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  "Package": "bnpsd",
  "Title": "Simulate Genotypes from the BN-PSD Admixture Model",
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  "Authors@R": "c(\nperson(given = \"Alejandro\",\nfamily = \"Ochoa\",\nrole = c(\"aut\", \"cre\"),\nemail = \"alejandro.ochoa@duke.edu\",\ncomment = c(ORCID = \"0000-0003-4928-3403\")),\nperson(given = \"John D.\",\nfamily = \"Storey\",\nrole = c(\"aut\"),\nemail = \"jstorey@princeton.edu\",\ncomment = c(ORCID = \"0000-0001-5992-402X\"))\n)",
  "Description": "The Pritchard-Stephens-Donnelly (PSD) admixture model has\nk intermediate subpopulations from which n individuals draw\ntheir alleles dictated by their individual-specific admixture\nproportions.  The BN-PSD model additionally imposes the\nBalding-Nichols (BN) allele frequency model to the intermediate\npopulations, which therefore evolved independently from a\ncommon ancestral population T with subpopulation-specific FST\n(Wright's fixation index) parameters.  The BN-PSD model can be\nused to yield complex population structures.  This simulation\napproach is now extended to subpopulations related by a tree.\nMethod described in Ochoa and Storey (2021)\n<doi:10.1371/journal.pgen.1009241>.",
  "License": "GPL (>= 3)",
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  "URL": "https://github.com/StoreyLab/bnpsd/",
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  "Repository": "https://storeylab.r-universe.dev",
  "Date/Publication": "2023-07-21 19:29:42 UTC",
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    "extra/citation.html",
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    "admix_prop_1d_linear",
    "admix_prop_indep_subpops",
    "coanc_admix",
    "coanc_to_kinship",
    "coanc_tree",
    "draw_all_admix",
    "draw_all_unstructured",
    "draw_genotypes_admix",
    "draw_p_anc",
    "draw_p_subpops",
    "draw_p_subpops_tree",
    "fit_tree",
    "fixed_loci",
    "fst_admix",
    "make_p_ind_admix",
    "scale_tree",
    "tree_additive",
    "tree_reindex_tips",
    "tree_reorder",
    "undiff_af"
  ],
  "_help": [
    {
      "page": "admix_prop_1d_circular",
      "title": "Construct admixture proportion matrix for circular 1D geography",
      "topics": [
        "admix_prop_1d_circular"
      ]
    },
    {
      "page": "admix_prop_1d_linear",
      "title": "Construct admixture proportion matrix for 1D geography",
      "topics": [
        "admix_prop_1d_linear"
      ]
    },
    {
      "page": "admix_prop_indep_subpops",
      "title": "Construct admixture proportion matrix for independent subpopulations",
      "topics": [
        "admix_prop_indep_subpops"
      ]
    },
    {
      "page": "bnpsd",
      "title": "A package for modeling and simulating an admixed population",
      "topics": [
        "bnpsd-package",
        "bnpsd"
      ]
    },
    {
      "page": "coanc_admix",
      "title": "Construct the coancestry matrix of an admixture model",
      "topics": [
        "coanc_admix"
      ]
    },
    {
      "page": "coanc_to_kinship",
      "title": "Transform coancestry matrix to kinship matrix",
      "topics": [
        "coanc_to_kinship"
      ]
    },
    {
      "page": "coanc_tree",
      "title": "Calculate coancestry matrix corresponding to a tree",
      "topics": [
        "coanc_tree"
      ]
    },
    {
      "page": "draw_all_admix",
      "title": "Simulate random allele frequencies and genotypes from the BN-PSD admixture model",
      "topics": [
        "draw_all_admix"
      ]
    },
    {
      "page": "draw_all_unstructured",
      "title": "Simulate random allele frequencies and genotypes from the unstructured model",
      "topics": [
        "draw_all_unstructured"
      ]
    },
    {
      "page": "draw_genotypes_admix",
      "title": "Draw genotypes from the admixture model",
      "topics": [
        "draw_genotypes_admix"
      ]
    },
    {
      "page": "draw_p_anc",
      "title": "Draw random Uniform or Beta ancestral allele frequencies",
      "topics": [
        "draw_p_anc"
      ]
    },
    {
      "page": "draw_p_subpops",
      "title": "Draw allele frequencies for independent subpopulations",
      "topics": [
        "draw_p_subpops"
      ]
    },
    {
      "page": "draw_p_subpops_tree",
      "title": "Draw allele frequencies for subpopulations related by a tree",
      "topics": [
        "draw_p_subpops_tree"
      ]
    },
    {
      "page": "fit_tree",
      "title": "Fit a tree structure to a coancestry matrix",
      "topics": [
        "fit_tree"
      ]
    },
    {
      "page": "fixed_loci",
      "title": "Identify fixed loci",
      "topics": [
        "fixed_loci"
      ]
    },
    {
      "page": "fst_admix",
      "title": "Calculate FST for the admixed individuals",
      "topics": [
        "fst_admix"
      ]
    },
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      "page": "make_p_ind_admix",
      "title": "Construct individual-specific allele frequency matrix under the PSD admixture model",
      "topics": [
        "make_p_ind_admix"
      ]
    },
    {
      "page": "scale_tree",
      "title": "Scale a coancestry tree",
      "topics": [
        "scale_tree"
      ]
    },
    {
      "page": "tree_additive",
      "title": "Calculate additive edges for a coancestry tree, or viceversa",
      "topics": [
        "tree_additive"
      ]
    },
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      "page": "tree_reindex_tips",
      "title": "Reindex tree tips in order of appearance in edges",
      "topics": [
        "tree_reindex_tips"
      ]
    },
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      "page": "tree_reorder",
      "title": "Reorder tree tips to best match a desired order",
      "topics": [
        "tree_reorder"
      ]
    },
    {
      "page": "undiff_af",
      "title": "Undifferentiate an allele distribution",
      "topics": [
        "undiff_af"
      ]
    }
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        "Customizing the allele frequency and genotype pipeline",
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