{
  "_id": "6a49cc6874d3c5f978be8efe",
  "Package": "pegas",
  "Version": "1.4",
  "Date": "2025-12-08",
  "Title": "Population and Evolutionary Genetics Analysis System",
  "Authors@R": "c(person(\"Emmanuel\", \"Paradis\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Emmanuel.Paradis@ird.fr\", comment = c(ORCID = \"0000-0003-3092-2199\")),\nperson(\"Thibaut\", \"Jombart\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0003-2226-8692\")),\nperson(\"Zhian N.\", \"Kamvar\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0003-1458-7108\")),\nperson(\"Brian\", \"Knaus\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0003-1665-4343\")),\nperson(\"Klaus\", \"Schliep\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0003-2941-0161\")),\nperson(\"Alastair\", \"Potts\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0003-0919-7279\")),\nperson(\"David\", \"Winter\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-6165-0029\")))",
  "ZipData": "no",
  "Description": "Functions for reading, writing, plotting, analysing, and\nmanipulating allelic and haplotypic data, including from VCF\nfiles, and for the analysis of population nucleotide sequences\nand micro-satellites including coalescent analyses, linkage\ndisequilibrium, population structure (Fst, Amova) and\nequilibrium (HWE), haplotype networks, minimum spanning tree\nand network, and median-joining networks.",
  "License": "GPL (>= 2)",
  "URL": "https://emmanuelparadis.github.io/pegas.html",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-16 07:50:11 UTC",
    "User": "root"
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  "Author": "Emmanuel Paradis [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0003-3092-2199>), Thibaut Jombart [aut,\ncph] (ORCID: <https://orcid.org/0000-0003-2226-8692>), Zhian N.\nKamvar [aut, cph] (ORCID:\n<https://orcid.org/0000-0003-1458-7108>), Brian Knaus [aut,\ncph] (ORCID: <https://orcid.org/0000-0003-1665-4343>), Klaus\nSchliep [aut, cph] (ORCID:\n<https://orcid.org/0000-0003-2941-0161>), Alastair Potts [aut,\ncph] (ORCID: <https://orcid.org/0000-0003-0919-7279>), David\nWinter [aut, cph] (ORCID:\n<https://orcid.org/0000-0002-6165-0029>)",
  "Maintainer": "Emmanuel Paradis <Emmanuel.Paradis@ird.fr>",
  "Repository": "https://emmanuelparadis.r-universe.dev",
  "Date/Publication": "2025-12-08 08:49:10 UTC",
  "RemoteUrl": "https://github.com/cran/pegas",
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  "_expires": "2026-10-13T03:15:50.000Z",
  "_created": "2026-06-16T07:50:11.000Z",
  "_published": "2026-07-05T03:15:52.613Z",
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  "_realowner": "emmanuelparadis",
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  "_releases": [
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    },
    {
      "version": "0.6",
      "date": "2014-08-21"
    },
    {
      "version": "0.7",
      "date": "2015-03-05"
    },
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      "version": "0.8",
      "date": "2015-05-19"
    },
    {
      "version": "0.8-1",
      "date": "2015-06-24"
    },
    {
      "version": "0.8-2",
      "date": "2015-09-25"
    },
    {
      "version": "0.9",
      "date": "2016-04-15"
    },
    {
      "version": "0.10",
      "date": "2017-05-03"
    },
    {
      "version": "0.11",
      "date": "2018-07-09"
    },
    {
      "version": "0.12",
      "date": "2019-10-05"
    },
    {
      "version": "0.13",
      "date": "2020-03-10"
    },
    {
      "version": "0.14",
      "date": "2020-09-16"
    },
    {
      "version": "1.0",
      "date": "2021-04-08"
    },
    {
      "version": "1.0-1",
      "date": "2021-05-17"
    },
    {
      "version": "1.1",
      "date": "2021-12-16"
    },
    {
      "version": "1.2",
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    },
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      "date": "2023-12-13"
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      "version": "1.4",
      "date": "2025-12-11"
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  "_exports": [
    "alleles2loci",
    "allelicrichness",
    "amova",
    "as.igraph.haploNet",
    "as.loci",
    "as.network.haploNet",
    "diffHaplo",
    "dist.asd",
    "dist.hamming",
    "dist.haplotype.loci",
    "expand.genotype",
    "F2",
    "F3",
    "F4",
    "Fst",
