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  "Title": "Importing and Analysing 'SNP' and 'Silicodart' Data Generated by\nGenome-Wide Restriction Fragment Analysis",
  "Version": "2.9.9.5",
  "Date": "2025-03-24",
  "Authors@R": "c(\nperson(\"Bernd\", \"Gruber\", email=\"bernd.gruber@canberra.edu.au\", role=c(\"aut\",\"cre\")),\nperson(\"Arthur\", \"Georges\", email=\"georges@aerg.edu.au\", role=\"aut\"),\nperson(\"Jose L.\", \"Mijangos\", email=\"Luis.MijangosAraujo@canberra.edu.au\", role=\"aut\"),\nperson(\"Carlo\", \"Pacioni\",email=\"carlo.pacioni@delwp.vic.gov.au\",role=\"aut\"),\nperson(\"Diana\", \"Robledo-Ruiz\",email=\"diana.robledoruiz1@monash.edu\",role =\"aut\"),\nperson(\"Peter J.\", \"Unmack\", email=\"peter.mail2@unmack.net\", role=\"ctb\"),\nperson(\"Oliver\", \"Berry\", email=\"oliver.berry@csiro.au\", role=\"ctb\" ),\nperson(\"Lindsay V.\", \"Clark\", email=\"lvclark@illinois.edu\", role=\"ctb\"),\nperson(\"Floriaan\", \"Devloo-Delva\",email=\"Floriaan.Devloo-Delva@csiro.au\", role=\"ctb\"),\nperson(\"Eric\",\"Archer\", email=\"eric.archer@noaa.gov\", role=\"ctb\")\n)",
  "Description": "Functions are provided that facilitate the import and\nanalysis of 'SNP' (single nucleotide polymorphism) and\n'silicodart' (presence/absence) data. The main focus is on data\ngenerated by 'DarT' (Diversity Arrays Technology), however,\ndata from other sequencing platforms can be used once 'SNP' or\nrelated fragment presence/absence data from any source is\nimported. Genetic datasets are stored in a derived 'genlight'\nformat (package 'adegenet'), that allows for a very compact\nstorage of data and metadata. Functions are available for\nimporting and exporting of 'SNP' and 'silicodart' data, for\nreporting on and filtering on various criteria (e.g.\n'CallRate', heterozygosity, reproducibility, maximum allele\nfrequency). Additional functions are available for\nvisualization (e.g. Principle Coordinate Analysis) and creating\na spatial representation using maps. 'dartR' supports also the\nanalysis of 3rd party software package such as 'newhybrid',\n'structure', 'NeEstimator' and 'blast'. Since version 2.0.3 we\nalso implemented simulation functions, that allow to forward\nsimulate 'SNP' dynamics under different population and\nevolutionary dynamics. Comprehensive tutorials and support can\nbe found at our 'github' repository:\ngithub.com/green-striped-gecko/dartR/. If you want to cite\n'dartR', you find the information by typing citation('dartR')\nin the console.",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-22 07:43:50 UTC",
    "User": "root"
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  "Author": "Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos\n[aut], Carlo Pacioni [aut], Diana Robledo-Ruiz [aut], Peter J.\nUnmack [ctb], Oliver Berry [ctb], Lindsay V. Clark [ctb],\nFloriaan Devloo-Delva [ctb], Eric Archer [ctb]",
  "URL": "https://green-striped-gecko.github.io/dartR/,\nhttps://github.com/green-striped-gecko/dartR",
  "BugReports": "https://groups.google.com/g/dartr?pli=1",
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  "Repository": "https://green-striped-gecko.r-universe.dev",
  "Date/Publication": "2025-03-27 23:13:38 UTC",
  "RemoteUrl": "https://github.com/green-striped-gecko/dartr",
  "RemoteRef": "HEAD",
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      "tojson": false
    },
    {
      "name": "possums.gl",
      "title": "A simulated genlight object created to run a landscape genetic example",
      "object": "possums.gl",
      "class": [
        "genlight"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "testset.gl",
      "title": "A genlight object created via the gl.read.dart function",
      "object": "testset.gl",
      "class": [
        "genlight"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "testset.gs",
      "title": "A genlight object created via the gl.read.silicodart function",
      "object": "testset.gs",
      "class": [
        "genlight"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "sub-dartR-ANY-ANY-ANY-method",
      "title": "indexing dartR objects correctly...",
      "topics": [
        "[,dartR,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "bandicoot.gl",
      "title": "A genlight object created via the read.dart functions",
      "topics": [
        "bandicoot.gl"
      ]
    },
    {
      "page": "cbind.dartR",
      "title": "adjust cbind for dartR",
      "topics": [
        "cbind.dartR"
      ]
    },
    {
      "page": "gi2gl",
      "title": "Converts a genind object into a genlight object",
      "topics": [
        "gi2gl"
      ]
    },
    {
      "page": "gl.alf",
      "title": "Calculates allele frequency of the first and second allele for each loci A very simple function to report allele frequencies",
      "topics": [
        "gl.alf"
      ]
    },
    {
      "page": "gl.allele.freq",
      "title": "Generates percentage allele frequencies by locus and population",
      "concept": [
        "unmatched report"
      ],
      "topics": [
        "gl.allele.freq"
      ]
    },
    {
      "page": "gl.amova",
      "title": "Performs AMOVA using genlight data",
      "topics": [
        "gl.amova"
      ]
    },
    {
      "page": "gl.assign.grm",
      "title": "Population assignment using grm",
      "topics": [
        "gl.assign.grm"
      ]
    },
    {
      "page": "gl.assign.mahalanobis",
      "title": "Assign an individual of unknown provenance to population based on Mahalanobis Distance",
      "topics": [
        "gl.assign.mahalanobis"
      ]
    },
    {
      "page": "gl.assign.pa",
      "title": "Eliminates populations as possible source populations for an individual of unknown provenance, using private alleles",
