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  "Title": "Stable Isotope Bayesian Ellipses in R",
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  "Description": "Fits bi-variate ellipses to stable isotope data using\nBayesian inference with the aim being to describe and compare\ntheir isotopic niche.",
  "License": "GPL (>= 2)",
  "Language": "en-GB",
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  "Date/Publication": "2026-02-09 14:34:35 UTC",
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  "_releases": [
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      "date": "2015-08-13"
    },
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      "version": "2.0.1",
      "date": "2016-01-27"
    },
    {
      "version": "2.0.2",
      "date": "2016-02-16"
    },
    {
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    {
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    },
    {
      "version": "2.1.3",
      "date": "2017-04-28"
    },
    {
      "version": "2.1.4",
      "date": "2019-02-24"
    },
    {
      "version": "2.1.5",
      "date": "2020-05-12"
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    {
      "version": "2.1.6",
      "date": "2021-04-13"
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      "version": "2.1.7",
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      "date": "2023-08-24"
    },
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      "version": "2.1.9",
      "date": "2023-10-19"
    },
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      "version": "2.1.10",
      "date": "2026-02-16"
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  "_exports": [
    "addEllipse",
    "allCentroidVectors",
    "bayesianLayman",
    "bayesianOverlap",
    "communityMetricsML",
    "createSiberObject",
    "ellipseInOut",
    "ellipsoidTransform",
    "extractPosteriorMeans",
    "fitEllipse",
    "generateSiberCommunity",
    "generateSiberData",
    "generateSiberGroup",
    "groupMetricsML",
    "laymanMetrics",
    "maxLikOverlap",
    "plotCommunityHulls",
    "plotGroupEllipses",
    "plotGroupHulls",
    "plotSiberObject",
    "pointsToEllipsoid",
    "posteriorSEA",
    "siberCentroids",
    "siberConvexhull",
    "siberDensityPlot",
    "siberEllipses",
    "siberMVN",
    "sigmaSEA",
    "specificCentroidVectors"
  ],
  "_datasets": [
    {
      "name": "allgroups",
      "title": "The entire set of Geese isotope data",
      "object": "allgroups",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "Group",
        "d15NPl",
        "d13CPl",
        "d15NCe",
        "d13CCe"
      ],
      "rows": 251,
      "table": true,
      "tojson": true
    },
    {
      "name": "concdepdemo",
      "title": "A set of concentration dependence values for stable isotope analysis",
      "object": "concdepdemo",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Sources",
        "Meand13C",
        "SDd13C",
        "Meand15N",
        "SDd15N"
      ],
      "rows": 4,
      "table": true,
      "tojson": true
    },
    {
      "name": "correctionsdemo",
      "title": "A set of trophic discrimination factors for brent geese feeding on their sources.",
      "object": "correctionsdemo",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Source",
        "Mean15N",
        "Sd15N",
        "Mean13C",
        "Sd13C"
      ],
      "rows": 4,
      "table": true,
      "tojson": true
    },
    {
      "name": "demo.siber.data",
      "title": "Simulated d13C and d15N isotope-space data",
      "object": "demo.siber.data",
      "class": [
        "data.frame"
      ],
      "fields": [
        "iso1",
        "iso2",
        "group",
        "community"
      ],
      "rows": 180,
      "table": true,
      "tojson": true
    },
    {
      "name": "demo.siber.data.2",
      "title": "Simulated d13C and d15N isotope-space data",
      "object": "demo.siber.data.2",
      "class": [
        "data.frame"
      ],
      "fields": [
        "iso1",
        "iso2",
        "group",
        "community"
      ],
      "rows": 150,
      "table": true,
      "tojson": true
    },
    {
      "name": "geese1demo",
      "title": "A single group of the geese data",
      "object": "geese1demo",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "d13CPl",
        "d15NPl"
      ],
      "rows": 9,
      "table": true,
      "tojson": true
    },
    {
      "name": "geese2demo",
      "title": "A single group of the geese data",
      "object": "geese2demo",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "Group",
