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  "Package": "VLF",
  "Type": "Package",
  "Title": "Frequency Matrix Approach for Assessing Very Low Frequency\nVariants in Sequence Records",
  "Version": "1.1-3",
  "Date": "2025-04-010",
  "Authors@R": "c(person(given = c(\"Taryn\", \"B.\", \"T.\"),\nfamily = \"Athey\",\nrole = \"cre\",\nemail = \"taryn.athey@gmail.com\"),\nperson(given = c(\"Paul\", \"D.\"),\nfamily = \"McNicholas\",\nrole = \"aut\"),\nperson(given = c(\"Jarrett\", \"D.\"),\nfamily = \"Phillips\",\nrole = \"ctb\"))",
  "Maintainer": "Taryn B. T. Athey <taryn.athey@gmail.com>",
  "Description": "Using frequency matrices, very low frequency variants\n(VLFs) are assessed for amino acid and nucleotide sequences.\nThe VLFs are then compared to see if they occur in only one\nmember of a species, singleton VLFs, or if they occur in\nmultiple members of a species, shared VLFs.  The amino acid and\nnucleotide VLFs are then compared to see if they are concordant\nwith one another.  Amino acid VLFs are also assessed to\ndetermine if they lead to a change in amino acid residue type,\nand potential changes to protein structures. Based on Stoeckle\nand Kerr (2012) <doi:10.1371/journal.pone.0043992> and Phillips\net al. (2023) <doi:10.3897/BDJ.11.e96480>.",
  "License": "GPL (>= 3)",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-10 16:27:54 UTC",
    "User": "root"
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  "Author": "Taryn B. T. Athey [cre], Paul D. McNicholas [aut], Jarrett D.\nPhillips [ctb]",
  "Repository": "https://tathey.r-universe.dev",
  "Date/Publication": "2025-04-10 19:20:36 UTC",
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  "_created": "2026-10-10T16:27:54.000Z",
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    "extra/citation.json",
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    "extra/readme.html",
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    "aa.conservation_two",
    "aa.count.function",
    "aa.find.singles",
    "aa.frequency.matrix.function",
    "aa.MODE",
    "aa.MODE.freq",
    "aa.MODE.second.freq",
    "aa.specimen.frequencies",
    "aa.VLF.convert.matrix",
    "aa.VLF.count.pos",
    "aa.VLF.count.spec",
    "aa.VLF.reduced",
    "aaVLFs.to.modalchanges",
    "aminoAcid.matching.positions",
    "aminoAcidFun",
    "compare",
    "concordanceFun",
    "concordant.to.modalchanges",
    "conservation_first",
    "conservation_two",
    "count.function",
    "Decile.Plot",
    "Error.Rate",
    "fasta.read",
    "ffrequency.matrix.function",
    "find.matching",
    "find.singles",
    "matched.codon.position",
    "MODE",
    "MODE.freq",
    "MODE.second.freq",
    "nucleotide.matching.positions",
    "overall.matched",
    "separate",
    "Sliding.Window",
    "specimen.frequencies",
    "VLF.aminoAcids",
    "VLF.convert.matrix",
    "VLF.count.pos",
    "VLF.count.spec",
    "VLF.nucleotides",
    "VLF.reduced",
    "vlfFun"
  ],
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      "name": "birds",
      "title": "Bird Nucleotide Sequences",
      "object": "birds",
      "file": "birds.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [],
      "rows": 11333,
      "table": true,
      "tojson": true
    },
    {
      "name": "birds_aminoAcids",
      "title": "Bird Amino Acid Sequences",
      "object": "birds_aminoAcids",
      "file": "birds_aminoAcids.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [],
      "rows": 11333,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "VLF-package",
      "title": "Frequency Matrix Approach for Assessing Very Low Frequency Variants in Sequence Records",
      "topics": [
        "VLF-package",
        "VLF"
      ]
    },
    {
      "page": "aa.compare",
      "title": "Amino Acid Comparison",
      "topics": [
        "aa.compare"
      ]
    },
    {
      "page": "aa.conservation_first",
      "title": "First Modal Amino Acid Conservation",
      "topics": [
        "aa.conservation_first"
      ]
    },
    {
      "page": "aa.conservation_two",
      "title": "First and Second Modal Amino Acid Conservation",
      "topics": [
        "aa.conservation_two"
      ]
    },
    {
      "page": "aa.count.function",
      "title": "Amino Acid Count",
      "topics": [
        "aa.count.function"
      ]
    },
    {
      "page": "aa.find.singles",
      "title": "Find amino acid singles",
      "topics": [
        "aa.find.singles"
      ]
    },
    {
      "page": "aa.frequency.matrix.function",
      "title": "Amino Acid Frequency Matrix",
      "topics": [
        "aa.frequency.matrix.function"
      ]
    },
    {
      "page": "aa.MODE",
      "title": "Amino Acid Modal Sequence",
      "topics": [
        "aa.MODE"
      ]
    },
    {
      "page": "aa.MODE.freq",
      "title": "Amino Acid Modal Frequencies",
      "topics": [
        "aa.MODE.freq"
      ]
    },
    {
      "page": "aa.MODE.second.freq",
      "title": "Amino Acid Second Modal Frequency",
      "topics": [
        "aa.MODE.second.freq"
      ]
    },
    {
      "page": "aa.specimen.frequencies",
      "title": "Specimen Nucleotide Frequencies",
      "topics": [