      "topics": [
        "gl.assign.pa"
      ]
    },
    {
      "page": "gl.assign.pca",
      "title": "Assign an individual of unknown provenance to population based on PCA",
      "topics": [
        "gl.assign.pca"
      ]
    },
    {
      "page": "gl.basic.stats",
      "title": "Calculates basic statistics for each loci (Hs, Ho, Fis etc.)",
      "topics": [
        "gl.basic.stats"
      ]
    },
    {
      "page": "gl.blast",
      "title": "Aligns nucleotides sequences against those present in a target database using blastn",
      "concept": [
        "reference genomes"
      ],
      "topics": [
        "gl.blast"
      ]
    },
    {
      "page": "gl.check.verbosity",
      "title": "Checks the current global verbosity",
      "topics": [
        "gl.check.verbosity"
      ]
    },
    {
      "page": "gl.check.wd",
      "title": "Checks the global working directory",
      "concept": [
        "environment"
      ],
      "topics": [
        "gl.check.wd"
      ]
    },
    {
      "page": "gl.collapse",
      "title": "Collapses a distance matrix by amalgamating populations with pairwise fixed difference count less that a threshold",
      "topics": [
        "gl.collapse"
      ]
    },
    {
      "page": "gl.colors",
      "title": "This is a helper function that supports the creation of color palettes for all plotting functions.",
      "topics": [
        "gl.colors"
      ]
    },
    {
      "page": "gl.compliance.check",
      "title": "Checks a genlight object to see if it complies with dartR expectations and amends it to comply if necessary",
      "topics": [
        "gl.compliance.check"
      ]
    },
    {
      "page": "gl.costdistances",
      "title": "Calculates cost distances for a given landscape (resistance matrix)",
      "topics": [
        "gl.costdistances"
      ]
    },
    {
      "page": "gl.define.pop",
      "title": "Defines a new population in a genlight object for specified individuals",
      "topics": [
        "gl.define.pop"
      ]
    },
    {
      "page": "gl.diagnostics.hwe",
      "title": "Provides descriptive stats and plots to diagnose potential problems with Hardy-Weinberg proportions",
      "concept": [
        "reporting functions"
      ],
      "topics": [
        "gl.diagnostics.hwe"
      ]
    },
    {
      "page": "gl.diagnostics.sim",
      "title": "Comparing simulations against theoretical expectations",
      "topics": [
        "gl.diagnostics.sim"
      ]
    },
    {
      "page": "gl.dist.ind",
      "title": "Calculates a distance matrix for individuals defined in a genlight object",
      "topics": [
        "gl.dist.ind"
      ]
    },
    {
      "page": "gl.dist.pop",
      "title": "Calculates a distance matrix for populations with SNP genotypes in a genlight object",
      "topics": [
        "gl.dist.pop"
      ]
    },
    {
      "page": "gl.drop.ind",
      "title": "Removes specified individuals from a dartR genlight object",
      "concept": [
        "dartR-base"
      ],
      "topics": [
        "gl.drop.ind"
      ]
    },
    {
      "page": "gl.drop.loc",
      "title": "Removes specified loci from a dartR genlight object",
      "concept": [
        "dartR-base"
      ],
      "topics": [
        "gl.drop.loc"
      ]
    },
    {
      "page": "gl.drop.pop",
      "title": "Removes specified populations from a dartR genlight object",
      "concept": [
        "dartR-base"
      ],
      "topics": [
        "gl.drop.pop"
      ]
    },
    {
      "page": "gl.edit.recode.ind",
      "title": "Creates or edits individual (=specimen) names, creates a recode_ind file and applies the changes to a genlight object",
      "concept": [
        "dartR-base"
      ],
      "topics": [
        "gl.edit.recode.ind"
      ]
    },
    {
      "page": "gl.edit.recode.pop",
      "title": "Creates or edits and applies a population re-assignment table",
      "concept": [
        "dartR-base"
      ],
      "topics": [
        "gl.edit.recode.pop"
      ]
    },
    {
      "page": "gl.evanno",
      "title": "Creates an Evanno plot from a STRUCTURE run object",
      "topics": [
        "gl.evanno"
      ]
    },
    {
      "page": "gl.fdsim",
      "title": "Estimates the rate of false positives in a fixed difference analysis",
      "topics": [
        "gl.fdsim"
      ]
    },
    {
      "page": "gl.filter.allna",
      "title": "Filters loci that are all NA across individuals and/or populations with all NA across loci",
      "concept": [
        "filter functions"
      ],
      "topics": [
        "gl.filter.allna"
      ]
    },
    {
      "page": "gl.filter.callrate",
      "title": "Filters loci or specimens in a genlight {adegenet} object based on call rate",
      "concept": [
        "filter functions"
      ],
      "topics": [
        "gl.filter.callrate"
      ]
    },
    {
      "page": "gl.filter.hamming",
      "title": "Filters loci based on pairwise Hamming distance between sequence tags",
      "concept": [
        "filters functions"
      ],
      "topics": [
        "gl.filter.hamming"
      ]
    },
    {
      "page": "gl.filter.heterozygosity",
      "title": "Filters individuals with average heterozygosity greater than a specified upper threshold or less than a specified lower threshold",
      "concept": [
        "filter functions"
      ],
      "topics": [
        "gl.filter.heterozygosity"
      ]
    },
    {
      "page": "gl.filter.hwe",
      "title": "Filters loci that show significant departure from Hardy-Weinberg Equilibrium",
      "concept": [
        "filter functions"
      ],
      "topics": [