        "d13CPl",
        "d15NPl"
      ],
      "rows": 251,
      "table": true,
      "tojson": true
    },
    {
      "name": "mongoose",
      "title": "A set of isotope observations for mongooses nested within packs",
      "object": "mongoose",
      "class": [
        "data.frame"
      ],
      "fields": [
        "indiv.id",
        "pack",
        "c13",
        "n15"
      ],
      "rows": 783,
      "table": true,
      "tojson": true
    },
    {
      "name": "sourcesdemo",
      "title": "A set of isotope observations on food sources of brent geese",
      "object": "sourcesdemo",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Sources",
        "Meand13C",
        "SDd13C",
        "Meand15N",
        "SDd15N"
      ],
      "rows": 4,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "addEllipse",
      "title": "Adds an ellipse around some data to an existing plot",
      "topics": [
        "addEllipse"
      ]
    },
    {
      "page": "allCentroidVectors",
      "title": "Plot the pairwise distances and angles describing the difference between centroids of all groups",
      "topics": [
        "allCentroidVectors"
      ]
    },
    {
      "page": "allgroups",
      "title": "The entire set of Geese isotope data",
      "topics": [
        "allgroups"
      ]
    },
    {
      "page": "bayesianLayman",
      "title": "Calculate Layman metrics on Bayesian posterior samples of a community",
      "topics": [
        "bayesianLayman"
      ]
    },
    {
      "page": "bayesianOverlap",
      "title": "Calculate the overlap between two ellipses based on their posterior distributions.",
      "topics": [
        "bayesianOverlap"
      ]
    },
    {
      "page": "communityMetricsML",
      "title": "Calculate the point estimates of the Layman metrics for each community",
      "topics": [
        "communityMetricsML"
      ]
    },
    {
      "page": "concdepdemo",
      "title": "A set of concentration dependence values for stable isotope analysis",
      "topics": [
        "concdepdemo"
      ]
    },
    {
      "page": "correctionsdemo",
      "title": "A set of trophic discrimination factors for brent geese feeding on their sources.",
      "topics": [
        "correctionsdemo"
      ]
    },
    {
      "page": "createSiberObject",
      "title": "Read in SIBER format data and generate the SIBER object",
      "topics": [
        "createSiberObject"
      ]
    },
    {
      "page": "demo.siber.data",
      "title": "Simulated d13C and d15N isotope-space data",
      "topics": [
        "demo.siber.data"
      ]
    },
    {
      "page": "demo.siber.data.2",
      "title": "Simulated d13C and d15N isotope-space data",
      "topics": [
        "demo.siber.data.2"
      ]
    },
    {
      "page": "ellipseBackTransform",
      "title": "Back-transform a z-score siber ellipse to original location and scale.",
      "topics": [
        "ellipseBackTransform"
      ]
    },
    {
      "page": "ellipseInOut",
      "title": "Test whether a set of points are inside or outside a defined circle",
      "topics": [
        "ellipseInOut"
      ]
    },
    {
      "page": "ellipsoidTransform",
      "title": "Apply a normalisation transformation to vectors of data onto ellipsoids",
      "topics": [
        "ellipsoidTransform"
      ]
    },
    {
      "page": "extractPosteriorMeans",
      "title": "Extract posterior means from call to 'siberMVN'",
      "topics": [
        "extractPosteriorMeans"
      ]
    },
    {
      "page": "fitEllipse",
      "title": "Fit a multivariate normal distribution to x and y data using jags",
      "topics": [
        "fitEllipse"
      ]
    },
    {
      "page": "geese1demo",
      "title": "A single group of the geese data",
      "topics": [
        "geese1demo"
      ]
    },
    {
      "page": "geese2demo",
      "title": "A single group of the geese data",
      "topics": [
        "geese2demo"
      ]
    },
    {
      "page": "genCircle",
      "title": "Create a sequence of points on a circle",
      "topics": [
        "genCircle"
      ]
    },
    {
      "page": "generateSiberCommunity",
      "title": "A utility function to simulate a single community comprised of groups",
      "topics": [
        "generateSiberCommunity"
      ]
    },
    {
      "page": "generateSiberData",
      "title": "A utility function to simulate isotope data for several communities",
      "topics": [
        "generateSiberData"
      ]
    },
    {
