{
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  "Package": "adiv",
  "Type": "Package",
  "Title": "Analysis of Diversity",
  "Version": "2.2.1",
  "Date": "2024-02-05",
  "Author": "Sandrine Pavoine",
  "Maintainer": "Sandrine Pavoine <sandrine.pavoine@mnhn.fr>",
  "Description": "Functions, data sets and examples for the calculation of\nvarious indices of biodiversity including species, functional\nand phylogenetic diversity. Part of the indices are expressed\nin terms of equivalent numbers of species. The package also\nprovides ways to partition biodiversity across spatial or\ntemporal scales (alpha, beta, gamma diversities). In addition\nto the quantification of biodiversity, ordination approaches\nare available which rely on diversity indices and allow the\ndetailed identification of species, functional or phylogenetic\ndifferences between communities.",
  "License": "GPL (>= 2)",
  "NeedsCompilation": "no",
  "Packaged": {
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  "Repository": "https://sandrinepavoine.r-universe.dev",
  "Date/Publication": "2024-02-20 02:29:25 UTC",
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  "_published": "2026-06-02T18:07:31.254Z",
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    "author": "Sandrine Pavoine <sandrine.pavoine@mnhn.fr>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 2.2.1\n",
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      "package": "rgl",
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    "extra/citation.cff",
    "extra/citation.html",
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    "extra/contents.json",
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      "date": "2017-07-19"
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      "date": "2018-08-24"
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    "abgdivparam",
    "abgevodivparam",
    "apd",
    "aptree",
    "barp4d",
    "betastatjac",
    "betastatsor",
    "betaTreeUniqueness",
    "betaUniqueness",
    "CFbinary",
    "CFprop",
    "crossdpcoa_maineffect",
    "crossdpcoa_version1",
    "crossdpcoa_version2",
    "dbMANOVAspecies",
    "dbMANOVAspecies_pairwise",
    "decdiv",
    "discomQE",
    "dislptransport",
    "dissABC",
    "dissRicotta",
    "distinctAb",
    "distinctDis",
    "distinctTopo",
    "distinctTree",
    "distinctUltra",
    "distMS",
    "divparam",
    "DJac",
    "dotp4d",
    "DP",
    "dsimcom",
    "dsimFun",
    "dsimTaxo",
    "dsimTree",
    "dspca",
    "EH",
    "EqRao",
    "EqRS",
    "EqRSintra",
    "eveparam",
    "evoCA",
    "evodiss",
    "evodiss_family",
    "evodiss_ternaryplot",
    "evodiv",
    "evodivparam",
    "evoeveparam",
    "evoNSCA",
    "evopcachord",
    "evopcahellinger",
    "evouniparam",
    "FPdivparam",
    "FunImbalance",
    "generalized_Tradidiss",
    "gridp4d",
    "Jac",
    "K",
    "Kstar",
    "Kw",
    "multiCFbinary",
    "multiCFprop",
    "optimEH",
    "orisaved",
    "PADDis",
    "pIa",
    "plot.abgdivparam",
    "plot.abgevodivparam",
    "plot.aptree",
    "plot.decdiv",
    "plot.divparam",
    "plot.dspca",
    "plot.eveparam",
    "plot.evoCA",
    "plot.evodivparam",
    "plot.evoeveparam",
    "plot.evouniparam",
    "plot.FPdivparam",
    "plot.phylo4d",
    "plot.rlqESLTP",
    "plot.rtestaptree",
    "qDT",
    "QE",
    "qHdiv",
    "randEH",
    "rare_Rao",
    "Rentropy",
    "rlqESLTP",
    "rtestaptree",
    "rtestdecdiv",
    "rtestEqRao",
    "rtestEqRS",
    "rtestEqRSintra",
    "rtestwapqe",
    "speciesdiv",
    "specieseve",
    "SQ",
    "summary.dbMANOVAspecies_pairwise",
    "summary.rlqESLTP",
    "tecAptree",
    "treeUniqueness",
    "twoHmax",
    "uniqueness",
    "wapqe"
  ],
  "_datasets": [
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      "name": "batcomm",
      "title": "Bat Abundance and Phylogeny Along a Disturbance Gradient in a Neotropical Rainforest",
      "object": "batcomm",
      "file": "batcomm.rda",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "birdData",
      "title": "Avian Communities along Successional Forest Gradients",
      "object": "birdData",
      "file": "birdData.rda",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "RDMCCP16",
      "title": "Theoretical Data Set used in Ricotta et al. (2016)",
      "object": "RDMCCP16",
      "file": "RDMCCP16.rda",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "rockfish",
      "title": "Rockfish Phylogenetic Diversity in Southern California Bight",
      "object": "rockfish",
      "file": "rockfish.rda",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
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      "name": "RP15EI",
      "title": "Theoretical Data Set used in Ricotta and Pavoine (2015) in Ecological Indicators",
      "object": "RP15EI",
      "file": "RP15EI.rda",
      "class": [
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      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "RP15JVS",
      "title": "Theoretical Data Set used in Ricotta and Pavoine (2015) in Journal of Vegetation Science",