        "gl.filter.hwe"
      ]
    },
    {
      "page": "gl.filter.locmetric",
      "title": "Filters loci on the basis of numeric information stored in other$loc.metrics in a genlight {adegenet} object",
      "concept": [
        "filter functions"
      ],
      "topics": [
        "gl.filter.locmetric"
      ]
    },
    {
      "page": "gl.filter.maf",
      "title": "Filters loci on the basis of minor allele frequency (MAF) in a genlight 'adegenet' object",
      "concept": [
        "filter functions"
      ],
      "topics": [
        "gl.filter.maf"
      ]
    },
    {
      "page": "gl.filter.monomorphs",
      "title": "Filters monomorphic loci, including those with all NAs",
      "concept": [
        "filter functions"
      ],
      "topics": [
        "gl.filter.monomorphs"
      ]
    },
    {
      "page": "gl.filter.overshoot",
      "title": "Filters loci for which the SNP has been trimmed from the sequence tag along with the adaptor",
      "concept": [
        "filter functions"
      ],
      "topics": [
        "gl.filter.overshoot"
      ]
    },
    {
      "page": "gl.filter.pa",
      "title": "Filters loci that contain private (and fixed alleles) between two populations",
      "concept": [
        "filter functions"
      ],
      "topics": [
        "gl.filter.pa"
      ]
    },
    {
      "page": "gl.filter.parent.offspring",
      "title": "Filters putative parent offspring within a population",
      "concept": [
        "filter functions"
      ],
      "topics": [
        "gl.filter.parent.offspring"
      ]
    },
    {
      "page": "gl.filter.rdepth",
      "title": "Filters loci based on counts of sequence tags scored at a locus (read depth)",
      "concept": [
        "filter functions"
      ],
      "topics": [
        "gl.filter.rdepth"
      ]
    },
    {
      "page": "gl.filter.reproducibility",
      "title": "Filters loci in a genlight {adegenet} object based on average repeatability of alleles at a locus",
      "concept": [
        "filter functions"
      ],
      "topics": [
        "gl.filter.reproducibility"
      ]
    },
    {
      "page": "gl.filter.secondaries",
      "title": "Filters loci that represent secondary SNPs in a genlight object",
      "concept": [
        "filter functions"
      ],
      "topics": [
        "gl.filter.secondaries"
      ]
    },
    {
      "page": "gl.filter.sexlinked",
      "title": "Filters loci that are sex linked",
      "concept": [
        "filter functions"
      ],
      "topics": [
        "gl.filter.sexlinked"
      ]
    },
    {
      "page": "gl.filter.taglength",
      "title": "Filters loci in a genlight {adegenet} object based on sequence tag length",
      "concept": [
        "filter functions"
      ],
      "topics": [
        "gl.filter.taglength"
      ]
    },
    {
      "page": "gl.fixed.diff",
      "title": "Generates a matrix of fixed differences and associated statistics for populations taken pairwise",
      "topics": [
        "gl.fixed.diff"
      ]
    },
    {
      "page": "gl.fst.pop",
      "title": "Calculates a pairwise Fst values for populations in a genlight object",
      "topics": [
        "gl.fst.pop"
      ]
    },
    {
      "page": "gl.genleastcost",
      "title": "Performs least-cost path analysis based on a friction matrix",
      "topics": [
        "gl.genleastcost"
      ]
    },
    {
      "page": "gl.grm",
      "title": "Calculates an identity by descent matrix",
      "concept": [
        "inbreeding functions"
      ],
      "topics": [
        "gl.grm"
      ]
    },
    {
      "page": "gl.grm.network",
      "title": "Represents a genomic relationship matrix (GRM) as a network",
      "concept": [
        "inbreeding functions"
      ],
      "topics": [
        "gl.grm.network"
      ]
    },
    {
      "page": "gl.He",
      "title": "Estimates expected Heterozygosity",
      "topics": [
        "gl.He"
      ]
    },
    {
      "page": "gl.Ho",
      "title": "Estimates observed Heterozygosity",
      "topics": [
        "gl.Ho"
      ]
    },
    {
      "page": "gl.hwe.pop",
      "title": "Performs Hardy-Weinberg tests over loci and populations",
      "topics": [
        "gl.hwe.pop"
      ]
    },
    {
      "page": "gl.ibd",
      "title": "Performs isolation by distance analysis",
      "topics": [
        "gl.ibd"
      ]
    },
    {
      "page": "gl.impute",
      "title": "Imputates missing data",
      "topics": [
        "gl.impute"
      ]
    },
    {
      "page": "gl.install.vanilla.dartR",
      "title": "Installs all required packages for using all functions available in dartR",
      "topics": [
        "gl.install.vanilla.dartR"
      ]
    },
    {
      "page": "gl.join",
      "title": "Combines two genlight objects",
      "topics": [
        "gl.join"
      ]
    },
    {
      "page": "gl.keep.ind",
      "title": "Removes all but the specified individuals from a dartR genlight object",
      "topics": [
        "gl.keep.ind"
      ]
    },
    {
      "page": "gl.keep.loc",
      "title": "Removes all but the specified loci from a genlight object",
      "concept": [
        "dartR-base"
      ],
      "topics": [
        "gl.keep.loc"
      ]
    },
    {
      "page": "gl.keep.pop",
      "title": "Removes all but the specified populations from a dartR genlight object",
      "topics": [
        "gl.keep.pop"
      ]
    },
    {
      "page": "gl.ld.distance",
      "title": "Plots linkage disequilibrium against distance by population disequilibrium patterns",
      "concept": [
        "ld functions"
      ],
      "topics": [
        "gl.ld.distance"
      ]
    },
    {
      "page": "gl.ld.haplotype",
