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  "Package": "BAT",
  "Title": "Biodiversity Assessment Tools",
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  "Date": "2026-08-26",
  "Authors@R": "c(\nperson(\"Pedro\", \"Cardoso\", email = \"pmcardoso@ciencias.ulisboa.pt\", role = c(\"aut\", \"cre\")),\nperson(\"Stefano\", \"Mammola\", role = c(\"aut\")),\nperson(\"Francois\", \"Rigal\", role = c(\"aut\")),\nperson(\"Renato\", \"Hilario\", role = c(\"aut\")),\nperson(\"Jose\", \"Carvalho\", role = c(\"aut\")))",
  "Description": "Includes algorithms to assess alpha and beta diversity in\nall their dimensions (taxonomic, phylogenetic and functional).\nIt allows performing a number of analyses based on species\nidentities/abundances, phylogenetic/functional distances,\ntrees, convex-hulls or kernel density n-dimensional\nhypervolumes depicting species relationships. Cardoso et al.\n(2015) <doi:10.1111/2041-210X.12310>.",
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  "Author": "Pedro Cardoso [aut, cre], Stefano Mammola [aut], Francois Rigal\n[aut], Renato Hilario [aut], Jose Carvalho [aut]",
  "Maintainer": "Pedro Cardoso <pmcardoso@ciencias.ulisboa.pt>",
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    "alpha",
    "alpha.accum",
    "alpha.estimate",
    "beta",
    "beta.accum",
    "beta.evenness",
    "beta.multi",
    "contribution",
    "coverage",
    "cwd",
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    "dummy",
    "evenness",
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    "gdm",
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    "hull.beta",
    "hull.build",
    "hull.contribution",
    "hull.gamma",
    "hull.sad",
    "hyper.arrangement",
    "hyper.build",
    "hyper.quality",
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    "kernel.alpha",
    "kernel.arrangement",
    "kernel.bandwidth",
    "kernel.beta",
    "kernel.beta.evenness",
    "kernel.build",
    "kernel.contribution",
    "kernel.dispersion",
    "kernel.evenness",
    "kernel.evenness.contribution",
    "kernel.gamma",
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    "kernel.originality",
    "kernel.sad",
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    "optim.alpha.stats",
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    "optim.beta.stats",
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    "originality",
    "r2",
    "rao",
    "raster.alpha",
    "raster.beta",
    "raster.dispersion",
    "raster.evenness",
    "sad",
    "sar",
    "ses",
    "sim.plot",
    "sim.sad",
    "sim.sample",
    "sim.spatial",
    "sim.tree",
    "slope",
    "standard",
    "tree.addTip",
    "tree.build",
    "tree.quality",
    "tree.zero",
    "uniqueness"
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      "name": "arrabida",
      "title": "Sample data of spiders in Arrabida (Portugal)",
      "object": "arrabida",
      "class": [
        "data.frame"
      ],
      "fields": [],
      "rows": 320,
      "table": true,
      "tojson": true
    },
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      "title": "Functional tree for 338 species of spiders",
      "object": "functree",
      "class": [
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      "table": false,
      "tojson": false
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      "title": "Sample data of spiders in Geres (Portugal)",
      "object": "geres",
      "class": [
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      "rows": 320,
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    },
    {
      "name": "guadiana",
      "title": "Sample data of spiders in Guadiana (Portugal)",
      "object": "guadiana",
      "class": [
        "data.frame"
      ],
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      "rows": 192,
      "table": true,
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    },
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      "title": "Taxonomic tree for 338 species of spiders (surrogate for phylogeny)",
      "object": "phylotree",
      "class": [
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      "fields": [],
      "table": false,
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  "_help": [
    {
      "page": "accuracy",
      "title": "Scaled mean squared error of accumulation curves.",
      "topics": [
        "accuracy"
      ]
    },
    {
      "page": "aic",
      "title": "Akaike Information Criterion.",
      "topics": [
        "aic"
      ]
    },
    {
      "page": "alpha",
      "title": "Auxiliary function, used only internally Alpha diversity (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).",
      "topics": [
        "alpha"
      ]
    },
    {
      "page": "alpha.accum",
      "title": "Alpha diversity accumulation curves (observed and estimated).",
      "topics": [
        "alpha.accum"
      ]
    },
    {
      "page": "alpha.estimate",
      "title": "Alpha diversity estimates.",
      "topics": [
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      ]
    },
    {
      "page": "arrabida",
      "title": "Sample data of spiders in Arrabida (Portugal)",
      "topics": [
        "arrabida"
      ]
    },
    {
      "page": "beta",
      "title": "Beta diversity (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).",
      "topics": [
        "beta"
      ]
    },
    {
      "page": "beta.accum",
      "title": "Beta diversity accumulation curves.",
      "topics": [
        "beta.accum"
      ]
    },
    {
      "page": "beta.evenness",
      "title": "Beta diversity evenness (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).",
      "topics": [
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      ]
    },
    {
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      "title": "Beta diversity among multiple communities.",
      "topics": [
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    },
    {
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      "title": "Contribution of species or individuals to total phylogenetic/functional diversity.",