      "object": "RP15JVS",
      "file": "RP15JVS.rda",
      "class": [
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      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "RPP16EE",
      "title": "Theoretical Data Set used in Ricotta et al. (2016) in Ecology and Evolution",
      "object": "RPP16EE",
      "file": "RPP16EE.rda",
      "class": [
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      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "RutorGlacier",
      "title": "Functional and phylogenetic composition of plant communities along a primary succession on glacial deposits.",
      "object": "RutorGlacier",
      "file": "RutorGlacier.rda",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "adiv-package",
      "title": "Analysis of Diversity",
      "topics": [
        "adiv-package",
        "adiv"
      ]
    },
    {
      "page": "abgdivparam",
      "title": "Apportionment of Parametric Indices of Diversity",
      "topics": [
        "abgdivparam",
        "plot.abgdivparam"
      ]
    },
    {
      "page": "abgevodivparam",
      "title": "Apportionment of Parametric Indices of Phylogenetic Diversity",
      "topics": [
        "abgevodivparam",
        "plot.abgevodivparam"
      ]
    },
    {
      "page": "aptree",
      "title": "Hierarchical Partitioning of Evolutionary and Ecological Patterns in the Organization of Phylogenetically-Structured Species Assemblages",
      "topics": [
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        "apd",
        "aptree",
        "pIa",
        "plot.aptree",
        "plot.rtestaptree",
        "rtestaptree",
        "tecAptree"
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    },
    {
      "page": "batcomm",
      "title": "Bat Abundance and Phylogeny Along a Disturbance Gradient in a Neotropical Rainforest",
      "topics": [
        "batcomm"
      ]
    },
    {
      "page": "betastat",
      "title": "Multiple-Site Dissimilarity Measure for Species Presence/Absence Data",
      "topics": [
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        "betastatsor"
      ]
    },
    {
      "page": "betaTreeUniqueness",
      "title": "Plot-to-plot functional or phylogenetic dissimilarity and uniqueness",
      "topics": [
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      ]
    },
    {
      "page": "betaUniqueness",
      "title": "Algorithmic index of plot-to-plot functional (or phylogenetic) dissimilarity and uniqueness",
      "topics": [
        "betaUniqueness"
      ]
    },
    {
      "page": "birdData",
      "title": "Avian Communities along Successional Forest Gradients",
      "topics": [
        "birdData"
      ]
    },
    {
      "page": "CF",
      "title": "Matrices of Intra- and Inter-Specific Similarities",
      "topics": [
        "CFbinary",
        "CFprop",
        "multiCFbinary",
        "multiCFprop"
      ]
    },
    {
      "page": "crossdpcoa",
      "title": "Crossed-DPCoA",
      "topics": [
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        "crossdpcoa_version1",
        "crossdpcoa_version2"
      ]
    },
    {
      "page": "dbMANOVAspecies",
      "title": "Indicator species analysis in the framework of multivariate analysis of variance",
      "topics": [
        "dbMANOVAspecies",
        "dbMANOVAspecies_pairwise",
        "summary.dbMANOVAspecies_pairwise"
      ]
    },
    {
      "page": "decdiv",
      "title": "Decomposition of trait-based diversity along the nodes of a phylogenetic tree",
      "topics": [
        "decdiv",
        "plot.decdiv",
        "rtestdecdiv"
      ]
    },
    {
      "page": "dislptransport",
      "title": "Algorithmic index of plot-to-plot functional (or phylogenetic) dissimilarity",
      "topics": [
        "dislptransport"
      ]
    },
    {
      "page": "dissABC",
      "title": "Phylogenetic and Functional Similarity between Communities",
      "topics": [
        "dissABC"
      ]
    },
    {
      "page": "dissRicotta",
      "title": "Plot-to-Plot Functional or Phylogenetic Dissimilarity",
      "topics": [
        "dissRicotta"
      ]
    },
    {
      "page": "distinctAb",
      "title": "Abundance-based measures of species' rarity, functional or phylogenetic distinctiveness and functional or phylogenetic effective originality",
      "topics": [
        "distinctAb"
      ]
    },
    {
      "page": "distinctDis",
      "title": "Dissimilarity-based Species' Originality",
      "topics": [
        "distinctDis"
      ]
    },
    {
      "page": "distinctTopo",
      "title": "Topology-based Species' Originality",
      "topics": [
        "distinctTopo"
      ]
    },
    {
      "page": "distinctTree",
      "title": "Tree-based Species' Originality",
      "topics": [
        "distinctTree"
      ]
    },
    {
      "page": "distinctUltra",
      "title": "Ultrametric Tree-based Species' Originality",
      "topics": [
        "distinctUltra"
      ]
    },
    {
      "page": "distMS",
      "title": "Marczewski-Steinhaus Coefficient",
