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  "Package": "coralesce",
  "Title": "Group Coral Colonies Based on Genetic Relatedness",
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  "Authors@R": "c(\nperson(\"Colin\", \"Shea\", email = \"Colin.Shea@MyFWC.com\", role = c(\"aut\", \"cre\")),\nperson(\"Lauren\", \"Gentry\", email = \"Lauren.Gentry@MyFWC.com\", role = \"aut\"),\nperson(\"Kristen\", \"Sauby\", email = \"Kristen.Sauby@MyFWC.com\", role = \"aut\"))",
  "Description": "Assigns coral colonies to clonal groups (genets) from\nsingle nucleotide polymorphism (SNP) data by comparing alleles\nat each locus across all pairwise combinations of colonies, and\ncomputes individual- and population-level mean kinship and gene\ndiversity (excluding invariant loci). Wrapper functions read\ngenotype CSV files from a 'Data' folder and write results to a\n'Results' folder.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
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  "Date/Publication": "2026-07-10 16:11:43 UTC",
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    "classifyAllelePairsOthers",
    "collapseToGenets",
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    "omitInvariantLoci",
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      "object": "IUPAC",
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      "table": true,
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    {
      "page": "calcPercentNotNull",
      "title": "Calculate percent not null",
      "topics": [
        "calcPercentNotNull"
      ]
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    {
      "page": "checkforAllowableData",
      "title": "Flag values that are valid IUPAC allele pairs",
      "topics": [
        "checkforAllowableData"
      ]
    },
    {
      "page": "classifyAllelePairs",
      "title": "Classify allele pairs at a single locus",
      "topics": [
        "classifyAllelePairs"
      ]
    },
    {
      "page": "classifyAllelePairsOthers",
      "title": "Classify allele pairs at a single locus (excluding self-comparisons)",
      "topics": [
        "classifyAllelePairsOthers"
      ]
    },
    {
      "page": "collapseToGenets",
      "title": "Collapse colonies to one representative per genet",
      "topics": [
        "collapseToGenets"
      ]
    },
    {
      "page": "computeGenets",
      "title": "Assign colonies to genets from a genotype data frame",
      "topics": [
        "computeGenets"
      ]
    },
    {
      "page": "computeKinship",
      "title": "Compute kinship and gene diversity from a genotype data frame",
      "topics": [
        "computeKinship"
      ]
    },
    {
      "page": "convertBasePairstoCodes",
      "title": "Convert base-pair genotypes to single-letter IUPAC codes",
      "topics": [
        "convertBasePairstoCodes"
      ]
    },
    {
      "page": "determineAllAlleleMatches",
      "title": "Assess allele matches across all loci (self and other comparisons)",
      "topics": [
        "determineAllAlleleMatches"
      ]
    },
    {
      "page": "determineAllAlleleMatchesOthers",
      "title": "Assess allele matches across all loci (other comparisons only)",
      "topics": [
        "determineAllAlleleMatchesOthers"
      ]
    },
    {
      "page": "find_dups",
      "title": "Stop if any colony has multiple rows of SNP data",
      "topics": [
        "find_dups"
      ]
    },
    {
      "page": "groupByGenets",
      "title": "Assign colonies to genets from pairwise allele matches",
      "topics": [
        "groupByGenets"
      ]
    },
    {
      "page": "handleError_allZeros",
      "title": "Identify colonies with no valid SNP data",
      "topics": [
        "handleError_allZeros"
      ]
    },
    {
      "page": "handleError_ColumnContract",
      "title": "Validate the required input-column contract",
      "topics": [
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      ]
    },
    {
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      "title": "Report columns that do not hold valid SNP data",
      "topics": [
        "handleError_ProhibitedData"
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    },
    {
      "page": "isolateAllNAColonies",
      "title": "Separate colonies with no valid SNP data from the rest",
      "topics": [
        "isolateAllNAColonies"
      ]
    },
    {
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        "IUPAC"
      ]
    },
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