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  "Package": "poolfstat",
  "Authors@R": "person(given = \"Mathieu\",family = \"Gautier\",role = c(\"aut\", \"cre\"),email = \"mathieu.gautier@inrae.fr\")",
  "Version": "3.1.0",
  "License": "GPL (>= 2)",
  "Title": "Computing f-Statistics and Building Admixture Graphs Based on\nAllele Count or Pool-Seq Read Count Data",
  "Description": "Functions for the computation of F-, f- and D-statistics\n(e.g., Fst, hierarchical F-statistics, Patterson's F2, F3, F3*,\nF4 and D parameters) in population genomics studies from allele\ncount or Pool-Seq read count data and for the fitting, building\nand visualization of admixture graphs. The package also\nincludes several utilities to manipulate Pool-Seq data stored\nin standard format (e.g., such as 'vcf' files or 'rsync' files\ngenerated by the the 'PoPoolation' software) and perform\nconversion to alternative format (as used in the 'BayPass' and\n'SelEstim' software). As of version 2.0, the package also\nincludes utilities to manipulate standard allele count data\n(e.g., stored in 'TreeMix', 'BayPass' and 'SelEstim' format,\nsee the Package vignette for details).",
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  "Packaged": {
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  "Author": "Mathieu Gautier [aut, cre]",
  "Maintainer": "Mathieu Gautier <mathieu.gautier@inrae.fr>",
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  "Repository": "https://mgautierinra.r-universe.dev",
  "Date/Publication": "2026-02-23 18:30:02 UTC",
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
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    ".block_sum",
    ".block_sum2",
    ".compute_blockDdenom",
    ".compute_F3fromF2",
    ".compute_F3fromF2samples",
    ".compute_F4DfromF2samples",
    ".compute_F4fromF2",
    ".compute_F4fromF2samples",
    ".compute_H1",
    ".compute_Q2",
    ".compute_QmatfromF2samples",
    ".compute_snpFstAov",
    ".compute_snpHierFstAov",
    ".compute_snpQ1",
    ".compute_snpQ1onepop",
    ".compute_snpQ1rw",
    ".compute_snpQ2",
    ".compute_snpQ2onepair",
    ".compute_snpQ2rw",
    ".extract_allele_names",
    ".extract_nonvscan_counts",
    ".extract_vscan_counts",
    ".find_indelneighbor_idx",
    ".generateF3names",
    ".generateF4names",
    ".scan_allele_info",
    ".simureads_mono",
    ".simureads_poly",
    "add.leaf",
    "compare.fitted.fstats",
    "compute.f4ratio",
    "compute.fstats",
    "compute.pairwiseFST",
    "computeFST",
    "countdata.subset",
    "countdata2genobaypass",
    "data.merge",
    "find.tree.popset",
    "fit.graph",
    "generate.graph.params",
    "generate.jackknife.blocks",
    "genobaypass2countdata",
    "genobaypass2pooldata",
    "genoselestim2pooldata",
    "genotreemix2countdata",
    "graph.builder",
    "graph.params2qpGraphFiles",
    "graph.params2symbolic.fstats",
    "heatmap",
    "is.countdata",
    "is.fitted.graph",
    "is.fstats",
    "is.graph.params",
    "is.pairwisefst",
    "is.pooldata",
    "make.example.files",
    "plot",
    "plot_fstats",
    "pooldata.subset",
    "pooldata2diyabc",
    "pooldata2genobaypass",
    "pooldata2genoselestim",
    "poolify",
    "popsync2pooldata",
    "randomallele.pca",
    "rooted.njtree.builder",
    "sim.readcounts",
    "sliding.windows.fstat",
    "vcf2pooldata"
  ],
  "_help": [
    {
      "page": "add.leaf",
      "title": "Test all possible connection of a leaf to a graph with non-admixed and or admixed edges",
      "topics": [
        "add.leaf"
      ]
    },
    {
      "page": "bjack_cov",
      "title": "bjack_cov",
      "topics": [
        "bjack_cov"
      ]
    },
    {
      "page": "block_sum",
      "title": "block_sum",
      "topics": [
        ".block_sum",
        "block_sum"
      ]
    },
    {
      "page": "block_sum2",
      "title": "block_sum2",
      "topics": [
        ".block_sum2",
        "block_sum2"
      ]
    },
    {
      "page": "compare.fitted.fstats",
      "title": "Compare fitted f2, f3 and f4 f-statistics of an admixture graph with estimated ones",
      "topics": [
        "compare.fitted.fstats"
      ]
    },
    {
      "page": "compute_blockDdenom",
      "title": "compute_blockDdenom",
      "topics": [
        ".compute_blockDdenom",
        "compute_blockDdenom"
      ]
    },
    {
      "page": "compute_F3fromF2",
      "title": "compute_F3fromF2",
      "topics": [