    "genind2loci",
    "geod",
    "geoTrans",
    "geoTrans2",
    "getAlleles",
    "getGenotypes",
    "getHaploNetOptions",
    "getINFO",
    "getPhi",
    "getPloidy",
    "H",
    "hap.div",
    "haploFreq",
    "haploNet",
    "haplotype",
    "heterozygosity",
    "hw.test",
    "is.phased",
    "is.snp",
    "LD",
    "LD2",
    "LDmap",
    "LDscan",
    "loci2alleles",
    "loci2genind",
    "loci2SnpMatrix",
    "mjn",
    "MMD",
    "msn",
    "mst",
    "mutations",
    "nuc.div",
    "nullAlleles2NA",
    "plotNetMDS",
    "proba.genotype",
    "R2.test",
    "rangePOS",
    "rarefactionplot",
    "read.gtx",
    "read.loci",
    "read.vcf",
    "replot",
    "rhost",
    "rmst",
    "rr.test",
    "Rst",
    "selectQUAL",
    "setHaploNetOptions",
    "site.spectrum",
    "stairway",
    "sw",
    "tajima.test",
    "theta.h",
    "theta.k",
    "theta.msat",
    "theta.s",
    "theta.tree",
    "theta.tree.hetero",
    "unphase",
    "VCFheader",
    "VCFlabels",
    "VCFloci",
    "write.loci",
    "write.pegas.amova",
    "write.vcf"
  ],
  "_datasets": [
    {
      "name": "jaguar",
      "title": "Jaguar Micro-Satellites",
      "object": "jaguar",
      "file": "jaguar.rda",
      "class": [
        "loci",
        "data.frame"
      ],
      "fields": [
        "FCA742",
        "FCA723",
        "FCA740",
        "FCA441",
        "FCA391",
        "F98",
        "F53",
        "F124",
        "F146",
        "F85",
        "F42",
        "FCA453",
        "FCA741",
        "population"
      ],
      "rows": 59,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "pegas-package",
      "title": "Population and Evolutionary Genetics Analysis System",
      "topics": [
        "pegas-package",
        "pegas"
      ]
    },
    {
      "page": "all.equal.haploNet",
      "title": "Compare Two Haplotype Networks",
      "topics": [
        "all.equal.haploNet"
      ]
    },
    {
      "page": "alleles2loci",
      "title": "Build Loci Object From Matrix of Alleles",
      "topics": [
        "alleles2loci",
        "loci2alleles"
      ]
    },
    {
      "page": "allelicrichness",
      "title": "Allelic Richness and Rarefaction Plots",
      "topics": [
        "allelicrichness",
        "rarefactionplot",
        "rhost"
      ]
    },
    {
      "page": "amova",
      "title": "Analysis of Molecular Variance",
      "topics": [
        "amova",
        "getPhi",
        "print.amova",
        "write.pegas.amova"
      ]
    },
    {
      "page": "conversion",
      "title": "Conversion Among Allelic Data Classes",
      "topics": [
        "as.loci",
        "as.loci.character",
        "as.loci.data.frame",
        "as.loci.factor",
        "as.loci.genind",
        "as.loci.matrix",
        "genind2loci",
        "loci2genind",
        "loci2SnpMatrix"
      ]
    },
    {
      "page": "bind.loci",
      "title": "Bind Loci Objects",
      "topics": [
        "bind.loci",
        "cbind.loci",
        "rbind.loci"
      ]
    },
    {
      "page": "by.loci",
      "title": "Summary by Population or Other Factor",
      "topics": [
        "by.loci"
      ]
    },
    {
      "page": "cophenetic.haploNet",
      "title": "Cophenetic Matrix on Haplotype Networks",
      "topics": [
        "cophenetic.haploNet"
      ]
    },
    {
      "page": "diffHaplo",
      "title": "Comparison Between Two Haplotypes",
      "topics": [
        "diffHaplo"
      ]
    },
    {
      "page": "dist.asd",
      "title": "Allelic Sharing Distance",
      "topics": [
        "dist.asd"
      ]
    },
    {
      "page": "dist.hamming",
      "title": "Hamming Distance",
      "topics": [
        "dist.hamming"
      ]
    },
    {
      "page": "edit.loci",
      "title": "Edit Allelic Data with R's Data Editor",
      "topics": [
        "edit.loci"
      ]
    },
    {
      "page": "F234",
      "title": "F-Statistics From Patterson et al",
      "topics": [
        "F2",
        "F3",
        "F4"
      ]
    },
    {
      "page": "Fst",
      "title": "F-Statistics",
      "topics": [
        "Fst",
        "Rst"
      ]
    },
    {
      "page": "geod",
      "title": "Geodesic Distances",
      "topics": [
        "geod"
      ]
    },
    {
      "page": "geoTrans",
      "title": "Manipulate Geographical Coordinates",
      "topics": [
        "geoTrans",
        "geoTrans2"
