{
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  "Package": "hierfstat",
  "Version": "0.5-11",
  "Date": "2022-05-03",
  "Title": "Estimation and Tests of Hierarchical F-Statistics",
  "Authors@R": "c(person(\"Jerome\",\"Goudet\",role=c(\"aut\",\"cre\"),email=\"jerome.goudet@unil.ch\"),\nperson(\"Thibaut\",\"Jombart\",role=\"aut\",email=\"t.jombart@imperial.ac.uk\"),\nperson(\"Zhian N.\",\"Kamvar\",role=\"ctb\"),\nperson(\"Eric\",\"Archer\",role=\"ctb\"),\nperson(\"Olivier\",\"Hardy\",role=\"ctb\"))",
  "Author": "Jerome Goudet [aut, cre], Thibaut Jombart [aut], Zhian N.\nKamvar [ctb], Eric Archer [ctb], Olivier Hardy [ctb]",
  "Maintainer": "Jerome Goudet <jerome.goudet@unil.ch>",
  "Description": "Estimates hierarchical F-statistics from haploid or\ndiploid genetic data with any numbers of levels in the\nhierarchy, following the algorithm of Yang (Evolution(1998),\n52:950). Tests via randomisations the significance of each F\nand variance components, using the likelihood-ratio statistics\nG (Goudet et al. (1996)\n<https://academic.oup.com/genetics/article/144/4/1933/6017091>).\nEstimates genetic diversity statistics for haploid and diploid\ngenetic datasets in various formats, including inbreeding and\ncoancestry coefficients, and population specific F-statistics\nfollowing Weir and Goudet (2017)\n<https://academic.oup.com/genetics/article/206/4/2085/6072590>.",
  "License": "GPL (>=2)",
  "URL": "https://www.r-project.org, https://github.com/jgx65/hierfstat",
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  "Date/Publication": "2024-11-20 20:18:59 UTC",
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    "AIc",
    "allele.count",
    "allelic.richness",
    "basic.stats",
    "beta.dosage",
    "betas",
    "biall2dos",
    "boot.ppbetas",
    "boot.ppfis",
    "boot.ppfst",
    "boot.vc",
    "fis.dosage",
    "fs.dosage",
    "fst.dosage",
    "fstat2dos",
    "g.stats",
    "g.stats.glob",
    "genet.dist",
    "genind2hierfstat",
    "genot2al",
    "getal",
    "getal.b",
    "grm2kinship",
    "Ho",
    "Hs",
    "ind.count",
    "indpca",
    "kinship2dist",
    "kinship2grm",
    "kinshipShift",
    "mat2vec",
    "matching",
    "ms2bed",
    "ms2dos",
    "nb.alleles",
    "pairwise.betas",
    "pairwise.fst.dosage",
    "pairwise.neifst",
    "pairwise.WCfst",
    "pcoa",
    "pi.dosage",
    "pop.freq",
    "pp.fst",
    "pp.sigma.loc",
    "qn2.read.fstat",
    "read.fstat",
    "read.fstat.data",
    "read.ms",
    "read.VCF",
    "samp.between",
    "samp.between.within",
    "samp.within",
    "sexbias.test",
    "sim.genot",
    "sim.genot.metapop.t",
    "sim.genot.t",
    "subsampind",
    "TajimaD.dosage",
    "test.between",
    "test.between.within",
    "test.g",
    "test.within",
    "theta.Watt.dosage",
    "varcomp",
    "varcomp.glob",
    "vec2mat",
    "wc",
    "write.bayescan",
    "write.fstat",
    "write.ped",
    "write.struct"
  ],
  "_datasets": [
    {
      "name": "cont.isl",
      "title": "A genetic dataset from a diploid organism in a continent-island model",
      "object": "cont.isl",
      "file": "cont.isl.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Pop",
        "loc.1",
        "loc.2",
        "loc.3",
        "loc.4",
        "loc.5"
      ],
      "rows": 150,
      "table": true,
      "tojson": true
    },
    {
      "name": "cont.isl99",
      "title": "A genetic dataset from a diploid organism in a continent-island model",
      "object": "cont.isl99",
      "file": "cont.isl99.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Pop",
        "loc.1",
        "loc.2",
        "loc.3",
        "loc.4",
        "loc.5"
      ],
      "rows": 150,
      "table": true,
      "tojson": true
    },
    {
      "name": "crocrussula",
      "title": "Genotypes and sex of 140 shrews Crocidura russula",
      "object": "crocrussula",
      "file": "crocrussula.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "diploid",
      "title": "A genetic dataset from a diploid organism",
      "object": "diploid",
      "file": "diploid.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Pop",
        "loc-1",
        "loc-2",
        "loc-3",
        "loc-4",
        "loc-5"
      ],
      "rows": 44,
      "table": true,
