{
  "_id": "6a1f1f93b401979e734201a4",
  "Package": "qfasar",
  "Type": "Package",
  "Title": "Quantitative Fatty Acid Signature Analysis in R",
  "Version": "1.2.1",
  "Authors@R": "person(\"Jeffrey F.\", \"Bromaghin\",\nemail = \"jbromaghin@usgs.gov\",\nrole = c(\"aut\", \"cre\"))",
  "Description": "An implementation of Quantitative Fatty Acid Signature\nAnalysis (QFASA) in R.  QFASA is a method of estimating the\ndiet composition of predators.  The fundamental unit of\ninformation in QFASA is a fatty acid signature (signature),\nwhich is a vector of proportions describing the composition of\nfatty acids within lipids. Signature data from at least one\npredator and from samples of all potential prey types are\nrequired.  Calibration coefficients, which adjust for the\ndifferential metabolism of individual fatty acids by predators,\nare also required. Given those data inputs, a predator\nsignature is modeled as a mixture of prey signatures and its\ndiet estimate is obtained as the mixture that minimizes a\nmeasure of distance between the observed and modeled\nsignatures.  A variety of estimation options and simulation\ncapabilities are implemented. Please refer to the vignette for\nadditional details and references.",
  "License": "Unlimited",
  "RoxygenNote": "7.1.0",
  "VignetteBuilder": "knitr",
  "Packaged": {
    "Date": "2026-05-16 08:03:07 UTC",
    "User": "root"
  },
  "Date": "2020-03-18",
  "NeedsCompilation": "no",
  "Author": "Jeffrey F. Bromaghin [aut, cre]",
  "Maintainer": "Jeffrey F. Bromaghin <jbromaghin@usgs.gov>",
  "Repository": "https://bromaghin.r-universe.dev",
  "Date/Publication": "2020-03-19 20:30:02 UTC",
  "RemoteUrl": "https://github.com/cran/qfasar",
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    "author": "Jeffrey F. Bromaghin <jbromaghin@usgs.gov>",
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    "message": "version 1.2.1\n",
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    "name": "Jeffrey F. Bromaghin",
    "email": "jbromaghin@usgs.gov",
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  "_tags": [],
  "_stars": 0,
  "_contributors": [
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      "count": 5,
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/qfasar"
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/qfasar.html",
    "manual.pdf"
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  "_realowner": "bromaghin",
  "_cranurl": false,
  "_releases": [
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      "version": "1.0.0",
      "date": "2016-08-25"
    },
    {
      "version": "1.1.0",
      "date": "2016-10-25"
    },
    {
      "version": "1.1.1",
      "date": "2016-12-02"
    },
    {
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      "date": "2017-01-09"
    },
    {
      "version": "1.2.1",
      "date": "2020-03-20"
    }
  ],
  "_exports": [
    "add_cc_err",
    "adj_diet_fat",
    "cc_aug",
    "comp_chi_gamma",
    "diet_pool",
    "dimac",
    "est_diet",
    "find_boot_ss",
    "gof",
    "lopo",
    "lopo_pool",
    "make_diet_grid",
    "make_diet_rand",
    "make_ghost",
    "make_pred_sigs",
    "make_prey_part",
    "pred_beyond_prey",
    "prep_fa",
    "prep_sig"
  ],
  "_help": [
    {
      "page": "add_cc_err",
      "title": "Add error to the calibration coefficients",
      "topics": [
        "add_cc_err"
      ]
    },
    {
      "page": "adj_diet_fat",
      "title": "Adjust diet composition estimates for prey fat content",
      "topics": [
        "adj_diet_fat"
      ]
    },
    {
      "page": "cc_aug",
      "title": "Calibration coefficient for an augmented signature proportion",
      "topics": [
        "cc_aug"
      ]
    },
    {
      "page": "comp_chi_gamma",
      "title": "Compute gamma parameter of chi-square distance measure",
      "topics": [
        "comp_chi_gamma"
      ]
    },
    {
      "page": "diet_obj_func",
      "title": "Diet estimation objective function",
      "topics": [
        "diet_obj_func"
      ]
    },
    {
      "page": "diet_pool",
      "title": "Pool diet estimates to combined prey types",
      "topics": [
        "diet_pool"
      ]
    },
    {
      "page": "dimac",
      "title": "Diversive magnetic clustering",
      "topics": [
        "dimac"
      ]
    },
    {
      "page": "dist_between_2_sigs",
      "title": "Compute the distance between two fatty acid signatures",
      "topics": [
        "dist_between_2_sigs"
      ]
    },
    {
      "page": "dist_pairs_map",
      "title": "Creats a map of the distance between pairs of fatty acid signatures",
      "topics": [
        "dist_pairs_map"
      ]
    },
    {
      "page": "dist_sigs_2_mean",
      "title": "Distance between fatty acid signatures and their mean",
      "topics": [
        "dist_sigs_2_mean"
      ]
    },
    {
      "page": "dist_sum_pairwise",
      "title": "Distance between pairs of fatty acid signatures",
      "topics": [
        "dist_sum_pairwise"
      ]
    },
    {
      "page": "est_diet",
      "title": "Estimate predator diet composition",
      "topics": [
        "est_diet"
      ]
    },
    {
      "page": "find_boot_ss",
      "title": "Find realistic bootstrap sample sizes",
      "topics": [
        "find_boot_ss"
      ]
    },
    {
      "page": "gof",
      "title": "Goodness-of-fit for modeled predator signatures",
      "topics": [
        "gof"
      ]
    },
    {
      "page": "lopo",
      "title": "Leave-one-prey-out analysis",
      "topics": [
        "lopo"
      ]
    },
    {
      "page": "lopo_pool",