      "title": "Visualize patterns of linkage disequilibrium and identification of haplotypes",
      "concept": [
        "ld functions"
      ],
      "topics": [
        "gl.ld.haplotype"
      ]
    },
    {
      "page": "gl.LDNe",
      "title": "Estimates effective population size using the Linkage Disequilibrium method based on NeEstimator (V2)",
      "topics": [
        "gl.LDNe"
      ]
    },
    {
      "page": "gl.list.reports",
      "title": "Prints dartR reports saved in tempdir",
      "topics": [
        "gl.list.reports"
      ]
    },
    {
      "page": "gl.load",
      "title": "Loads an object from compressed binary format produced by gl.save()",
      "topics": [
        "gl.load"
      ]
    },
    {
      "page": "gl.make.recode.ind",
      "title": "Creates a proforma recode_ind file for reassigning individual (=specimen) names",
      "concept": [
        "dartR-base"
      ],
      "topics": [
        "gl.make.recode.ind"
      ]
    },
    {
      "page": "gl.make.recode.pop",
      "title": "Creates a proforma recode_pop_table file for reassigning population names",
      "topics": [
        "gl.make.recode.pop"
      ]
    },
    {
      "page": "gl.map.interactive",
      "title": "Creates an interactive map (based on latlon) from a genlight object",
      "topics": [
        "gl.map.interactive"
      ]
    },
    {
      "page": "gl.map.structure",
      "title": "Maps a STRUCTURE plot using a genlight object",
      "topics": [
        "gl.map.structure"
      ]
    },
    {
      "page": "gl.merge.pop",
      "title": "Merges two or more populations in a genlight object into one population",
      "topics": [
        "gl.merge.pop"
      ]
    },
    {
      "page": "gl.nhybrids",
      "title": "Creates an input file for the program NewHybrids and runs it if NewHybrids is installed",
      "concept": [
        "phylo"
      ],
      "topics": [
        "gl.nhybrids"
      ]
    },
    {
      "page": "gl.outflank",
      "title": "Identifies loci under selection per population using the outflank method of Whitlock and Lotterhos (2015)",
      "topics": [
        "gl.outflank"
      ]
    },
    {
      "page": "gl.pcoa",
      "title": "Ordination applied to genotypes in a genlight object (PCA), in an fd object, or to a distance matrix (PCoA)",
      "concept": [
        "data exploration functions"
      ],
      "topics": [
        "gl.pcoa"
      ]
    },
    {
      "page": "gl.pcoa.plot",
      "title": "Bivariate or trivariate plot of the results of an ordination generated using gl.pcoa()",
      "concept": [
        "Exploration/visualisation functions"
      ],
      "topics": [
        "gl.pcoa.plot"
      ]
    },
    {
      "page": "gl.percent.freq",
      "title": "Generates percentage allele frequencies by locus and population",
      "topics": [
        "gl.percent.freq"
      ]
    },
    {
      "page": "gl.play.history",
      "title": "Replays the history and applies it to a genlight object",
      "topics": [
        "gl.play.history"
      ]
    },
    {
      "page": "gl.plot.faststructure",
      "title": "Plots fastStructure analysis results (Q-matrix)",
      "topics": [
        "gl.plot.faststructure"
      ]
    },
    {
      "page": "gl.plot.heatmap",
      "title": "Represents a distance matrix as a heatmap",
      "concept": [
        "graphics"
      ],
      "topics": [
        "gl.plot.heatmap"
      ]
    },
    {
      "page": "gl.plot.network",
      "title": "Represents a distance or dissimilarity matrix as a network",
      "topics": [
        "gl.plot.network"
      ]
    },
    {
      "page": "gl.plot.structure",
      "title": "Plots STRUCTURE analysis results (Q-matrix)",
      "topics": [
        "gl.plot.structure"
      ]
    },
    {
      "page": "gl.print.history",
      "title": "Prints history of a genlight object",
      "topics": [
        "gl.print.history"
      ]
    },
    {
      "page": "gl.print.reports",
      "title": "Prints dartR reports saved in tempdir",
      "topics": [
        "gl.print.reports"
      ]
    },
    {
      "page": "gl.propShared",
      "title": "Calculates a similarity (distance) matrix for individuals on the proportion of shared alleles",
      "topics": [
        "gl.propShared"
      ]
    },
    {
      "page": "gl.random.snp",
      "title": "Randomly changes the allocation of 0's and 2's in a genlight object",
      "topics": [
        "gl.random.snp"
      ]
    },
    {
      "page": "gl.read.csv",
      "title": "Reads SNP data from a csv file into a genlight object",
      "topics": [
        "gl.read.csv"
      ]
    },
    {
      "page": "gl.read.dart",
      "title": "Imports DArT data into dartR and converts it into a dartR genlight object",
      "concept": [
        "dartR-base"
      ],
      "topics": [
        "gl.read.dart"
      ]
    },
    {
      "page": "gl.read.fasta",
      "title": "Reads FASTA files and converts them to genlight object",
      "concept": [
        "reading functions"
      ],
      "topics": [
        "gl.read.fasta"
      ]
    },
    {
      "page": "gl.read.silicodart",
      "title": "Imports presence/absence data from SilicoDArT to genlight {agegenet} format (ploidy=1)",
      "topics": [
        "gl.read.silicodart"
      ]
    },
    {
      "page": "gl.read.vcf",
      "title": "Converts a vcf file into a genlight object",
      "topics": [
        "gl.read.vcf"
      ]
    },
    {
      "page": "gl.reassign.pop",
      "title": "Assigns an individual metric as pop in a genlight {adegenet} object",
      "topics": [
        "gl.reassign.pop"
      ]
    },
    {
      "page": "gl.recalc.metrics",
