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  "Title": "Measurement and Partitioning of Similarity-Sensitive\nBiodiversity",
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  "Maintainer": "Richard Reeve <richard.reeve@glasgow.ac.uk>",
  "URL": "https://github.com/boydorr/rdiversity",
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  "Description": "Provides a framework for the measurement and partitioning\nof the (similarity-sensitive) biodiversity of a metacommunity\nand its constituent subcommunities. Richard Reeve, et al.\n(2016) <arXiv:1404.6520v3>.",
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  "Repository": "https://boydorr.r-universe.dev",
  "Date/Publication": "2022-05-05 23:27:20 UTC",
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  "Author": "Sonia Mitchell [aut] (ORCID: <https://orcid.org/0000-0003-1536-2066>),\nRichard Reeve [cre, aut, ths] (ORCID:\n<https://orcid.org/0000-0003-2589-8091>),\nTom White [ctb] (ORCID: <https://orcid.org/0000-0002-9639-3800>),\nDaniel Dörrhöfer [ctb],\nAaron Rudkin [ctb]",
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  "_topics": [
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  "_realowner": "boydorr",
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      "date": "2017-06-27"
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    "as.binary",
    "chainsaw",
    "dist2sim",
    "distance",
    "gen2dist",
    "inddiv",
    "meta_gamma",
    "metacommunity",
    "metadiv",
    "norm_alpha",
    "norm_beta",
    "norm_meta_alpha",
    "norm_meta_beta",
    "norm_meta_rho",
    "norm_rho",
    "norm_sub_alpha",
    "norm_sub_beta",
    "norm_sub_rho",
    "phy_abundance",
    "phy_struct",
    "phy2branch",
    "phy2dist",
    "power_mean",
    "raw_alpha",
    "raw_beta",
    "raw_gamma",
    "raw_meta_alpha",
    "raw_meta_beta",
    "raw_meta_rho",
    "raw_rho",
    "raw_sub_alpha",
    "raw_sub_beta",
    "raw_sub_rho",
    "repartition",
    "similarity",
    "sub_gamma",
    "subdiv",
    "tax2dist"
  ],
  "_help": [
    {
      "page": "rdiversity-package",
      "title": "rdiversity: diversity measurement in R",
      "topics": [
        "rdiversity-package",
        "rdiversity"
      ]
    },
    {
      "page": "as.binary",
      "title": "as binary digit.",
      "topics": [
        "as.binary"
      ]
    },
    {
      "page": "binAdd",
      "title": "Binary Addition (+)",
      "topics": [
        "binAdd"
      ]
    },
    {
      "page": "binary",
      "title": "Binary digit.",
      "topics": [
        "binary"
      ]
    },
    {
      "page": "binSeq",
      "title": "Binary sequence",
      "topics": [
        "binSeq"
      ]
    },
    {
      "page": "byte",
      "title": "A simple helper function to return the size of one byte",
      "topics": [
        "byte"
      ]
    },
    {
      "page": "bytesNeeded",
      "title": "Minimum number of \"byte\" needed to hold n \"bit\"",
      "topics": [
        "bytesNeeded"
      ]
    },
    {
      "page": "chainsaw",
      "title": "Function to cut the phylogeny to a specified depth from the tip with the greatest distance from the root.",
      "topics": [
        "chainsaw"
      ]
    },
    {
      "page": "dist2sim",
      "title": "Distance to similarity",
      "topics": [
        "dist2sim"
      ]
    },
    {
      "page": "distance-methods",
      "title": "Generate distance object",
      "topics": [
        "distance",
        "distance,matrix,character-method",
        "distance,matrix,missing-method"
      ]
    },
    {
      "page": "distance-class",
      "title": "distance-class",
      "topics": [
        "distance-class",
        "show,distance-method"
      ]
    },
    {
      "page": "fillUpToBit",
      "title": "Fill up to bit (000..)",
      "topics": [
        "fillUpToBit"
      ]
    },
    {
      "page": "fillUpToByte",
      "title": "Fill up to Byte (00000000..)",
      "topics": [
        "fillUpToByte"
      ]
    },
    {
      "page": "gen2dist",
      "title": "Genetic distance matrix",
      "topics": [
        "gen2dist"
      ]
    },
    {
      "page": "inddiv",
      "title": "Calculate individual-level diversity",
      "topics": [
        "inddiv",
        "inddiv,metacommunity-method",