        "aa.specimen.frequencies"
      ]
    },
    {
      "page": "aa.VLF.convert.matrix",
      "title": "Convert Amino Acid Matrix",
      "topics": [
        "aa.VLF.convert.matrix"
      ]
    },
    {
      "page": "aa.VLF.count.pos",
      "title": "VLF position count",
      "topics": [
        "aa.VLF.count.pos"
      ]
    },
    {
      "page": "aa.VLF.count.spec",
      "title": "VLF Specimen Count",
      "topics": [
        "aa.VLF.count.spec"
      ]
    },
    {
      "page": "aa.VLF.reduced",
      "title": "Amino Acid Reduced",
      "topics": [
        "aa.VLF.reduced"
      ]
    },
    {
      "page": "aaVLFs.to.modalchanges",
      "title": "Amino Acid Changes",
      "topics": [
        "aaVLFs.to.modalchanges"
      ]
    },
    {
      "page": "aminoAcid.matching.positions",
      "title": "Matching Amino Acid Positions",
      "topics": [
        "aminoAcid.matching.positions"
      ]
    },
    {
      "page": "aminoAcidFun",
      "title": "Amino Acid VLF Analysis Function",
      "topics": [
        "aminoAcidFun"
      ]
    },
    {
      "page": "birds",
      "title": "Bird Nucleotide Sequences",
      "topics": [
        "birds"
      ]
    },
    {
      "page": "birds_aminoAcids",
      "title": "Bird Amino Acid Sequences",
      "topics": [
        "birds_aminoAcids"
      ]
    },
    {
      "page": "compare",
      "title": "Compare VLFs within Species",
      "topics": [
        "compare"
      ]
    },
    {
      "page": "concordanceFun",
      "title": "VLF Concordance Check Function",
      "topics": [
        "concordanceFun"
      ]
    },
    {
      "page": "concordant.to.modalchanges",
      "title": "Concordant Residue Changes",
      "topics": [
        "concordant.to.modalchanges"
      ]
    },
    {
      "page": "conservation_first",
      "title": "First Modal Conserved",
      "topics": [
        "conservation_first"
      ]
    },
    {
      "page": "conservation_two",
      "title": "First and Second Modal Conserved",
      "topics": [
        "conservation_two"
      ]
    },
    {
      "page": "count.function",
      "title": "Nucleotide Count",
      "topics": [
        "count.function"
      ]
    },
    {
      "page": "Decile.Plot",
      "title": "VLF Decile Plot",
      "topics": [
        "Decile.Plot"
      ]
    },
    {
      "page": "Error.Rate",
      "title": "Error Rate",
      "topics": [
        "Error.Rate"
      ]
    },
    {
      "page": "fasta.read",
      "title": "Read Fasta Files",
      "topics": [
        "fasta.read"
      ]
    },
    {
      "page": "ffrequency.matrix.function",
      "title": "Frequency Matrix",
      "topics": [
        "ffrequency.matrix.function"
      ]
    },
    {
      "page": "find.matching",
      "title": "Find Matching ntVLF and aaVLF Specimen.",
      "topics": [
        "find.matching"
      ]
    },
    {
      "page": "find.singles",
      "title": "Single and Shared VLF Find",
      "topics": [
        "find.singles"
      ]
    },
    {
      "page": "matched.codon.position",
      "title": "Codon Position of Matching aa and ntVLFs",
      "topics": [
        "matched.codon.position"
      ]
    },
    {
      "page": "MODE",
      "title": "Modal Sequence",
      "topics": [
        "MODE"
      ]
    },
    {
      "page": "MODE.freq",
      "title": "Modal Frequencies",
      "topics": [
        "MODE.freq"
      ]
    },
    {
      "page": "MODE.second.freq",
      "title": "Second Modal Frequency",
      "topics": [
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      ]
    },
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      "page": "nucleotide.matching.positions",
      "title": "Matching Nucleotide Positions",
      "topics": [
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      ]
    },
    {
      "page": "overall.matched",
      "title": "Final Matching",
      "topics": [
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      ]
    },
    {
      "page": "separate",
      "title": "Separate Specimen by Species Names",
      "topics": [
        "separate"
      ]
    },
    {
      "page": "Sliding.Window",
      "title": "Sliding Window",
      "topics": [
        "Sliding.Window"
      ]
    },
    {
      "page": "specimen.frequencies",
      "title": "Specimen Nucleotide Frequencies",
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        "specimen.frequencies"
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    },
    {
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      "title": "Amino Acid VLFs",
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      "topics": [
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      "title": "VLF Count for Sequence Positions",
      "topics": [
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      ]
    },
    {
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      "title": "VLF Count for Specimens",
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    },
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    },
    {
      "page": "vlfFun",
      "title": "Nucleotide VLF Assessment Function",
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