      ]
    },
    {
      "page": "options_themes_haploNet",
      "title": "Options to Plot haploNet Objects",
      "topics": [
        "getHaploNetOptions",
        "setHaploNetOptions"
      ]
    },
    {
      "page": "hap.div",
      "title": "Haplotype Diversity",
      "topics": [
        "hap.div",
        "hap.div.DNAbin",
        "hap.div.haplotype"
      ]
    },
    {
      "page": "haploFreq",
      "title": "Haplotype Frequencies With a Covariate",
      "topics": [
        "haploFreq"
      ]
    },
    {
      "page": "haploNet",
      "title": "Haplotype Networks",
      "topics": [
        "as.evonet.haploNet",
        "as.igraph.haploNet",
        "as.network.haploNet",
        "as.phylo.haploNet",
        "haploNet",
        "plot.haploNet",
        "print.haploNet"
      ]
    },
    {
      "page": "haplotype",
      "title": "Haplotype Extraction and Frequencies",
      "topics": [
        "haplotype",
        "haplotype.character",
        "haplotype.DNAbin",
        "haplotype.numeric",
        "plot.haplotype",
        "print.haplotype",
        "sort.haplotype",
        "summary.haplotype",
        "[.haplotype"
      ]
    },
    {
      "page": "haplotype.loci",
      "title": "Haplotype Extraction and Frequencies From Allelic Data",
      "topics": [
        "dist.haplotype.loci",
        "haplotype.loci",
        "plot.haplotype.loci"
      ]
    },
    {
      "page": "heterozygosity",
      "title": "Heterozygosity at a Locus Using Gene Frequencies",
      "topics": [
        "H",
        "H.default",
        "H.loci",
        "heterozygosity"
      ]
    },
    {
      "page": "hw.test",
      "title": "Test of Hardy-Weinberg Equilibrium",
      "topics": [
        "hw.test",
        "hw.test.genind",
        "hw.test.loci"
      ]
    },
    {
      "page": "jaguar",
      "title": "Jaguar Micro-Satellites",
      "topics": [
        "jaguar"
      ]
    },
    {
      "page": "LD",
      "title": "Linkage Disequilibrium",
      "topics": [
        "LD",
        "LD2"
      ]
    },
    {
      "page": "LDscan",
      "title": "Multi-Locus Linkage Disequilibrium",
      "topics": [
        "LDmap",
        "LDscan",
        "LDscan.DNAbin",
        "LDscan.loci"
      ]
    },
    {
      "page": "mjn",
      "title": "Median-Joining Network",
      "topics": [
        "mjn",
        "plot.mjn"
      ]
    },
    {
      "page": "MMD",
      "title": "Mismatch Distribution",
      "topics": [
        "MMD"
      ]
    },
    {
      "page": "mst",
      "title": "Minimum Spanning Tree and Network",
      "topics": [
        "msn",
        "mst",
        "rmst"
      ]
    },
    {
      "page": "mutations",
      "title": "Plot Mutations on Networks",
      "topics": [
        "mutations"
      ]
    },
    {
      "page": "na.omit.loci",
      "title": "Missing Allelic Data",
      "topics": [
        "na.omit.loci",
        "nullAlleles2NA"
      ]
    },
    {
      "page": "nuc.div",
      "title": "Nucleotide Diversity",
      "topics": [
        "nuc.div",
        "nuc.div.DNAbin",
        "nuc.div.haplotype"
      ]
    },
    {
      "page": "plotNetMDS",
      "title": "Plot Networks With MDS Layout",
      "topics": [
        "plotNetMDS"
      ]
    },
    {
      "page": "R2.test",
      "title": "Ramos-Onsins-Rozas Test of Neutrality",
      "topics": [
        "R2.test"
      ]
    },
    {
      "page": "read.gtx",
      "title": "Read Genetix Data Files",
      "topics": [
        "read.gtx"
      ]
    },
    {
      "page": "read.loci",
      "title": "Read Allelic Data Files",
      "topics": [
        "loci",
        "read.loci"
      ]
    },
    {
      "page": "read.vcf",
      "title": "Read Variant Calling Format Files",
      "topics": [
        "read.vcf",
        "write.vcf"
      ]
    },
    {
      "page": "replot",
      "title": "Edit the Layout of a Haplotype Network",
      "topics": [
        "replot"
      ]
    },
    {
      "page": "rr.test",
      "title": "Tajima Relative Rate Test of Molecular Clock",
      "topics": [
        "rr.test"
      ]
    },
    {
      "page": "site.spectrum",
      "title": "Site Frequency Spectrum",
      "topics": [
        "plot.spectrum",
        "site.spectrum",
        "site.spectrum.DNAbin",
        "site.spectrum.loci"
      ]
    },
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