      "tojson": true
    },
    {
      "name": "exhier",
      "title": "Example data set with 4 levels, one diploid and one haploid locus",
      "object": "exhier",
      "file": "exhier.txt.gz",
      "class": [
        "data.frame"
      ],
      "fields": [
        "lev1",
        "lev2",
        "lev3",
        "lev4",
        "loc1",
        "haplo"
      ],
      "rows": 500,
      "table": true,
      "tojson": true
    },
    {
      "name": "gtrunchier",
      "title": "Genotypes at 6 microsatellite loci of Galba truncatula from different patches in Western Switzerland",
      "object": "gtrunchier",
      "file": "gtrunchier.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Locality",
        "Patch",
        "L21.V",
        "L37.J",
        "L20.B",
        "L29.V",
        "L36.B",
        "L16.J"
      ],
      "rows": 370,
      "table": true,
      "tojson": true
    },
    {
      "name": "yangex",
      "title": "Example data set from Yang (1998) appendix",
      "object": "yangex",
      "file": "yangex.txt.gz",
      "class": [
        "data.frame"
      ],
      "fields": [
        "pop",
        "spop",
        "sspop",
        "genot"
      ],
      "rows": 232,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "AIc",
      "title": "Calculates corrected Assignment Index",
      "topics": [
        "AIc"
      ]
    },
    {
      "page": "allele.count",
      "title": "Allelic counts",
      "topics": [
        "allele.count"
      ]
    },
    {
      "page": "allelic.richness",
      "title": "Estimates allelic richness",
      "topics": [
        "allelic.richness"
      ]
    },
    {
      "page": "basic.stats",
      "title": "Basic diversity and differentiation statistics",
      "topics": [
        "basic.stats",
        "Ho",
        "Hs",
        "print.basic.stats"
      ]
    },
    {
      "page": "beta.dosage",
      "title": "Estimates pairwise kinships and individual inbreeding coefficients from dosage data",
      "topics": [
        "beta.dosage",
        "kas.dosage"
      ]
    },
    {
      "page": "betas",
      "title": "Estimates betas per population and a bootstrap confidence interval",
      "topics": [
        "betas",
        "print.betas"
      ]
    },
    {
      "page": "biall2dos",
      "title": "Converts bi-allelic SNPs from hierfstat format to dosage format",
      "topics": [
        "biall2dos"
      ]
    },
    {
      "page": "boot.ppbetas",
      "title": "Estimates bootstrap confidence intervals for pairwise betas FST estimates",
      "topics": [
        "boot.ppbetas"
      ]
    },
    {
      "page": "boot.ppfis",
      "title": "Performs bootstrapping over loci of population's Fis",
      "topics": [
        "boot.ppfis"
      ]
    },
    {
      "page": "boot.ppfst",
      "title": "Performs bootstrapping over loci of pairwise Fst",
      "topics": [
        "boot.ppfst",
        "print.boot.ppfst"
      ]
    },
    {
      "page": "boot.vc",
      "title": "Bootstrap confidence intervals for variance components",
      "topics": [
        "boot.vc"
      ]
    },
    {
      "page": "cont.isl",
      "title": "A genetic dataset from a diploid organism in a continent-island model",
      "topics": [
        "cont.isl"
      ]
    },
    {
      "page": "cont.isl99",
      "title": "A genetic dataset from a diploid organism in a continent-island model",
      "topics": [
        "cont.isl99"
      ]
    },
    {
      "page": "crocrussula",
      "title": "Genotypes and sex of 140 shrews Crocidura russula",
      "topics": [
        "crocrussula"
      ]
    },
    {
      "page": "diploid",
      "title": "A genetic dataset from a diploid organism",
      "topics": [
        "diploid"
      ]
    },
    {
      "page": "exhier",
      "title": "Example data set with 4 levels, one diploid and one haploid locus",
      "topics": [
        "exhier"
      ]
    },
    {
      "page": "fs.dosage",
      "title": "Estimates F-statistics from dosage data",
      "topics": [
        "fis.dosage",
        "fs.dosage",
        "fst.dosage",
        "pairwise.fst.dosage",
        "plot.fs.dosage",
        "print.fs.dosage"
      ]
    },
    {
      "page": "fstat2dos",
      "title": "Converts a hierfstat genetic data frame to dosage data",