      "topics": [
        "distMS"
      ]
    },
    {
      "page": "divparam",
      "title": "Parametric Indices of Species Diversity",
      "topics": [
        "divparam",
        "plot.divparam"
      ]
    },
    {
      "page": "DP",
      "title": "Plot-to-plot functional or phylogenetic dissimilarity",
      "topics": [
        "DP"
      ]
    },
    {
      "page": "dsimcom",
      "title": "Functional or Phylogenetic Similarity between Species and Communities",
      "topics": [
        "dsimcom",
        "dsimFun",
        "dsimTaxo",
        "dsimTree",
        "SQ"
      ]
    },
    {
      "page": "dspca",
      "title": "Double similarity principal component analysis",
      "topics": [
        "dspca",
        "plot.dspca"
      ]
    },
    {
      "page": "EH",
      "title": "Faith Phylogenetic Diversity",
      "topics": [
        "EH"
      ]
    },
    {
      "page": "EqRao",
      "title": "Apportionment of Diversity",
      "topics": [
        "EqRao",
        "EqRS",
        "EqRSintra",
        "rtestEqRao",
        "rtestEqRS",
        "rtestEqRSintra",
        "rtestwapqe",
        "wapqe"
      ]
    },
    {
      "page": "eveparam",
      "title": "Parametric Indices of Species Evenness",
      "topics": [
        "eveparam",
        "plot.eveparam"
      ]
    },
    {
      "page": "evoCA",
      "title": "Evolutionary Correspondence Analysis",
      "topics": [
        "evoCA",
        "plot.evoCA"
      ]
    },
    {
      "page": "evodiss",
      "title": "Pair-wise Phylogenetic Dissimilarities between Communities",
      "topics": [
        "evodiss"
      ]
    },
    {
      "page": "evodiss_family",
      "title": "A Family of Indices Dedicated to Pair-wise Phylogenetic Dissimilarities between Communities",
      "topics": [
        "evodiss_family",
        "evodiss_ternaryplot"
      ]
    },
    {
      "page": "evodiv",
      "title": "Indices of Phylogenetic Diversity",
      "topics": [
        "evodiv"
      ]
    },
    {
      "page": "evodivparam",
      "title": "Parametric Indices of Phylogenetic Diversity",
      "topics": [
        "evodivparam",
        "plot.evodivparam"
      ]
    },
    {
      "page": "evoeveparam",
      "title": "Parametric Indices of Phylogenetic evenness",
      "topics": [
        "evoeveparam",
        "plot.evoeveparam"
      ]
    },
    {
      "page": "evoNSCA",
      "title": "Evolutionary Non-Symmetric Correspondence Analysis",
      "topics": [
        "evoNSCA"
      ]
    },
    {
      "page": "evopca",
      "title": "Evolutionary Principal Component analyses",
      "topics": [
        "evopcachord",
        "evopcahellinger"
      ]
    },
    {
      "page": "evouniparam",
      "title": "Parametric Indices of Phylogenetic Uniqueness",
      "topics": [
        "evouniparam",
        "plot.evouniparam"
      ]
    },
    {
      "page": "FPdivparam",
      "title": "Parametric Indices of Functional and Phylogenetic Diversity",
      "topics": [
        "FPdivparam",
        "plot.FPdivparam"
      ]
    },
    {
      "page": "FunImbalance",
      "title": "Indices of functional imbalance",
      "topics": [
        "FunImbalance"
      ]
    },
    {
      "page": "generalized_Tradidiss",
      "title": "Plot-to-plot dissimilarity taking account of functional dissimilarities between species",
      "topics": [
        "generalized_Tradidiss"
      ]
    },
    {
      "page": "K",
      "title": "Indices K, Kstar and Kw of Phylogenetic Signal",
      "topics": [
        "K",
        "Kstar",
        "Kw"
      ]
    },
    {
      "page": "optimEH",
      "title": "Nee and May's Optimizing Process",
      "topics": [
        "optimEH"
      ]
    },
    {
      "page": "orisaved",
      "title": "Maximal or Minimal Amount of Originality Saved under Optimal Conditions",
      "topics": [
        "orisaved"
      ]
    },
    {
      "page": "PADDis",
      "title": "Functional Dissimilarity Measures for Presence-Absence Data",
      "topics": [
        "DJac",
        "Jac",
        "PADDis"
      ]
    },
    {
      "page": "plot.phylo4d",
      "title": "Plots for phylogenetic tree and data",
      "topics": [
        "barp4d",
        "dotp4d",
        "gridp4d",
        "plot.phylo4d"
      ]
    },
    {
      "page": "qDT",
      "title": "Mean Diversity along a Phylogenetic Tree",
      "topics": [
        "qDT"
      ]
    },
    {
      "page": "QE",
      "title": "Quadratic Entropy",
      "topics": [
        "discomQE",
        "QE"
      ]
    },
    {
      "page": "qHdiv",
      "title": "Biodiversity Measure that Includes Consistent Interspecific and Intraspecific Components",
      "topics": [
        "qHdiv"
      ]
    },
    {
      "page": "randEH",
      "title": "Amount of Evolutionary History Preserved when Random Species are Saved",
      "topics": [
        "randEH"
      ]
    },
    {
      "page": "rare_Rao",
      "title": "Functional Rarefaction for Species Abundance Data",
      "topics": [
        "rare_Rao"
      ]
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