{
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  "Package": "HAPTRACE",
  "Title": "Haplotype-Based Tracking of Admixed Population for Breed\nComposition Estimation",
  "Version": "0.1.2",
  "Authors@R": "c(\nperson(\"Shweta\", \"Sahoo\", , \"queryhap01@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-5154-5719\")),\nperson(\"Sara de las\", \"Heras-Saldana\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-8665-6160\")),\nperson(\"Julius H. J.\", \"van der Werf\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-2512-1696\")),\nperson(\"Mohammad H.\", \"Ferdosi\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-5385-4913\"))\n)",
  "Maintainer": "Shweta Sahoo <queryhap01@gmail.com>",
  "Description": "Simulate populations and track haplotypes over generations\nto evaluate population admixture. The 'HAPTRACE' supports\ncustomisable population parameters, including size, number of\nmarkers, mutation rates and recombination.",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
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  "Author": "Shweta Sahoo [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-5154-5719>), Sara de las\nHeras-Saldana [aut] (ORCID:\n<https://orcid.org/0000-0002-8665-6160>), Julius H. J. van der\nWerf [aut] (ORCID: <https://orcid.org/0000-0003-2512-1696>),\nMohammad H. Ferdosi [aut] (ORCID:\n<https://orcid.org/0000-0001-5385-4913>)",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2026-09-10 04:10:02 UTC",
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  "_created": "2026-10-11T15:42:26.000Z",
  "_published": "2026-10-11T15:46:35.464Z",
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  "_topics": [
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  "_exports": [
    "Admixplot",
    "AlleleFreq",
    "BreedEff_Haplo",
    "BreedPopCross",
    "BreedPopSelect",
    "CalQTLeffect",
    "Coded_to_Haplo",
    "DamSample",
    "Ext_Pheno",
    "GenBreedPop",
    "generateHP",
    "generateMAP",
    "GenOnePopulation",
    "MakeGeno",
    "mapQTLfile",
    "MatingPop",
    "MutationRate",
    "Ped_Pheno",
    "plinkped",
    "plotHaplo",
    "PopSelect",
    "PopulationID",
    "QMSim_PlinkMAP",
    "QTL_densityplot",
    "QTLeffects",
    "Random_gametes",
    "read_qmsim_geno",
    "ReadQTL",
    "Recode_Haplotype",
    "RecombinationPoint",
    "recProbplot",
    "Reformat_BLUPF90",
    "Rescale",
    "SireSample",
    "TBV_Haplo",
    "trueBreedComp",
    "TwoPopCross",
    "Var_PhenoRecords"
  ],
  "_help": [
    {
      "page": "Admixplot",
      "title": "Plot for True Breed Composition",
      "topics": [
        "Admixplot"
      ]
    },
    {
      "page": "AlleleFreq",
      "title": "Calculate Allele Frequency",
      "topics": [
        "AlleleFreq"
      ]
    },
    {
      "page": "BreedEff_Haplo",
      "title": "True Breeding Value (TBV) estimation according to breed of origin",
      "topics": [
        "BreedEff_Haplo"
      ]
    },
    {
      "page": "BreedPopCross",
      "title": "Function for crossing two population with breed effects according to breed of origin",
      "topics": [
        "BreedPopCross"
      ]
    },
    {
      "page": "BreedPopSelect",
      "title": "Selecting Population with breed effect according to breed of origin",
      "topics": [
        "BreedPopSelect"
      ]
    },
    {
      "page": "CalQTLeffect",
      "title": "Calculate QTL effect from file generated from ReadQTL (For QMSim generated files)",
      "topics": [
        "CalQTLeffect"
      ]
    },
    {
      "page": "Coded_to_Haplo",
      "title": "Recode Coded haplotypes according to breed of origin into 0 and 1 format",
      "topics": [
        "Coded_to_Haplo"
      ]
    },
    {
      "page": "DamSample",
      "title": "Select Dams",
      "topics": [
        "DamSample"
      ]
    },
    {
      "page": "Ext_Pheno",
      "title": "Extract TBV and Phenotype",
      "topics": [
        "Ext_Pheno"
      ]
    },
    {
      "page": "GenBreedPop",
      "title": "Generate Population with specific breed effect",
      "topics": [
        "GenBreedPop"
      ]
    },
    {
      "page": "generateHP",
      "title": "Generate Historical Population",
      "topics": [
        "generateHP"
      ]
    },
    {
      "page": "generateMAP",
      "title": "Generate MAP file",
      "topics": [
        "generateMAP"
      ]
    },
    {
      "page": "GenOnePopulation",
      "title": "Simulate Population",
      "topics": [
        "GenOnePopulation"
      ]
    },
    {
      "page": "MakeGeno",
      "title": "Make Genotype from Haplotype",