      "title": "Recalculates locus metrics when individuals or populations are deleted from a genlight {adegenet} object",
      "topics": [
        "gl.recalc.metrics"
      ]
    },
    {
      "page": "gl.recode.ind",
      "title": "Recodes individual (=specimen = sample) labels in a genlight object",
      "concept": [
        "dartR-base"
      ],
      "topics": [
        "gl.recode.ind"
      ]
    },
    {
      "page": "gl.recode.pop",
      "title": "Recodes population assignments in a genlight object",
      "concept": [
        "dartR-base"
      ],
      "topics": [
        "gl.recode.pop"
      ]
    },
    {
      "page": "gl.rename.pop",
      "title": "Renames a population in a genlight object",
      "topics": [
        "gl.rename.pop"
      ]
    },
    {
      "page": "gl.report.bases",
      "title": "Reports summary of base pair frequencies",
      "concept": [
        "report functions"
      ],
      "topics": [
        "gl.report.bases"
      ]
    },
    {
      "page": "gl.report.callrate",
      "title": "Reports summary of Call Rate for loci or individuals",
      "concept": [
        "report functions"
      ],
      "topics": [
        "gl.report.callrate"
      ]
    },
    {
      "page": "gl.report.diversity",
      "title": "Calculates diversity indexes for SNPs",
      "concept": [
        "report functions"
      ],
      "topics": [
        "gl.report.diversity"
      ]
    },
    {
      "page": "gl.report.fstat",
      "title": "Reports various statistics of genetic differentiation between populations with confident intervals",
      "concept": [
        "matched reports"
      ],
      "topics": [
        "gl.report.fstat"
      ]
    },
    {
      "page": "gl.report.hamming",
      "title": "Calculates the pairwise Hamming distance between DArT trimmed DNA sequences",
      "concept": [
        "report functions"
      ],
      "topics": [
        "gl.report.hamming"
      ]
    },
    {
      "page": "gl.report.heterozygosity",
      "title": "Reports observed, expected and unbiased heterozygosities and FIS (inbreeding coefficient) by population or by individual from SNP data",
      "concept": [
        "unmatched report"
      ],
      "topics": [
        "gl.report.heterozygosity"
      ]
    },
    {
      "page": "gl.report.hwe",
      "title": "Reports departure from Hardy-Weinberg proportions",
      "concept": [
        "report functions"
      ],
      "topics": [
        "gl.report.hwe"
      ]
    },
    {
      "page": "gl.report.ld.map",
      "title": "Calculates pairwise linkage disequilibrium by population",
      "concept": [
        "report functions"
      ],
      "topics": [
        "gl.report.ld.map"
      ]
    },
    {
      "page": "gl.report.locmetric",
      "title": "Reports summary of the slot $other$loc.metrics",
      "concept": [
        "report functions"
      ],
      "topics": [
        "gl.report.locmetric"
      ]
    },
    {
      "page": "gl.report.maf",
      "title": "Reports minor allele frequency (MAF) for each locus in a SNP dataset",
      "concept": [
        "report functions"
      ],
      "topics": [
        "gl.report.maf"
      ]
    },
    {
      "page": "gl.report.monomorphs",
      "title": "Reports monomorphic loci",
      "concept": [
        "report functions"
      ],
      "topics": [
        "gl.report.monomorphs"
      ]
    },
    {
      "page": "gl.report.overshoot",
      "title": "Reports loci for which the SNP has been trimmed from the sequence tag along with the adaptor",
      "concept": [
        "report functions"
      ],
      "topics": [
        "gl.report.overshoot"
      ]
    },
    {
      "page": "gl.report.pa",
      "title": "Reports private alleles (and fixed alleles) per pair of populations",
      "concept": [
        "report functions"
      ],
      "topics": [
        "gl.report.pa"
      ]
    },
    {
      "page": "gl.report.parent.offspring",
      "title": "Identifies putative parent offspring within a population",
      "concept": [
        "report functions"
      ],
      "topics": [
        "gl.report.parent.offspring"
      ]
    },
    {
      "page": "gl.report.rdepth",
      "title": "Reports summary of Read Depth for each locus",
      "concept": [
        "report functions"
      ],
      "topics": [
        "gl.report.rdepth"
      ]
    },
    {
      "page": "gl.report.replicates",
      "title": "Identify replicated individuals",
      "concept": [
        "report functions"
      ],
      "topics": [
        "gl.report.replicates"
      ]
    },
    {
      "page": "gl.report.reproducibility",
      "title": "Reports summary of RepAvg (repeatability averaged over both alleles for each locus) or reproducibility (repeatability of the scores for fragment presence/absence)",
      "concept": [
        "report functions"
      ],
      "topics": [
        "gl.report.reproducibility"
      ]
    },
    {
      "page": "gl.report.secondaries",
      "title": "Reports loci containing secondary SNPs in sequence tags and calculates number of invariant sites",
      "concept": [
        "report functions"
      ],
      "topics": [
        "gl.report.secondaries"
      ]
    },
    {
      "page": "gl.report.sexlinked",
      "title": "Identifies loci that are sex linked",
      "concept": [
        "report functions"
      ],
      "topics": [
        "gl.report.sexlinked"
      ]
    },
    {
      "page": "gl.report.taglength",
      "title": "Reports summary of sequence tag length across loci",
      "concept": [
        "report functions"
      ],
      "topics": [
        "gl.report.taglength"
      ]
    },
    {
      "page": "gl.run.faststructure",