      "topics": [
        "fstat2dos"
      ]
    },
    {
      "page": "g.stats",
      "title": "Calculates likelihood-ratio G-statistic on contingency table",
      "topics": [
        "g.stats"
      ]
    },
    {
      "page": "g.stats.glob",
      "title": "Likelihood ratio G-statistic over loci",
      "topics": [
        "g.stats.glob"
      ]
    },
    {
      "page": "genet.dist",
      "title": "Classical genetic distances estimation",
      "topics": [
        "genet.dist"
      ]
    },
    {
      "page": "genind2hierfstat",
      "title": "Converts genind objects from adegenet into a hierfstat data frame",
      "topics": [
        "genind2hierfstat"
      ]
    },
    {
      "page": "genot2al",
      "title": "Separates diploid genotypes in its constituant alleles",
      "topics": [
        "genot2al"
      ]
    },
    {
      "page": "getal",
      "title": "Converts diploid genotypic data into allelic data",
      "topics": [
        "getal"
      ]
    },
    {
      "page": "getal.b",
      "title": "Converts diploid genotypic data into allelic data",
      "topics": [
        "getal.b"
      ]
    },
    {
      "page": "grm2kinship",
      "title": "Converts a Genetic Relationship Matrix (GRM) to a kinship matrix",
      "topics": [
        "grm2kinship"
      ]
    },
    {
      "page": "gtrunchier",
      "title": "Genotypes at 6 microsatellite loci of Galba truncatula from different patches in Western Switzerland",
      "topics": [
        "gtrunchier"
      ]
    },
    {
      "page": "hierfstat",
      "title": "General information on the hierfstat package",
      "topics": [
        "hierfstat"
      ]
    },
    {
      "page": "ind.count",
      "title": "individual counts",
      "topics": [
        "ind.count"
      ]
    },
    {
      "page": "indpca",
      "title": "PCA on a matrix of individuals genotypes frequencies",
      "topics": [
        "indpca",
        "plot.indpca",
        "print.indpca"
      ]
    },
    {
      "page": "is.genind",
      "title": "Test if object is of class 'genind'",
      "topics": [
        "is.genind"
      ]
    },
    {
      "page": "kinship2dist",
      "title": "Converts a kinship matrix to a distance matrix",
      "topics": [
        "kinship2dist"
      ]
    },
    {
      "page": "kinship2grm",
      "title": "Converts a kinship matrix to a Genetic Relation Matrix (GRM)",
      "topics": [
        "kinship2grm"
      ]
    },
    {
      "page": "kinshipShift",
      "title": "Shifts a kinship matrix",
      "topics": [
        "kinshipShift"
      ]
    },
    {
      "page": "mat2vec",
      "title": "Creates a vector from a matrix",
      "topics": [
        "mat2vec"
      ]
    },
    {
      "page": "matching",
      "title": "Estimates matching between pairs of individuals",
      "topics": [
        "AlleleSharing",
        "matching"
      ]
    },
    {
      "page": "ms2bed",
      "title": "Import the output of the 'ms' program in a 'BED' object",
      "topics": [
        "ms2bed"
      ]
    },
    {
      "page": "ms2dos",
      "title": "Import 'ms' output",
      "topics": [
        "ms2dos"
      ]
    },
    {
      "page": "nb.alleles",
      "title": "Number of different alleles",
      "topics": [
        "nb.alleles"
      ]
    },
    {
      "page": "pairwise.betas",
      "title": "Estimates pairwise betas according to Weir and Goudet (2017)",
      "topics": [
        "pairwise.betas"
      ]
    },
    {
      "page": "pairwise.neifst",
      "title": "Estimates pairwise FSTs according to Nei (1987)",
      "topics": [
        "pairwise.neifst"
      ]
    },
    {
      "page": "pairwise.WCfst",
      "title": "Estimates pairwise FSTs according to Weir and Cockerham (1984)",
      "topics": [
        "pairwise.WCfst"
      ]
    },
    {
      "page": "pcoa",
      "title": "Principal coordinate analysis",
      "topics": [
        "pcoa"
      ]
    },
    {
      "page": "pi.dosage",
      "title": "Estimates nucleotide diversity (pi) from dosage data",
      "topics": [
        "pi.dosage"
      ]
    },
    {
      "page": "pop.freq",
      "title": "Allelic frequencies",
      "topics": [
        "pop.freq"
      ]
    },
    {