      "topics": [
        "MakeGeno"
      ]
    },
    {
      "page": "mapQTLfile",
      "title": "Create combined map and qtl file",
      "topics": [
        "mapQTLfile"
      ]
    },
    {
      "page": "MatingPop",
      "title": "Function for mating sire and dam",
      "topics": [
        "MatingPop"
      ]
    },
    {
      "page": "MutationRate",
      "title": "Adding Mutation",
      "topics": [
        "MutationRate"
      ]
    },
    {
      "page": "Ped_Pheno",
      "title": "Combine Pedigree and Phenotype data",
      "topics": [
        "Ped_Pheno"
      ]
    },
    {
      "page": "plinkped",
      "title": "Generate PLINK pedigree file",
      "topics": [
        "plinkped"
      ]
    },
    {
      "page": "plotHaplo",
      "title": "Plot for Haplotype segments",
      "topics": [
        "plotHaplo"
      ]
    },
    {
      "page": "PopSelect",
      "title": "Selecting Population with selection criteria random, phenotype and true breeding value",
      "topics": [
        "PopSelect"
      ]
    },
    {
      "page": "PopulationID",
      "title": "Adding Population Code before simulating the population",
      "topics": [
        "PopulationID"
      ]
    },
    {
      "page": "QMSim_PlinkMAP",
      "title": "Format PLINK MAP file from QMSim",
      "topics": [
        "QMSim_PlinkMAP"
      ]
    },
    {
      "page": "QTL_densityplot",
      "title": "Plot for the QTL effect",
      "topics": [
        "QTL_densityplot"
      ]
    },
    {
      "page": "QTLeffects",
      "title": "Calculation QTL effects",
      "topics": [
        "QTLeffects"
      ]
    },
    {
      "page": "Random_gametes",
      "title": "Random selection of sire and dam gametes",
      "topics": [
        "Random_gametes"
      ]
    },
    {
      "page": "read_qmsim_geno",
      "title": "Read QMSim Marker/QTL Genotype File",
      "topics": [
        "read_qmsim_geno"
      ]
    },
    {
      "page": "ReadQTL",
      "title": "Read QTL file obtained from QMSim",
      "topics": [
        "ReadQTL"
      ]
    },
    {
      "page": "Recode_Haplotype",
      "title": "Recode Haplotype with different breed codes",
      "topics": [
        "Recode_Haplotype"
      ]
    },
    {
      "page": "RecombinationPoint",
      "title": "Add Recombination",
      "topics": [
        "RecombinationPoint"
      ]
    },
    {
      "page": "recProbplot",
      "title": "Plot for recombination points and recombination probability",
      "topics": [
        "recProbplot"
      ]
    },
    {
      "page": "Reformat_BLUPF90",
      "title": "Reformat genotype data for BLUPF90 analysis",
      "topics": [
        "Reformat_BLUPF90"
      ]
    },
    {
      "page": "Rescale",
      "title": "Rescaling SNP Effect",
      "topics": [
        "Rescale"
      ]
    },
    {
      "page": "SireSample",
      "title": "Select Sires",
      "topics": [
        "SireSample"
      ]
    },
    {
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      "title": "Calculation of True breeding Value (TBV)",
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        "TBV_Haplo"
      ]
    },
    {
      "page": "trueBreedComp",
      "title": "Calculate True Breed Proportion with coded haplotype",
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        "trueBreedComp"
      ]
    },
    {
      "page": "TwoPopCross",
      "title": "Function for crossing two populations",
      "topics": [
        "TwoPopCross"
      ]
    },
    {
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      "title": "Generate variance components and phenotypic records",
      "topics": [
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      ]
    }
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      "source": "Introduction_HAPTRACE.Rmd",
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      "title": "Introduction to HAPTRACE",
      "author": "Shweta Sahoo, Sara de las Heras-Saldana, Julius H. J. van der Werf, Mohammad H. Ferdosi",
      "engine": "knitr::rmarkdown",
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        "Input data for simulating the population",
        "Creating MAP and QTL file",
        "Creating a historical population",
        "Assigning of population code and haplotype recording",
        "Modelling the breeding program",
        "Visualization of an admixed population",
        "Haplotype plot",
        "References"
      ],
      "created": "2026-07-30 18:52:13",
      "modified": "2026-09-10 04:10:02",
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