      "topics": [
        "contribution"
      ]
    },
    {
      "page": "coverage",
      "title": "Coverage of datasets.",
      "topics": [
        "coverage"
      ]
    },
    {
      "page": "cwd",
      "title": "Community Weighted Dispersion.",
      "topics": [
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      ]
    },
    {
      "page": "cwe",
      "title": "Community Weighted Evenness.",
      "topics": [
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    },
    {
      "page": "cwm",
      "title": "Community Weighted Mean.",
      "topics": [
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      ]
    },
    {
      "page": "dispersion",
      "title": "Phylogenetic/functional dispersion of species or individuals.",
      "topics": [
        "dispersion"
      ]
    },
    {
      "page": "dummy",
      "title": "Dummify variables.",
      "topics": [
        "dummy"
      ]
    },
    {
      "page": "evenness",
      "title": "Taxonomic/phylogenetic/functional evenness of species or individuals.",
      "topics": [
        "evenness"
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    },
    {
      "page": "evenness.contribution",
      "title": "Contribution of each species or individual to the total taxonomic/phylogenetic/functional evenness.",
      "topics": [
        "evenness.contribution"
      ]
    },
    {
      "page": "fill",
      "title": "Filling missing data.",
      "topics": [
        "fill"
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    },
    {
      "page": "functree",
      "title": "Functional tree for 338 species of spiders",
      "topics": [
        "functree"
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    },
    {
      "page": "gamma",
      "title": "Gamma diversity (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).",
      "topics": [
        "gamma"
      ]
    },
    {
      "page": "gdm",
      "title": "General dynamic model of oceanic island biogeography (GDM).",
      "topics": [
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    },
    {
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      "title": "Sample data of spiders in Geres (Portugal)",
      "topics": [
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    },
    {
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      "topics": [
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    },
    {
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      "title": "Sample data of spiders in Guadiana (Portugal)",
      "topics": [
        "guadiana"
      ]
    },
    {
      "page": "hill",
      "title": "Hill numbers.",
      "topics": [
        "hill"
      ]
    },
    {
      "page": "hull.alpha",
      "title": "Alpha diversity using convex hull hypervolumes.",
      "topics": [
        "hull.alpha"
      ]
    },
    {
      "page": "hull.beta",
      "title": "Beta diversity partitioning using convex hull hypervolumes.",
      "topics": [
        "hull.beta"
      ]
    },
    {
      "page": "hull.build",
      "title": "Build convex hull hypervolumes.",
      "topics": [
        "hull.build"
      ]
    },
    {
      "page": "hull.contribution",
      "title": "Contribution of each observation to a convex hull hypervolume.",
      "topics": [
        "hull.contribution"
      ]
    },
    {
      "page": "hull.gamma",
      "title": "Gamma diversity using convex hull hypervolumes.",
      "topics": [
        "hull.gamma"
      ]
    },
    {
      "page": "hull.sad",
      "title": "Species-abundance distribution (SAD) using convex hulls.",
      "topics": [
        "hull.sad"
      ]
    },
    {
      "page": "hyper.arrangement",
      "title": "Functional arrangement within a functional space (generic function).",
      "topics": [
        "hyper.arrangement"
      ]
    },
    {
      "page": "hyper.build",
      "title": "Build hyperspace.",
      "topics": [
        "hyper.build"
      ]
    },
    {
      "page": "hyper.quality",
      "title": "Quality of hyperspace.",
      "topics": [
        "hyper.quality"
      ]
    },
    {
      "page": "iaor",
      "title": "Interspecific abundance-occupancy relationship (IAOR).",
      "topics": [
        "iaor"
      ]
    },
    {
      "page": "kernel.alpha",
      "title": "Alpha diversity using kernel density hypervolumes.",
      "topics": [
        "kernel.alpha"
      ]
    },
    {
      "page": "kernel.arrangement",
      "title": "Functional arrangement of kernel density hypervolumes.",
      "topics": [
        "kernel.arrangement"
      ]
    },
    {
      "page": "kernel.bandwidth",
      "title": "Kernel bandwidth estimation by median heuristic method with bootstrap CI",
      "topics": [
        "kernel.bandwidth"
      ]
    },
    {
      "page": "kernel.beta",
      "title": "Beta diversity partitioning using kernel density hypervolumes.",
      "topics": [
        "kernel.beta"
      ]
    },
    {
      "page": "kernel.beta.evenness",
      "title": "Functional beta diversity evenness using kernel density hypervolumes.",
      "topics": [
        "kernel.beta.evenness"
      ]
    },
    {
      "page": "kernel.build",
      "title": "Build kernel hypervolumes.",
      "topics": [
        "kernel.build"
      ]
    },
    {
      "page": "kernel.contribution",
      "title": "Contribution of each observation to the kernel density hypervolume.",
      "topics": [
        "kernel.contribution"
      ]
    },
    {
      "page": "kernel.dispersion",
      "title": "Functional dispersion of kernel density hypervolumes.",
      "topics": [
        "kernel.dispersion"
      ]
    },
    {
      "page": "kernel.evenness",
      "title": "Functional evenness of kernel density hypervolumes.",
      "topics": [
        "kernel.evenness"
      ]
    },
    {
      "page": "kernel.evenness.contribution",
      "title": "Contribution of each observation to the evenness of a kernel density hypervolume.",
      "topics": [
        "kernel.evenness.contribution"
      ]
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