      "page": "ppfst",
      "title": "fst per pair",
      "topics": [
        "pp.fst"
      ]
    },
    {
      "page": "pp.sigma.loc",
      "title": "wrapper to return per locus variance components",
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      "title": "print function for pp.fst",
      "topics": [
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      "page": "qn2.read.fstat",
      "title": "Read QuantiNemo extended format for genotype files Read QuantiNemo (<http://www2.unil.ch/popgen/softwares/quantinemo/>) genotype files extended format (option 2)",
      "topics": [
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      "title": "Reads data from a FSTAT file",
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      "title": "Reads data from a FSTAT file",
      "topics": [
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      "title": "Read data generated by Hudson ms program Read data generated by Hudson ms program, either as Haplotypes or as SNPs.",
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    {
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      "title": "Reads a VCF file into a BED object",
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    {
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      "title": "Shuffles a sequence among groups defined by the input vector",
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    {
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      "title": "Shuffles a sequence",
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    {
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      "title": "Shuffles a sequence within groups defined by the input vector",
      "topics": [
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    {
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      "title": "Test for sex biased dispersal",
      "topics": [
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    },
    {
      "page": "sim.freq",
      "title": "Simulates frequencies, for internal use only",
      "topics": [
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    {
      "page": "sim.genot",
      "title": "Simulates genotypes in an island model at equilibrium",
      "topics": [
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    },
    {
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      "title": "Simulate genetic data from a metapopulation model",
      "topics": [
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    },
    {
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      "title": "Simulate data from a non equilibrium continent-island model",
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    {
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      "title": "Subsample a FSTAT data frame",
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    {
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      "title": "Estimates Tajima's D",
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    {
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      "title": "Tests the significance of the effect of test.lev on genetic differentiation",
      "topics": [
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    {
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      "title": "Tests the significance of the effect of test.lev on genetic differentiation",
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      "title": "Tests the significance of the effect of level on genetic differentiation",
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      "title": "Estimates variance components for each allele of a locus",
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      "title": "Estimate variance components and hierarchical F-statistics over all loci",
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      "title": "Fills a triangular matrix from the inputed vector",
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      "title": "Computes Weir and Cockrham estimates of Fstatistics",
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      "title": "Hierfstat latest features",
      "author": "Jerome Goudet",
      "engine": "knitr::rmarkdown",
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