      "title": "Runs a faststructure analysis using a genlight object",
      "topics": [
        "gl.run.faststructure"
      ]
    },
    {
      "page": "gl.run.structure",
      "title": "Runs a STRUCTURE analysis using a genlight object",
      "topics": [
        "gl.run.structure"
      ]
    },
    {
      "page": "gl.sample",
      "title": "Samples individuals from populations",
      "concept": [
        "base dartR"
      ],
      "topics": [
        "gl.sample"
      ]
    },
    {
      "page": "gl.save",
      "title": "Saves an object in compressed binary format for later rapid retrieval",
      "topics": [
        "gl.save"
      ]
    },
    {
      "page": "gl.select.colors",
      "title": "Selects colors from one of several palettes and output as a vector",
      "concept": [
        "Exploration/visualisation functions"
      ],
      "topics": [
        "gl.select.colors"
      ]
    },
    {
      "page": "gl.select.shapes",
      "title": "Selects shapes from the base R shape palette and outputs as a vector",
      "concept": [
        "Exploration/visualisation functions"
      ],
      "topics": [
        "gl.select.shapes"
      ]
    },
    {
      "page": "gl.set.verbosity",
      "title": "Sets the default verbosity level",
      "concept": [
        "dartR-base"
      ],
      "topics": [
        "gl.set.verbosity"
      ]
    },
    {
      "page": "gl.sfs",
      "title": "Creates a site frequency spectrum based on a dartR or genlight object",
      "topics": [
        "gl.sfs"
      ]
    },
    {
      "page": "gl.sim.create_dispersal",
      "title": "Creates a dispersal file as input for the function gl.sim.WF.run",
      "concept": [
        "simulation functions"
      ],
      "topics": [
        "gl.sim.create_dispersal"
      ]
    },
    {
      "page": "gl.sim.emigration",
      "title": "Simulates emigration between populations",
      "topics": [
        "gl.sim.emigration"
      ]
    },
    {
      "page": "gl.sim.ind",
      "title": "Simulates individuals based on the allele frequencies provided via a genlight object.",
      "topics": [
        "gl.sim.ind"
      ]
    },
    {
      "page": "gl.sim.mutate",
      "title": "Simulates mutations within a genlight object",
      "topics": [
        "gl.sim.mutate"
      ]
    },
    {
      "page": "gl.sim.offspring",
      "title": "Simulates a specified number of offspring based on alleles provided by potential father(s) and mother(s)",
      "topics": [
        "gl.sim.offspring"
      ]
    },
    {
      "page": "gl.sim.WF.run",
      "title": "Runs Wright-Fisher simulations",
      "concept": [
        "simulation functions"
      ],
      "topics": [
        "gl.sim.WF.run"
      ]
    },
    {
      "page": "gl.sim.WF.table",
      "title": "Creates the reference table for running gl.sim.WF.run",
      "concept": [
        "simulation functions"
      ],
      "topics": [
        "gl.sim.WF.table"
      ]
    },
    {
      "page": "gl.smearplot",
      "title": "Smear plot of SNP or presence/absence (SilicoDArT) data",
      "concept": [
        "Exploration/visualisation functions"
      ],
      "topics": [
        "gl.smearplot"
      ]
    },
    {
      "page": "gl.sort",
      "title": "re-sorts genlight objects",
      "concept": [
        "base dartR"
      ],
      "topics": [
        "gl.sort"
      ]
    },
    {
      "page": "gl.spatial.autoCorr",
      "title": "Spatial autocorrelation following Smouse and Peakall 1999",
      "topics": [
        "gl.spatial.autoCorr"
      ]
    },
    {
      "page": "gl.subsample.loci",
      "title": "Subsamples n loci from a genlight object and return it as a genlight object",
      "topics": [
        "gl.subsample.loci"
      ]
    },
    {
      "page": "gl.test.heterozygosity",
      "title": "Tests the difference in heterozygosity between populations taken pairwise",
      "concept": [
        "Genetic variation within populations"
      ],
      "topics": [
        "gl.test.heterozygosity"
      ]
    },
    {
      "page": "gl.tree.nj",
      "title": "Outputs an nj tree to summarize genetic similarity among populations",
      "topics": [
        "gl.tree.nj"
      ]
    },
    {
      "page": "gl.write.csv",
      "title": "Writes out data from a genlight object to csv file",
      "topics": [
        "gl.write.csv"
      ]
    },
    {
      "page": "gl2bayescan",
      "title": "Converts a genlight object into a format suitable for input to Bayescan",
      "topics": [
        "gl2bayescan"
      ]
    },
    {
      "page": "gl2bpp",
      "title": "Converts a genlight object into a format suitable for input to the BPP program",
      "topics": [
        "gl2bpp"
      ]
    },
    {
      "page": "gl2dartR",
      "title": "Convert a genlight object to a dartR object",
      "topics": [
        "gl2dartR"
      ]
    },
    {
      "page": "gl2demerelate",
      "title": "Creates a dataframe suitable for input to package {Demerelate} from a genlight {adegenet} object",
      "topics": [
        "gl2demerelate"
      ]
    },
    {
      "page": "gl2eigenstrat",
      "title": "Converts a genlight object into eigenstrat format",
      "topics": [
        "gl2eigenstrat"
      ]
    },
    {
      "page": "gl2fasta",
      "title": "Concatenates DArT trimmed sequences and outputs a FASTA file",
      "topics": [
        "gl2fasta"
      ]
    },
    {
      "page": "gl2faststructure",
      "title": "Converts a genlight object into faststructure format (to run faststructure elsewhere)",
      "topics": [
        "gl2faststructure"
      ]
    },
    {
      "page": "gl2gds",
      "title": "Converts a genlight object into gds format",
      "topics": [