        ".compute_F3fromF2",
        "compute_F3fromF2"
      ]
    },
    {
      "page": "compute_F3fromF2samples",
      "title": "compute_F3fromF2samples",
      "topics": [
        ".compute_F3fromF2samples",
        "compute_F3fromF2samples"
      ]
    },
    {
      "page": "compute_F4DfromF2samples",
      "title": "compute_F4DfromF2samples",
      "topics": [
        ".compute_F4DfromF2samples",
        "compute_F4DfromF2samples"
      ]
    },
    {
      "page": "compute_F4fromF2",
      "title": "compute_F4fromF2",
      "topics": [
        ".compute_F4fromF2",
        "compute_F4fromF2"
      ]
    },
    {
      "page": "compute_F4fromF2samples",
      "title": "compute_F4fromF2samples",
      "topics": [
        ".compute_F4fromF2samples",
        "compute_F4fromF2samples"
      ]
    },
    {
      "page": "compute_H1",
      "title": "compute_H1",
      "topics": [
        ".compute_H1",
        "compute_H1"
      ]
    },
    {
      "page": "compute_Q2",
      "title": "compute_Q2",
      "topics": [
        ".compute_Q2",
        "compute_Q2"
      ]
    },
    {
      "page": "compute_QmatfromF2samples",
      "title": "compute_QmatfromF2samples",
      "topics": [
        ".compute_QmatfromF2samples",
        "compute_QmatfromF2samples"
      ]
    },
    {
      "page": "compute_snpFstAov",
      "title": "compute_snpFstAov",
      "topics": [
        ".compute_snpFstAov",
        "compute_snpFstAov"
      ]
    },
    {
      "page": "compute_snpHierFstAov",
      "title": "compute_snpHierFstAov",
      "topics": [
        ".compute_snpHierFstAov",
        "compute_snpHierFstAov"
      ]
    },
    {
      "page": "compute_snpQ1",
      "title": "compute_snpQ1",
      "topics": [
        ".compute_snpQ1",
        "compute_snpQ1"
      ]
    },
    {
      "page": "compute_snpQ1onepop",
      "title": "compute_snpQ1onepop",
      "topics": [
        ".compute_snpQ1onepop",
        "compute_snpQ1onepop"
      ]
    },
    {
      "page": "compute_snpQ1rw",
      "title": "compute_snpQ1rw",
      "topics": [
        ".compute_snpQ1rw",
        "compute_snpQ1rw"
      ]
    },
    {
      "page": "compute_snpQ2",
      "title": "compute_snpQ2",
      "topics": [
        ".compute_snpQ2",
        "compute_snpQ2"
      ]
    },
    {
      "page": "compute_snpQ2onepair",
      "title": "compute_snpQ2onepair",
      "topics": [
        ".compute_snpQ2onepair",
        "compute_snpQ2onepair"
      ]
    },
    {
      "page": "compute_snpQ2w",
      "title": "compute_snpQ2rw",
      "topics": [
        ".compute_snpQ2rw",
        "compute_snpQ2rw"
      ]
    },
    {
      "page": "compute.f4ratio",
      "title": "Compute F4ratio (estimation of admixture rate) from an fstats object",
      "topics": [
        "compute.f4ratio"
      ]
    },
    {
      "page": "compute.fstats",
      "title": "Estimate the F-statistics (F2, F3, F3star, F4, Dstat) and within and across population diversity",
      "topics": [
        "compute.fstats"
      ]
    },
    {
      "page": "compute.pairwiseFST",
      "title": "Compute pairwise population population FST matrix (and possibly all pairwise SNP-specific FST)",
      "topics": [
        "compute.pairwiseFST"
      ]
    },
    {
      "page": "computeFST",
      "title": "Compute Fst from Pool-Seq data or Count data",
      "topics": [
        "computeFST"
      ]
    },
    {
      "page": "countdata-class",
      "title": "S4 class to represent a Count data set.",
      "topics": [
        "countdata",
        "countdata-class"
      ]
    },
    {
      "page": "countdata.subset",
      "title": "Create a subset of a countdata object that contains count data as a function of pop or SNP indexes",
      "topics": [
        "countdata.subset"
      ]
    },
    {
      "page": "countdata2genobaypass",
      "title": "Convert a countdata object into BayPass input files.",
      "topics": [
        "countdata2genobaypass"
      ]
    },
    {
      "page": "data.merge",
      "title": "Merge two pooldata or countdata objects",
      "topics": [
        "data.merge"
      ]
    },
    {
      "page": "extract_allele_names",
      "title": "extract_allele_names",
      "topics": [
        ".extract_allele_names",
        "extract_allele_names"
      ]
    },
    {
      "page": "extract_nonvscan_counts",
      "title": "extract_nonvscan_counts",
      "topics": [
        ".extract_nonvscan_counts",
        "extract_nonvscan_counts"