        "inddiv,powermean-method",
        "inddiv,relativeentropy-method"
      ]
    },
    {
      "page": "is.binary",
      "title": "is Binary Vector",
      "topics": [
        "is.binary"
      ]
    },
    {
      "page": "loadAttributes",
      "title": "loadAttributes",
      "topics": [
        "loadAttributes"
      ]
    },
    {
      "page": "meta_gamma",
      "title": "Metacommunity gamma diversity",
      "topics": [
        "meta_gamma"
      ]
    },
    {
      "page": "metacommunity-methods",
      "title": "Metacommunity",
      "topics": [
        "metacommunity",
        "metacommunity,data.frame,missing-method",
        "metacommunity,data.frame,similarity-method",
        "metacommunity,data.frame-method",
        "metacommunity,matrix,missing-method",
        "metacommunity,matrix,similarity-method",
        "metacommunity,matrix-method",
        "metacommunity,missing,similarity-method",
        "metacommunity,numeric,missing-method",
        "metacommunity,numeric,similarity-method",
        "metacommunity,numeric-method",
        "metacommunity,similarity-method"
      ]
    },
    {
      "page": "metacommunity-class",
      "title": "metacommunity-class",
      "topics": [
        "metacommunity-class",
        "show,metacommunity-method"
      ]
    },
    {
      "page": "metadiv",
      "title": "Metacommunity-level diversity",
      "topics": [
        "metadiv",
        "metadiv,metacommunity-method",
        "metadiv,powermean-method",
        "metadiv,relativeentropy-method"
      ]
    },
    {
      "page": "negate",
      "title": "Binary Negation (!)",
      "topics": [
        "negate"
      ]
    },
    {
      "page": "norm_alpha",
      "title": "Normalised alpha (low level diversity component)",
      "topics": [
        "norm_alpha"
      ]
    },
    {
      "page": "norm_beta",
      "title": "Normalised beta (low level diversity component)",
      "topics": [
        "norm_beta"
      ]
    },
    {
      "page": "norm_meta_alpha",
      "title": "Normalised metacommunity alpha diversity",
      "topics": [
        "norm_meta_alpha"
      ]
    },
    {
      "page": "norm_meta_beta",
      "title": "Normalised metacommunity beta diversity",
      "topics": [
        "norm_meta_beta"
      ]
    },
    {
      "page": "norm_meta_rho",
      "title": "Normalised metacommunity rho diversity",
      "topics": [
        "norm_meta_rho"
      ]
    },
    {
      "page": "norm_rho",
      "title": "Normalised rho (low level diversity component)",
      "topics": [
        "norm_rho"
      ]
    },
    {
      "page": "norm_sub_alpha",
      "title": "Normalised subcommunity alpha diversity",
      "topics": [
        "norm_sub_alpha"
      ]
    },
    {
      "page": "norm_sub_beta",
      "title": "Normalised subcommunity beta diversity",
      "topics": [
        "norm_sub_beta"
      ]
    },
    {
      "page": "norm_sub_rho",
      "title": "Normalised subcommunity rho diversity",
      "topics": [
        "norm_sub_rho"
      ]
    },
    {
      "page": "Ops.binary",
      "title": "Group Generic Ops",
      "topics": [
        "Ops.binary"
      ]
    },
    {
      "page": "phy_abundance",
      "title": "Relative abundance of historical species",
      "topics": [
        "phy_abundance"
      ]
    },
    {
      "page": "phy_struct",
      "title": "Calculate phylogenetic structure matrix",
      "topics": [
        "phy_struct"
      ]
    },
    {
      "page": "phy2branch",
      "title": "Phylogenetic similarity",
      "topics": [
        "phy2branch"
      ]
    },
    {
      "page": "phy2dist",
      "title": "Phylogenetic pairwise tip distance matrix",
      "topics": [
        "phy2dist"
      ]
    },
    {
      "page": "power_mean",
      "title": "Power mean of vector elements",
      "topics": [
        "power_mean"
      ]
    },
    {
      "page": "powermean-class",
      "title": "powermean-class",
      "topics": [
        "powermean-class"
      ]
    },
    {
      "page": "print.binary",
      "title": "Print method for binary number.",
      "topics": [
        "print.binary"
      ]
    },
    {
      "page": "raw_alpha",
      "title": "Raw alpha (low level diversity component)",
      "topics": [
        "raw_alpha"
      ]
    },
