{
  "_id": "6a13ea94acfb0bcc41d2e130",
  "Package": "QFASA",
  "Title": "Quantitative Fatty Acid Signature Analysis",
  "Version": "1.2.1",
  "Date": "2024-08-27",
  "Authors@R": "c(\nperson(\"Connie\", \"Stewart\", email = \"connie.stewart@unb.ca\", role = c(\"cre\",\"aut\", \"cph\")),\nperson(\"Sara\", \"Iverson\", email = \"Sara.Iverson@dal.ca\", role = c(\"aut\",\"cph\")),\nperson(\"Chris\", \"Field\", email = \"field@mathstat.dal.ca\", role = c(\"aut\")),\nperson(\"Don\", \"Bowen\", email = \"Don.Bowen@dfo-mpo.gc.ca\", role = c(\"aut\")),\nperson(\"Wade\", \"Blanchard\", email = \"wade.blanchard@anu.edu.au\", role = c(\"aut\")),\nperson(\"Shelley\", \"Lang\", email = \"shelley.lang@dfo-mpo.gc.ca\", role = c(\"aut\")),\nperson(\"Justin\", \"Kamerman\", email = \"justin@kaleco.net\", role = c(\"aut\")),\nperson(\"Hongchang\", \"Bao\", email = \"hbao@unb.ca\", role = c(\"ctb\")),\nperson(\"Holly\", \"Steeves\", email = \"holly.steeves@uwo.ca\", role = c(\"aut\")),\nperson(\"Jennifer\", \"McNichol\", email = \"jmcnicho@unb.ca\", role = c(\"aut\")),\nperson(\"Tyler\", \"Rideout\", email = \"trideou2@unb.ca\", role = c(\"aut\")))",
  "Description": "Accurate estimates of the diets of predators are required\nin many areas of ecology, but for many species current methods\nare imprecise, limited to the last meal, and often biased. The\ndiversity of fatty acids and their patterns in organisms,\ncoupled with the narrow limitations on their biosynthesis,\nproperties of digestion in monogastric animals, and the\nprevalence of large storage reservoirs of lipid in many\npredators, led to the development of quantitative fatty acid\nsignature analysis (QFASA) to study predator diets.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
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  "RoxygenNote": "7.3.2",
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  "BugReports": "https://github.com/cstewartGH/QFASA/issues",
  "URL": "https://CRAN.R-project.org/package=QFASA",
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  "Repository": "https://cstewartgh.r-universe.dev",
  "Date/Publication": "2024-08-27 17:23:11 UTC",
  "RemoteUrl": "https://github.com/cstewartgh/qfasa",
  "RemoteRef": "HEAD",
  "RemoteSha": "fe5a5bbccf104dfeddd539c8f5a976c2e3f0fb61",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-25 06:12:50 UTC",
    "User": "root"
  },
  "Author": "Connie Stewart [cre, aut, cph],\nSara Iverson [aut, cph],\nChris Field [aut],\nDon Bowen [aut],\nWade Blanchard [aut],\nShelley Lang [aut],\nJustin Kamerman [aut],\nHongchang Bao [ctb],\nHolly Steeves [aut],\nJennifer McNichol [aut],\nTyler Rideout [aut]",
  "Maintainer": "Connie Stewart <connie.stewart@unb.ca>",
  "MD5sum": "27f8070bc41778574e1fb7009b873c31",
  "_user": "cstewartgh",
  "_type": "src",
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  "_created": "2026-05-25T06:12:50.000Z",
  "_published": "2026-05-25T06:22:12.797Z",
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    "message": "New version\n",
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    "AIT.more",
    "AIT.obj",
    "backward.elimination",
    "chisq.CA",
    "chisq.dist",
    "comp.rep",
    "conf.meth",
    "create.d.mat",
    "CS.more",
    "CS.obj",
    "forward.selection",
    "KL.dist",
    "KL.more",
    "KL.obj",
    "MEANmeth",
    "multiplicativeReplacement",
    "p.MLE",
    "p.MUFASA",
    "p.QFASA",
    "p.sim.QFASA",
    "p.SMUFASA",
    "POOLVARmeth",
    "prey.cluster",
    "prey.on.prey",
    "pseudo.pred",
    "pseudo.pred.norm",
    "testfordiff.ind.boot",
    "testfordiff.ind.boot.fun",
    "testfordiff.ind.pval"
  ],
  "_datasets": [
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      "name": "bal.diet.data",
      "title": "Sample example of balanced repeatability diet estimates data with only two repeated measurements per predator.",
      "object": "bal.diet.data",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Seal.ID",
        "Year",
        "capelin",
        "coho",
        "eulachon",
        "herring",
        "mackerel",
        "pilchard",
        "pollock",
        "sandlance",
        "squid",
        "sufsmelt_lg",
        "surfsmelt_s"
      ],
      "rows": 100,
      "table": true,
      "tojson": true
    },
    {
      "name": "CC",
      "title": "Fatty acid calibration coefficients.",
      "object": "CC",
      "class": [
        "data.frame"
      ],
      "fields": [
        "FA",
        "CC"
      ],
      "rows": 66,
      "table": true,
      "tojson": true
    },
    {
      "name": "FAset",
      "title": "List of fatty acids used in sample prey and predator data sets, 'preyFAs' and 'predatorFAs' respectively.",
      "object": "FAset",
      "class": [
        "data.frame"
      ],
      "fields": [
        "FA"
      ],
      "rows": 39,
      "table": true,
      "tojson": true
    },
    {
      "name": "predatorFAs",
      "title": "Predator fatty acid signatures. Each predator signature is a row with fatty acid proportions in columns.",
      "object": "predatorFAs",
      "class": [
        "data.frame"
      ],
      "fields": [
        "SampleCode",
        "AnimalCode",
        "SampleGroup",
        "Biopsy",
        "c12.0",
        "c13.0",
        "Iso14",
        "c14.0",
        "c14.1w9",
        "c14.1w7",
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        "Anti15",
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        "c15.1w6",
        "Iso16",
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        "c16.1w11",
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        "c16.1w7",
        "c7Mec16.0",
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        "c18.1w11",
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      "rows": 10,
      "table": true,
      "tojson": true
    },