      "page": "generateSiberGroup",
      "title": "A utility function to simulate a single group of data",
      "topics": [
        "generateSiberGroup"
      ]
    },
    {
      "page": "groupMetricsML",
      "title": "Calculate maximum likelihood based measures of dispersion of bivariate data",
      "topics": [
        "groupMetricsML"
      ]
    },
    {
      "page": "hullArea",
      "title": "Calculate the area of a convex hull given its coordinates",
      "topics": [
        "hullArea"
      ]
    },
    {
      "page": "laymanMetrics",
      "title": "Calculates the 6 Layman metrics on a vector of x and y data",
      "topics": [
        "laymanMetrics"
      ]
    },
    {
      "page": "maxLikOverlap",
      "title": "Calculate the overlap between two ellipses based on the maximum likelihood fitted ellipses.",
      "topics": [
        "maxLikOverlap"
      ]
    },
    {
      "page": "mongoose",
      "title": "A set of isotope observations for mongooses nested within packs",
      "topics": [
        "mongoose"
      ]
    },
    {
      "page": "plotCommunityHulls",
      "title": "Adds convex hulls to each community to an existing plot",
      "topics": [
        "plotCommunityHulls"
      ]
    },
    {
      "page": "plotGroupEllipses",
      "title": "Adds ellipses to an existing plot for each of your groups",
      "topics": [
        "plotGroupEllipses"
      ]
    },
    {
      "page": "plotGroupHulls",
      "title": "Plots illustrative convex hulls for each group within all communities",
      "topics": [
        "plotGroupHulls"
      ]
    },
    {
      "page": "plotSiberObject",
      "title": "Creates an isotope scatterplot and provides a wrapper to ellipse and hull plotting",
      "topics": [
        "plotSiberObject"
      ]
    },
    {
      "page": "pointsToEllipsoid",
      "title": "Test whether a set of points are inside or outside a defined ellipse",
      "topics": [
        "pointsToEllipsoid"
      ]
    },
    {
      "page": "posteriorSEA",
      "title": "Calculate the SEA based on a posterior distribution of Sigma",
      "topics": [
        "posteriorSEA"
      ]
    },
    {
      "page": "siberCentroids",
      "title": "Calculate the polar form of the vector between pairs of ellipse centroids",
      "topics": [
        "siberCentroids"
      ]
    },
    {
      "page": "siberConvexhull",
      "title": "Calculate metrics and plotting information for convex hulls",
      "topics": [
        "siberConvexhull"
      ]
    },
    {
      "page": "siberdensityplot",
      "title": "Plot credible intervals as shaded boxplots using 'hdr.boxplot'",
      "topics": [
        "siberDensityPlot"
      ]
    },
    {
      "page": "siberEllipses",
      "title": "Calculate the Bayesian Standard Ellipse Area for all groups",
      "topics": [
        "siberEllipses"
      ]
    },
    {
      "page": "siberMVN",
      "title": "Fit Bayesian bivariate normal distributions to each group in each community",
      "topics": [
        "siberMVN"
      ]
    },
    {
      "page": "sigmaSEA",
      "title": "Calculate metrics corresponding to the Standard Ellipse based on a covariance matrix",
      "topics": [
        "sigmaSEA"
      ]
    },
    {
      "page": "sourcesdemo",
      "title": "A set of isotope observations on food sources of brent geese",
      "topics": [
        "sourcesdemo"
      ]
    },
    {
      "page": "specificCentroidVectors",
      "title": "Calculate the pairwise distances and angles describing the difference between centroids of paired groups",
      "topics": [
        "specificCentroidVectors"
      ]
    }
  ],
  "_readme": "https://github.com/andrewljackson/siber/raw/HEAD/README.md",
  "_rundeps": [
    "ash",
    "cli",
    "coda",
    "cpp11",
    "dplyr",
    "farver",
    "FNN",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "hdrcde",
    "isoband",
    "kernlab",
    "KernSmooth",
    "ks",
    "labeling",
    "lattice",
    "lifecycle",
    "locfit",
    "magrittr",
    "Matrix",
    "mclust",
    "mgcv",
    "mnormt",
    "multicool",
    "mvtnorm",
    "nlme",
    "pillar",
    "pkgconfig",
    "pracma",
    "purrr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "rjags",
    "rlang",
    "S7",
    "scales",
    "spatstat.utils",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_sysdeps": [
    {
      "shlib": "libjags",
      "package": "jags",
      "headers": "jags",
      "source": "jags",
      "version": "4.3.2-2.2404.0",
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