      ]
    },
    {
      "page": "extract_vscan_counts",
      "title": "extract_vscan_counts",
      "topics": [
        ".extract_vscan_counts",
        "extract_vscan_counts"
      ]
    },
    {
      "page": "find_indelneighbor_idx",
      "title": "find_indelneighbor_idx",
      "topics": [
        ".find_indelneighbor_idx",
        "find_indelneighbor_idx"
      ]
    },
    {
      "page": "find.tree.popset",
      "title": "Find sets of populations that may used as scaffold tree",
      "topics": [
        "find.tree.popset"
      ]
    },
    {
      "page": "fit.graph",
      "title": "Estimate parameters of an admixture graph",
      "topics": [
        "fit.graph"
      ]
    },
    {
      "page": "fitted.graph-class",
      "title": "S4 class to represent a population tree or admixture graph and its underlying fitted parameter.",
      "topics": [
        "fitted.graph",
        "fitted.graph-class",
        "gen.fitted.graph"
      ]
    },
    {
      "page": "fstats-class",
      "title": "S4 class to represent fstats results obtained with computeFstats.",
      "topics": [
        "fstats",
        "fstats-class"
      ]
    },
    {
      "page": "generate.graph.params",
      "title": "Generate a graph parameter object to fit admixture graph to observed fstats",
      "topics": [
        "generate.graph.params"
      ]
    },
    {
      "page": "generate.jackknife.blocks",
      "title": "Generate block coordinates for block-jackknife",
      "topics": [
        "generate.jackknife.blocks"
      ]
    },
    {
      "page": "generateF3names",
      "title": "generateF3names",
      "topics": [
        ".generateF3names",
        "generateF3names"
      ]
    },
    {
      "page": "generateF4names",
      "title": "generateF4names",
      "topics": [
        ".generateF4names",
        "generateF4names"
      ]
    },
    {
      "page": "genobaypass2countdata",
      "title": "Convert BayPass allele count input files into a coundata object",
      "topics": [
        "genobaypass2countdata"
      ]
    },
    {
      "page": "genobaypass2pooldata",
      "title": "Convert BayPass read count and haploid pool size input files into a pooldata object",
      "topics": [
        "genobaypass2pooldata"
      ]
    },
    {
      "page": "genoselestim2pooldata",
      "title": "Convert SelEstim read count input files into a pooldata object",
      "topics": [
        "genoselestim2pooldata"
      ]
    },
    {
      "page": "genotreemix2countdata",
      "title": "Convert allele count input files from the Treemix program into a coundata object",
      "topics": [
        "genotreemix2countdata"
      ]
    },
    {
      "page": "graph.builder",
      "title": "Implement a graph builder heuristic by successively adding leaves to an initial graph",
      "topics": [
        "graph.builder"
      ]
    },
    {
      "page": "graph.params-class",
      "title": "S4 class to represent a population tree or admixture graph and its underlying parameter.",
      "topics": [
        "graph.params",
        "graph.params-class"
      ]
    },
    {
      "page": "graph.params2qpGraphFiles",
      "title": "Generate files for the qpGraph software from a graph.params object",
      "topics": [
        "graph.params2qpGraphFiles"
      ]
    },
    {
      "page": "graph.params2symbolic.fstats",
      "title": "Provide a symbolic representation of all the F-statistics and the model system of equations",
      "topics": [
        "graph.params2symbolic.fstats"
      ]
    },
    {
      "page": "heatmap-pairwisefst-method",
      "title": "Show pairwisefst object",
      "topics": [
        "heatmap,pairwisefst-method"
      ]
    },
    {
      "page": "is.countdata",
      "title": "Check countdata objects",
      "topics": [
        "is.countdata"
      ]
    },
    {
      "page": "is.fitted.graph",
      "title": "Check fitted.graph objects",
      "topics": [
        "is.fitted.graph"
      ]
    },
    {
      "page": "is.fstats",
      "title": "Check fstats objects",
      "topics": [
        "is.fstats"
      ]
    },
    {
      "page": "is.graph.params",
      "title": "Check graph.params objects",
      "topics": [
        "is.graph.params"
      ]
    },
    {
      "page": "is.pairwisefst",
      "title": "Check pairwisefst objects",
      "topics": [
        "is.pairwisefst"
      ]
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