Ratio Test",
      "topics": [
        "LRTest"
      ]
    },
    {
      "page": "makeA",
      "title": "Creates the additive genetic relationship matrix",
      "topics": [
        "makeA"
      ]
    },
    {
      "page": "makeAA",
      "title": "Creates the additive by additive epistatic genetic relationship matrix",
      "topics": [
        "makeAA"
      ]
    },
    {
      "page": "makeAinv",
      "title": "Creates the inverse additive genetic relationship matrix",
      "topics": [
        "makeAinv",
        "makeAinv.default",
        "makeAinv.fuzzy",
        "makeGGAinv"
      ]
    },
    {
      "page": "makeAstarMult",
      "title": "Creates the inverse additive genetic relationship matrix with genetic groups",
      "topics": [
        "makeAstarMult"
      ]
    },
    {
      "page": "makeD",
      "title": "Create the dominance genetic relationship matrix",
      "topics": [
        "makeD",
        "makeSd"
      ]
    },
    {
      "page": "makeDomEpi",
      "title": "Creates the additive by dominance and dominance by dominance epistatic genetic relationship matrices",
      "topics": [
        "makeDomEpi"
      ]
    },
    {
      "page": "makeDsim",
      "title": "Create the dominance genetic relationship matrix through an iterative (simulation) process",
      "topics": [
        "makeDsim",
        "makeSdsim"
      ]
    },
    {
      "page": "makeM",
      "title": "Creates the (additive) mutational effects relationship matrix",
      "topics": [
        "makeM"
      ]
    },
    {
      "page": "makeMinv",
      "title": "Create the inverse (additive) mutational effects relationship matrix",
      "topics": [
        "makeMinv",
        "makeMinvML"
      ]
    },
    {
      "page": "makeS",
      "title": "Creates the additive genetic relationship matrix for the shared sex chromosomes",
      "topics": [
        "makeS"
      ]
    },
    {
      "page": "makeTinv",
      "title": "Creates components of the additive genetic relationship matrix and its inverse",
      "topics": [
        "makeDiiF",
        "makeDiiF.default",
        "makeDiiF.numPed",
        "makeT",
        "makeT.default",
        "makeT.numPed",
        "makeTinv",
        "makeTinv.default",
        "makeTinv.numPed"
      ]
    },
    {
      "page": "Mrode2",
      "title": "Pedigree from Table 2.1 of Mrode (2005)",
      "topics": [
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    {
      "page": "Mrode3",
      "title": "Pedigree, from chapter 3 of Mrode (2005) with genetic groups and a trait column",
      "topics": [
        "Mrode3"
      ]
    },
    {
      "page": "Mrode9",
      "title": "Pedigree, adapted from example 9.1 of Mrode (2005)",
      "topics": [
        "Mrode9"
      ]
    },
    {
      "page": "numPed",
      "title": "Integer Format Pedigree",
      "topics": [
        "numPed",
        "ronPed"
      ]
    },
    {
      "page": "pcc",
      "title": "REML convergence checks",
      "topics": [
        "pcc"
      ]
    },
    {
      "page": "prepPed",
      "title": "Prepares a pedigree by sorting and adding 'founders'",
      "topics": [
        "prepPed"
      ]
    },
    {
      "page": "prunePed",
      "title": "Prunes a pedigree based on individuals with phenotypes",
      "topics": [
        "prunePed",
        "prunePed.default",
        "prunePed.numPed"
      ]
    },
    {
      "page": "Q1988",
      "title": "Pedigree with genetic groups adapted from Quaas (1988) equation [5]",
      "topics": [
        "Q1988"
      ]
    },
    {
      "page": "simGG",
      "title": "Genetic group pedigree and data simulation",
      "topics": [
        "simGG"
      ]
    },
    {
      "page": "simPedDFC",
      "title": "Double first cousin pedigree construction",
      "topics": [
        "simPedDFC"
      ]
    },
    {
      "page": "simPedHS",
      "title": "Half-sib pedigree construction",
      "topics": [
        "simPedHS"
      ]
    },
    {
      "page": "simPedMCN",
      "title": "Middle Class Neighborhood pedigree construction",
      "topics": [
        "simPedMCN"
      ]
    },
    {
      "page": "sm2list",
      "title": "Converts a sparse matrix into a three column format.",
      "topics": [
        "sm2list"
      ]
    },
    {
      "page": "varTrans",
      "title": "Transforms ASReml-R gamma sampling variances to component scale",
      "topics": [
        "varTrans"
      ]
    },
    {
      "page": "warcolak",
      "title": "Pedigree and phenotypic values for a mythical population of Warcolaks",
      "topics": [
        "warcolak"
      ]
    },
    {
      "page": "Wray90",
      "title": "Pedigree, adapted from Wray (1990)",
      "topics": [
        "Wray90"
      ]
    }
  ],
  "_readme": "https://github.com/matthewwolak/nadiv/raw/HEAD/README.md",
  "_rundeps": [
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