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  "Title": "Epistatic Network Modelling with Forward-Time Simulation",
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  "Description": "Allows for forward-in-time simulation of epistatic\nnetworks with associated phenotypic output.",
  "URL": "https://github.com/diondetterer/epinetr",
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    "runSim"
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        "V2",
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      "page": "addEffects",
      "title": "Attach additive effects to population.",
      "topics": [
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      ]
    },
    {
      "page": "attachEpiNet",
      "title": "Attach epistatic network to population.",
      "topics": [
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      ]
    },
    {
      "page": "epinetr",
      "title": "epinetr",
      "topics": [
        "epinetr"
      ]
    },
    {
      "page": "geno100snp",
      "title": "Example genotype matrix.",
      "topics": [
        "geno100snp"
      ]
    },
    {
      "page": "getAddCoefs",
      "title": "Get additive coefficients.",
      "topics": [
        "getAddCoefs"
      ]
    },
    {
      "page": "getAddOffset",
      "title": "Retrieve additive offset.",
      "topics": [
        "getAddOffset"
      ]
    },
    {
      "page": "getAlleleFreqRun",
      "title": "Get allele frequencies.",
      "topics": [
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      ]
    },
    {
      "page": "getComponents",
      "title": "Get phenotypic components.",
      "topics": [
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      ]
    },
    {
      "page": "getEpiNet",
      "title": "Epistatic network retrieval.",
      "topics": [
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    },
    {
      "page": "getEpiOffset",
      "title": "Retrieve epistatic offset.",
      "topics": [
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      ]
    },
    {
      "page": "getEpistasis",
      "title": "Calculate epistatic interactions.",
      "topics": [
        "getEpistasis"
      ]
    },
    {
      "page": "getGeno",
      "title": "Get population unphased genotypes.",
      "topics": [
        "getGeno"
      ]
    },
    {
      "page": "getHaplo",
      "title": "Retrieve haplotypes.",
      "topics": [
        "getHaplo"
      ]
    },
    {
      "page": "getIncMatrix",
      "title": "Incidence matrix retrieval.",
      "topics": [
        "getIncMatrix"
      ]
    },
    {
      "page": "getInteraction",
      "title": "Retrieve interaction values.",
      "topics": [
        "getInteraction"
      ]
    },
    {
      "page": "getPedigree",
      "title": "Get population pedigree.",
      "topics": [
        "getPedigree"
      ]
    },
    {
      "page": "getPhased",
      "title": "Get population phased genotypes.",
      "topics": [
        "getPhased"
      ]
    },
    {
      "page": "getQTL",
      "title": "QTL retrieval.",
      "topics": [
        "getQTL"
      ]
    },
    {
      "page": "getSubPop",
      "title": "Get subpopulation",
      "topics": [
        "getSubPop"
      ]
    },
    {
      "page": "loadGeno",
      "title": "Load epinetr genotype file.",
      "topics": [
        "loadGeno"
      ]
    },
    {
      "page": "map100snp",
      "title": "Example map.",
      "topics": [
        "map100snp"
      ]
    },
    {
      "page": "plot.EpiNet",
      "title": "Plot epistatic network.",
      "topics": [
        "plot.EpiNet"
      ]
    },
    {
      "page": "plot.Population",
      "title": "Plot phenotypic value for a population.",
      "topics": [
        "plot.Population"
      ]
    },
    {
      "page": "Population",
      "title": "Population constructor.",
      "topics": [
        "Population"
      ]
    },
    {
      "page": "print.Population",
      "title": "Print function for population.",
      "topics": [
        "print.Population"
      ]
    },
    {
      "page": "rincmat100snp",
      "title": "Example incidence matrix.",
      "topics": [
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    },
    {
      "page": "runSim",
      "title": "Run simulation on population.",
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  "_vignettes": [
    {
      "source": "epinetr-vignette.Rmd",
      "filename": "epinetr-vignette.html",
      "title": "Using the epinetr package",
      "author": "Dion Detterer, Paul Kwan, Cedric Gondro",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Constructing the initial population",
        "Constructing a population using a genotype matrix",
        "Modifying an existing population",
        "Attaching effects to the population",
        "Attaching an epistatic network to the population",
        "Supplying a user-defined network",
        "Creating purely epistatic QTL",
        "Calculating effects",
        "Inspecting additive, epistatic and environmental components",
        "Deriving additive and epistatic components",
        "Running the simulation",
        "Using the pedigree dropper",
        "Conclusion",
        "References"
      ],
      "created": "2019-11-13 22:59:13",
      "modified": "2022-03-09 01:22:57",
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