      "title": "Pool lopo results to original prey types",
      "topics": [
        "lopo_pool"
      ]
    },
    {
      "page": "make_diet_grid",
      "title": "Generate a regular grid of diet compositions",
      "topics": [
        "make_diet_grid"
      ]
    },
    {
      "page": "make_diet_rand",
      "title": "Generate random diet compositions",
      "topics": [
        "make_diet_rand"
      ]
    },
    {
      "page": "make_ghost",
      "title": "Make a ghost prey signature",
      "topics": [
        "make_ghost"
      ]
    },
    {
      "page": "make_pred_sigs",
      "title": "Simulate predator signatures",
      "topics": [
        "make_pred_sigs"
      ]
    },
    {
      "page": "make_prey_part",
      "title": "Make prey partition",
      "topics": [
        "make_prey_part"
      ]
    },
    {
      "page": "pm_obj_func",
      "title": "Parameterized mean objective function",
      "topics": [
        "pm_obj_func"
      ]
    },
    {
      "page": "pred_beyond_prey",
      "title": "Identify predator signature proportions beyond range of prey",
      "topics": [
        "pred_beyond_prey"
      ]
    },
    {
      "page": "prep_fa",
      "title": "Prepare fatty acid information analysis",
      "topics": [
        "prep_fa"
      ]
    },
    {
      "page": "prep_sig",
      "title": "Prepare fatty acid signature data for analysis",
      "topics": [
        "prep_sig"
      ]
    },
    {
      "page": "sig_rep_zero",
      "title": "Replace invalid fatty acid signature proportions",
      "topics": [
        "sig_rep_zero"
      ]
    },
    {
      "page": "sig_scale",
      "title": "Scale fatty acid signature proportions",
      "topics": [
        "sig_scale"
      ]
    }
  ],
  "_rundeps": [
    "codetools",
    "digest",
    "future",
    "future.apply",
    "globals",
    "listenv",
    "numDeriv",
    "parallelly",
    "Rcpp",
    "RcppArmadillo",
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    "truncnorm"
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  "_vignettes": [
    {
      "source": "qfasar.Rmd",
      "filename": "qfasar.html",
      "title": "Package qfasar",
      "author": "Jeffrey F. Bromaghin",
      "engine": "knitr::rmarkdown",
      "headings": [
        "<a name=\"Introduction\"></a> Introduction",
        "",
        "<a name=\"Getting started\"></a> Getting started",
        "<a name=\"Getting help within R\"></a> Getting help within R",
        "<a name=\"Distribution list\"></a> Distribution list",
        "<a name=\"Data frames\"></a> Data frames",
        "<a name=\"Prey signature data\"></a> Prey signature data",
        "<a name=\"Predator signature data\"></a> Predator signature data",
        "<a name=\"Fatty acid suite data\"></a> Fatty acid suite data",
        "<a name=\"Preparing for an analysis\"></a> Preparing for an analysis",
        "<a name=\"Preparing fatty acid suite information\"></a> Preparing fatty acid suite information",
        "<a name=\"Preparing signature data\"></a> Preparing signature data",
        "<a name=\"Modifying invalid signature proportions\"></a> Modifying invalid signature proportions",
        "<a name=\"Scaling signatures\"></a> Scaling signatures",
        "<a name=\"Calibration coefficient for an augmented proportion\"></a> Calibration coefficient for an augmented proportion",
        "<a name=\"Distance measures\"></a> Distance measures",
        "<a name=\"Chi-square distance power parameter\"></a> Chi-square distance power parameter",
        "<a name=\"Estimation spaces\"></a> Estimation spaces",
        "<a name=\"Diet estimation\"></a> Diet estimation",
        "<a name=\"Estimating individual diet and variance\"></a> Estimating individual diet and variance",
        "<a name=\"Estimating mean diet and variance\"></a> Estimating mean diet and variance",
        "<a name=\"Adjusting for fat content\"></a> Adjusting for fat content",
        "<a name=\"Diagnostic functionality\"></a> Diagnostic functionality",
        "<a name=\"Exploring signatures for structure\"></a> Exploring signatures for structure",
        "<a name=\"Using a prey partition\"></a> Using a prey partition",
        "<a name=\"Pooling partitioned estimates to the original prey types\"></a> Pooling partitioned estimates to the original prey types",
        "<a name=\"Leave-one-prey-out analysis\"></a>Leave-one-prey-out analysis",
        "<a name=\"Pool leave-one-prey-out results to the original prey types\"></a> Pool leave-one-prey-out results to the original prey types",
        "<a name=\"Signature & calibration coefficient consistency\"></a> Signature & calibration coefficient consistency",
        "<a name=\"Goodness of fit\"></a> Goodness of fit",
        "<a name=\"Simulation functionality\"></a> Simulation functionality",
        "<a name=\"Predator diet composition\"></a> Predator diet composition",
        "<a name=\"Realistic diets\"></a> Realistic diets",
        "<a name=\"Random diets\"></a> Random diets",
        "<a name=\"Diet grid\"></a> Diet grid",
        "<a name=\"Simulating predator signatures\"></a>Simulating predator signatures",
        "<a name=\"Bootstrap sample size algorithm\"></a> Bootstrap sample size algorithm",
        "<a name=\"Generating a ghost prey signature\"></a> Generating a ghost prey signature",
        "<a name=\"Adding error to calibration coefficients\"></a> Adding error to calibration coefficients",
        "References"
      ],
      "created": "2016-08-25 10:00:58",
      "modified": "2020-03-19 20:30:02",
      "commits": 4
    }
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