    {
      "name": "preyFAs",
      "title": "Prey fatty acid signatures. Each prey signature is a row with fatty acid proportions in columns.",
      "object": "preyFAs",
      "class": [
        "data.frame"
      ],
      "fields": [
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        "Species",
        "lipid",
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      "rows": 302,
      "table": true,
      "tojson": true
    },
    {
      "name": "unbal.diet.data",
      "title": "Sample example of unbalanced repeatability diet estimates data with a max of two repeated measurements per predator.",
      "object": "unbal.diet.data",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Seal.ID",
        "Year",
        "capelin",
        "coho",
        "eulachon",
        "herring",
        "mackerel",
        "pilchard",
        "pollock",
        "sandlance",
        "squid",
        "sufsmelt_lg",
        "surfsmelt_s"
      ],
      "rows": 96,
      "table": true,
      "tojson": true
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  "_help": [
    {
      "page": "AIT.dist",
      "title": "Returns the distance between two compositional vectors using Aitchison's distance measure.",
      "topics": [
        "AIT.dist"
      ]
    },
    {
      "page": "AIT.more",
      "title": "Used to provide additional information on various model components evaluated at the optimal solution, i.e., using the QFASA diet estimates and Aitchison distance measure.",
      "topics": [
        "AIT.more"
      ]
    },
    {
      "page": "AIT.obj",
      "title": "Used in 'solnp()' as the objective function to be minimized when Aitchison distance measure is chosen.",
      "topics": [
        "AIT.obj"
      ]
    },
    {
      "page": "backward.elimination",
      "title": "Returns diet estimates corresponding to a sample of predators based on a backward elimination algorithm that chooses the prey species to be included in the modelling.",
      "topics": [
        "backward.elimination"
      ]
    },
    {
      "page": "bal.diet.data",
      "title": "Sample example of balanced repeatability diet estimates data with only two repeated measurements per predator.",
      "topics": [
        "bal.diet.data"
      ]
    },
    {
      "page": "CC",
      "title": "Fatty acid calibration coefficients.",
      "topics": [
        "CC"
      ]
    },
    {
      "page": "chisq.CA",
      "title": "Called by 'create.d.mat()' to compute the chi-square distance.",
      "topics": [
        "chisq.CA"
      ]
    },
    {
      "page": "chisq.dist",
      "title": "Returns the distance between two compositional vectors using the chi-square distance.",
      "topics": [
        "chisq.dist"
      ]
    },
    {
      "page": "comp.rep",
      "title": "Repeatability in Diet Estimates",
      "topics": [
        "comp.rep"
      ]
    },
    {
      "page": "conf.meth",
      "title": "Confidence Intervals for Diet Proportions",
      "topics": [
        "conf.meth"
      ]
    },
    {
      "page": "create.d.mat",
      "title": "Called by 'testfordiff.ind.boot.fun()' to create a matrix of distances.",
      "topics": [
        "create.d.mat"
      ]
    },
    {
      "page": "CS.more",
      "title": "Used to provide additional information on various model components evaluated at the optimal solution, i.e., using the QFASA diet estimates and chi-square distance measure.",
      "topics": [
        "CS.more"
      ]
    },
    {
      "page": "CS.obj",
      "title": "Used in 'solnp()' as the objective function to be minimized when chi-square distance measure is chosen. Unlike 'AIT.obj()' and 'KL.obj()', does not require modifying zeros.",
      "topics": [
        "CS.obj"
      ]
    },
    {
      "page": "FAset",
      "title": "List of fatty acids used in sample prey and predator data sets, 'preyFAs' and 'predatorFAs' respectively.",
      "topics": [
        "FAset"
      ]
    },
    {
      "page": "forward.selection",
      "title": "Returns diet estimates corresponding to a sample of predators based on a forward selection algorithm that chooses the prey species to be included in the modelling.",
      "topics": [
        "forward.selection"
      ]
    },
    {
      "page": "KL.dist",
      "title": "Returns the distance between two compositional vectors using Kullback-Leibler distance measure.",
      "topics": [
        "KL.dist"
      ]
    },
    {
      "page": "KL.more",
      "title": "Used to provide additional information on various model components evaluated at the optimal solution, i.e., using the QFASA diet estimates and Kullback-Leibler distance measure.",
      "topics": [
        "KL.more"
      ]
    },
    {
      "page": "KL.obj",
      "title": "Used in 'solnp()' as the objective function to be minimized when Kullback-Leibler distance measure is chosen.",
      "topics": [
        "KL.obj"
      ]
    },
    {
      "page": "mean_geometric",
      "title": "Returns the geometric mean of a compositional vector",
      "topics": [
        "mean_geometric"
      ]
    },
    {
      "page": "MEANmeth",
      "title": "Returns the multivariate mean FA signature of each prey group entered into the QFASA model. Result can be passed to prey.mat in 'p.QFASA()'.",
      "topics": [
        "MEANmeth"
      ]
    },
    {
      "page": "multiplicativeReplacement",
      "title": "Multiplicative replacement of zeroes",
      "topics": [
        "multiplicativeReplacement"
      ]
    },
    {
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      "title": "Returns MUFASA diet estimates corresponding to a sample of predators.",
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      "title": "Returns QFASA diet estimates corresponding to a sample of predators.",
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