        "gl2gds"
      ]
    },
    {
      "page": "gl2genalex",
      "title": "Converts a genlight object into a format suitable for input to genalex",
      "topics": [
        "gl2genalex"
      ]
    },
    {
      "page": "gl2genepop",
      "title": "Converts a genlight object into genepop format (and file)",
      "topics": [
        "gl2genepop"
      ]
    },
    {
      "page": "gl2geno",
      "title": "Converts a genlight object to geno format from package LEA",
      "topics": [
        "gl2geno"
      ]
    },
    {
      "page": "gl2gi",
      "title": "Converts a genlight object to genind object",
      "topics": [
        "gl2gi"
      ]
    },
    {
      "page": "gl2hiphop",
      "title": "Converts a genlight objects into hiphop format",
      "topics": [
        "gl2hiphop"
      ]
    },
    {
      "page": "gl2phylip",
      "title": "Creates a Phylip input distance matrix from a genlight (SNP) {adegenet} object",
      "topics": [
        "gl2phylip"
      ]
    },
    {
      "page": "gl2plink",
      "title": "Converts a genlight object into PLINK format",
      "topics": [
        "gl2plink"
      ]
    },
    {
      "page": "gl2related",
      "title": "Converts a genlight object to format suitable to be run with Coancestry",
      "topics": [
        "gl2related"
      ]
    },
    {
      "page": "gl2sa",
      "title": "Converts genlight objects to the format used in the SNPassoc package",
      "topics": [
        "gl2sa"
      ]
    },
    {
      "page": "gl2sfs",
      "title": "Converts a genlight object into a sfs input file",
      "topics": [
        "gl2sfs"
      ]
    },
    {
      "page": "gl2shp",
      "title": "Converts a genlight object to ESRI shapefiles or kml files",
      "topics": [
        "gl2shp"
      ]
    },
    {
      "page": "gl2snapp",
      "title": "Converts a genlight object to nexus format suitable for phylogenetic analysis by SNAPP (via BEAUti)",
      "topics": [
        "gl2snapp"
      ]
    },
    {
      "page": "gl2structure",
      "title": "Converts a genlight object to STRUCTURE formatted files",
      "topics": [
        "gl2structure"
      ]
    },
    {
      "page": "gl2svdquartets",
      "title": "Converts a genlight object to nexus format PAUP SVDquartets",
      "topics": [
        "gl2svdquartets"
      ]
    },
    {
      "page": "gl2treemix",
      "title": "Converts a genlight object to a treemix input file",
      "topics": [
        "gl2treemix"
      ]
    },
    {
      "page": "gl2vcf",
      "title": "Converts a genlight object into vcf format",
      "topics": [
        "gl2vcf"
      ]
    },
    {
      "page": "interactive_reference",
      "title": "Shiny app for the input of the reference table for the simulations",
      "topics": [
        "interactive_reference"
      ]
    },
    {
      "page": "interactive_sim_run",
      "title": "Shiny app for the input of the simulations variables",
      "topics": [
        "interactive_sim_run"
      ]
    },
    {
      "page": "is.fixed",
      "title": "Tests if two populations are fixed at a given locus",
      "topics": [
        "is.fixed"
      ]
    },
    {
      "page": "platy",
      "title": "Example data set as text file to be imported into a genlight object",
      "topics": [
        "platy"
      ]
    },
    {
      "page": "possums.gl",
      "title": "A simulated genlight object created to run a landscape genetic example",
      "topics": [
        "possums.gl"
      ]
    },
    {
      "page": "rbind.dartR",
      "title": "adjust rbind for dartR",
      "topics": [
        "rbind.dartR"
      ]
    },
    {
      "page": "testset_metadata",
      "title": "Metadata file. Can be integrated via the dart2genlight function.",
      "topics": [
        "testset_metadata"
      ]
    },
    {
      "page": "testset_pop_recode",
      "title": "Recode file to be used with the function.",
      "topics": [
        "testset_pop_recode"
      ]
    },
    {
      "page": "testset_SNPs_2Row",
      "title": "Testfile in DArT format (as provided by DArT)",
      "topics": [
        "testset_SNPs_2Row"
      ]
    },
    {
      "page": "testset.gl",
      "title": "A genlight object created via the gl.read.dart function",
      "topics": [
        "testset.gl"
      ]
    },
    {
      "page": "testset.gs",
      "title": "A genlight object created via the gl.read.silicodart function",
      "topics": [
        "testset.gs"
      ]
    },
    {
      "page": "theme_dartR",
      "title": "dartR theme",
      "topics": [
        "theme_dartR"
      ]
    },
    {
      "page": "utils.assignment",
      "title": "Population assignment probabilities",
      "topics": [
        "utils.assignment"
      ]
    },
    {
      "page": "utils.assignment_2",
      "title": "Population assignment probabilities",
      "topics": [
        "utils.assignment_2"
      ]
    },
    {
      "page": "utils.assignment_3",
      "title": "Population assignment probabilities",
      "topics": [
        "utils.assignment_3"
      ]
    },
    {
      "page": "utils.assignment_4",
      "title": "Population assignment probabilities",
      "topics": [
        "utils.assignment_4"
      ]
    },
    {
      "page": "utils.basic.stats",
      "title": "Calculates mean observed heterozygosity, mean expected heterozygosity and Fis per locus, per population and various population differentiation measures",
      "topics": [
        "utils.basic.stats"
      ]
    },
    {
      "page": "utils.check.datatype",
      "title": "Utility function to check the class of an object passed to a function",
      "topics": [
        "utils.check.datatype"
      ]
    },
    {