    {
      "page": "raw_beta",
      "title": "Raw beta (low level diversity component)",
      "topics": [
        "raw_beta"
      ]
    },
    {
      "page": "raw_gamma",
      "title": "Gamma (low level diversity component)",
      "topics": [
        "raw_gamma"
      ]
    },
    {
      "page": "raw_meta_alpha",
      "title": "Raw metacommunity alpha diversity",
      "topics": [
        "raw_meta_alpha"
      ]
    },
    {
      "page": "raw_meta_beta",
      "title": "Raw metacommunity beta diversity",
      "topics": [
        "raw_meta_beta"
      ]
    },
    {
      "page": "raw_meta_rho",
      "title": "Raw metacommunity rho diversity",
      "topics": [
        "raw_meta_rho"
      ]
    },
    {
      "page": "raw_rho",
      "title": "Raw rho (low level diversity component)",
      "topics": [
        "raw_rho"
      ]
    },
    {
      "page": "raw_sub_alpha",
      "title": "Raw subcommunity alpha diversity",
      "topics": [
        "raw_sub_alpha"
      ]
    },
    {
      "page": "raw_sub_beta",
      "title": "Raw subcommunity beta diversity",
      "topics": [
        "raw_sub_beta"
      ]
    },
    {
      "page": "raw_sub_rho",
      "title": "Raw subcommunity rho diversity",
      "topics": [
        "raw_sub_rho"
      ]
    },
    {
      "page": "relativeentropy-class",
      "title": "relativeentropy-class",
      "topics": [
        "relativeentropy-class"
      ]
    },
    {
      "page": "repartition",
      "title": "Repartition metacommunity",
      "topics": [
        "repartition"
      ]
    },
    {
      "page": "saveAttributes",
      "title": "saveAttributes",
      "topics": [
        "saveAttributes"
      ]
    },
    {
      "page": "similarity-methods",
      "title": "Generate similarity object",
      "topics": [
        "similarity",
        "similarity,matrix,character-method",
        "similarity,matrix,missing-method"
      ]
    },
    {
      "page": "similarity-class",
      "title": "similarity-class",
      "topics": [
        "show,similarity-method",
        "similarity-class"
      ]
    },
    {
      "page": "sub_gamma",
      "title": "Subcommunity gamma diversity",
      "topics": [
        "sub_gamma"
      ]
    },
    {
      "page": "subdiv",
      "title": "Calculate subcommunity-level diversity",
      "topics": [
        "subdiv",
        "subdiv,metacommunity-method",
        "subdiv,powermean-method",
        "subdiv,relativeentropy-method"
      ]
    },
    {
      "page": "summary.binary",
      "title": "Summary method for binary number.",
      "topics": [
        "summary.binary"
      ]
    },
    {
      "page": "switchEndianess",
      "title": "Switch Endianess.",
      "topics": [
        "switchEndianess"
      ]
    },
    {
      "page": "tax2dist",
      "title": "Generate taxonomic distance matrix",
      "topics": [
        "tax2dist"
      ]
    }
  ],
  "_readme": "https://github.com/boydorr/rdiversity/raw/HEAD/README.md",
  "_rundeps": [
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    "magrittr",
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    "Rcpp",
    "reshape2",
    "rlang",
    "stringdist",
    "stringi",
    "stringr",
    "vctrs"
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  "_vignettes": [
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      "source": "examples.Rmd",
      "filename": "examples.html",
      "title": "rdiversity examples",
      "author": "Sonia Mitchell",
      "engine": "knitr::knitr",
      "headings": [
        "Generating a metacommunity",
        "Calculating diversity",
        "Method 1",
        "Method 2",
        "Taxonomic diversity",
        "Phylogenetic diversity",
        "Distance-based phylogenetic diversity",
        "Branch-based phylogenetic diversity",
        "Genetic diversity",
        "User defined distance",
        "User defined similarity",
        "Additional tools",
        "repartition()"
      ],
      "created": "2020-12-21 11:25:15",
      "modified": "2020-12-21 13:36:29",
      "commits": 4
    }
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  "_nocasepkg": "rdiversity",
  "_universes": [
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    "richardreeve"
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