      "page": "utils.clumpp",
      "title": "Functions from package starmie for merging Q matrices from Structure runs using the CLUMPP algorithms.",
      "topics": [
        "utils.clumpp"
      ]
    },
    {
      "page": "utils.dart2genlight",
      "title": "Converts DarT to genlight.",
      "topics": [
        "utils.dart2genlight"
      ]
    },
    {
      "page": "utils.dist.binary",
      "title": "Calculates a distance matrix for individuals defined in a dartR genlight object using binary P/A data (SilicoDArT)",
      "topics": [
        "utils.dist.binary"
      ]
    },
    {
      "page": "utils.dist.ind.snp",
      "title": "Calculates a distance matrix for individuals defined in a dartR genlight object using SNP data (DArTseq)",
      "topics": [
        "utils.dist.ind.snp"
      ]
    },
    {
      "page": "utils.flag.start",
      "title": "A utility script to flag the start of a script",
      "topics": [
        "utils.flag.start"
      ]
    },
    {
      "page": "utils.hamming",
      "title": "Calculates the Hamming distance between two DArT trimmed DNA sequences",
      "topics": [
        "utils.hamming"
      ]
    },
    {
      "page": "utils.het.pop",
      "title": "Calculates expected mean expected heterozygosity per population",
      "topics": [
        "utils.het.pop"
      ]
    },
    {
      "page": "utils.jackknife",
      "title": "Conducts jackknife resampling using a genlight object",
      "topics": [
        "utils.jackknife"
      ]
    },
    {
      "page": "utils.n.var.invariant",
      "title": "A utility script to calculate the number of variant and invariant sites by locus",
      "topics": [
        "utils.n.var.invariant"
      ]
    },
    {
      "page": "utils.outflank",
      "title": "OutFLANK: An Fst outlier approach by Mike Whitlock and Katie Lotterhos, University of British Columbia.",
      "topics": [
        "utils.outflank"
      ]
    },
    {
      "page": "utils.outflank.MakeDiploidFSTMat",
      "title": "Creates OutFLANK input file from individual genotype info.",
      "topics": [
        "utils.outflank.MakeDiploidFSTMat"
      ]
    },
    {
      "page": "utils.outflank.plotter",
      "title": "Plotting functions for Fst distributions after OutFLANK",
      "topics": [
        "utils.outflank.plotter"
      ]
    },
    {
      "page": "utils.plot.save",
      "title": "An internal function to save a ggplot object to disk in RDS binary format",
      "concept": [
        "utilities"
      ],
      "topics": [
        "utils.plot.save"
      ]
    },
    {
      "page": "utils.read.dart",
      "title": "utility function to read in DArT data",
      "topics": [
        "utils.read.dart"
      ]
    },
    {
      "page": "utils.recalc.avgpic",
      "title": "A utility script to recalculate the OneRatioRef, OneRatioSnp, PICRef, PICSnp, and AvgPIC by locus after some individuals or populations have been deleted.",
      "topics": [
        "utils.recalc.avgpic"
      ]
    },
    {
      "page": "utils.recalc.callrate",
      "title": "A utility script to recalculate the callrate by locus after some populations have been deleted",
      "topics": [
        "utils.recalc.callrate"
      ]
    },
    {
      "page": "utils.recalc.freqhets",
      "title": "A utility script to recalculate the frequency of the heterozygous SNPs by locus after some populations have been deleted",
      "topics": [
        "utils.recalc.freqhets"
      ]
    },
    {
      "page": "utils.recalc.freqhomref",
      "title": "A utility script to recalculate the frequency of the homozygous reference SNP by locus after some populations have been deleted",
      "topics": [
        "utils.recalc.freqhomref"
      ]
    },
    {
      "page": "utils.recalc.freqhomsnp",
      "title": "A utility script to recalculate the frequency of the homozygous alternate SNP by locus after some populations have been deleted",
      "topics": [
        "utils.recalc.freqhomsnp"
      ]
    },
    {
      "page": "utils.recalc.maf",
      "title": "A utility script to recalculate the minor allele frequency by locus, typically after some populations have been deleted",
      "topics": [
        "utils.recalc.maf"
      ]
    },
    {
      "page": "utils.reset.flags",
      "title": "A utility script to reset to FALSE (or TRUE) the locus metric flags after some individuals or populations have been deleted.",
      "topics": [
        "utils.reset.flags"
      ]
    },
    {
      "page": "utils.spautocor",
      "title": "Spatial autocorrelation coefficient calculations",
      "topics": [
        "utils.spautocor"
      ]
    },
    {
      "page": "utils.structure.evanno",
      "title": "Util function for evanno plots",
      "topics": [
        "utils.structure.evanno"
      ]
    },
    {
      "page": "utils.structure.genind2gtypes",
      "title": "structure util functions",
      "topics": [
        "utils.structure.genind2gtypes"
      ]
    },
    {
      "page": "utils.structure.run",
      "title": "Utility function to run Structure",
      "topics": [
        "utils.structure.run"
      ]
    },
    {
      "page": "zzz",
      "title": "Setting up the package",
      "topics": [
        "zzz"
      ]
    }
  ],
  "_readme": "https://github.com/green-striped-gecko/dartr/raw/HEAD/README.md",
  "_rundeps": [
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  "_vignettes": [
    {
      "source": "dartRTutorials.Rmd",
      "filename": "dartRTutorials.pdf",
      "title": "dartR Tutorials",
      "author": "Bernd Gruber, Peter Unmack, Oliver Berry, Luis Mijangos & Arthur Georges",
      "engine": "knitr::rmarkdown",
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