{
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  "Title": "Parallel and Memory-Efficient Ecological Diversity Metrics",
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  "Authors@R": "c(\nperson(\n\"Daniel P.\", \"Smith\",\nemail   = \"dansmith01@gmail.com\",\nrole    = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-2479-2044\")),\nperson(\n\"Melissa\", \"O'Neill\",\nrole    = c(\"ctb\", \"cph\"),\ncomment = \"PCG random number generator\"),\nperson(\n\"Alkek Center for Metagenomics and Microbiome Research\",\nrole = c(\"cph\", \"fnd\") ))",
  "Description": "Computes alpha and beta diversity metrics in a parallel,\nmemory-efficient manner using 'C' and 'pthreads'. Implements 51\nclassic, compositional, and phylogenetic indices including\nShannon, Bray-Curtis, Faith, JSD, Hellinger, Robust Aitchison,\nand the UniFrac family. Provides random sub-sampling for table\nrarefaction and parses Newick trees into 'phylo' objects.\nIntegrates with data structures from 'phyloseq', 'rbiom', and\nother common bioinformatics packages. Algorithms are described\nin Smith et al. (2026) <doi:10.21105/joss.09777>.",
  "URL": "https://cmmr.github.io/ecodive/, https://github.com/cmmr/ecodive",
  "BugReports": "https://github.com/cmmr/ecodive/issues",
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  "Encoding": "UTF-8",
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  "Repository": "https://cmmr.r-universe.dev",
  "Date/Publication": "2026-06-04 20:50:50 UTC",
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  "Author": "Daniel P. Smith [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-2479-2044>),\nMelissa O'Neill [ctb, cph] (PCG random number generator),\nAlkek Center for Metagenomics and Microbiome Research [cph, fnd]",
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    "jensen",
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    "manhattan",
    "margalef",
    "match_metric",
    "matusita",
    "mcintosh",
    "menhinick",
    "minkowski",
    "morisita",
    "motyka",
    "n_cpus",
    "normalized_unifrac",
    "observed",
    "ochiai",
    "psym_chisq",
    "rarefy",
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    "robust_aitchison",
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    "soergel",
    "sorensen",
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    "squared_chord",
    "squared_euclidean",
    "squares",
    "topsoe",
    "unweighted_unifrac",
    "variance_adjusted_unifrac",
    "wave_hedges",
    "weighted_unifrac"
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      "class": [
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        "array"
      ],
      "fields": [
        "Streptococcus",
        "Bacteroides",
        "Corynebacterium",
        "Haemophilus",
        "Propionibacterium",
        "Staphylococcus"
      ],
      "rows": 4,
      "table": true,
      "tojson": true
    },
    {
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      "title": "Example phylogenetic tree",
      "object": "ex_tree",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "ace",
      "title": "Abundance-based Coverage Estimator (ACE)",
      "concept": [
        "Richness metrics"
      ],
      "topics": [
        "ace"
      ]
    },
    {
      "page": "aitchison",
      "title": "Aitchison distance",
      "concept": [
        "Abundance metrics"
      ],
      "topics": [
        "aitchison"
      ]
    },
    {
      "page": "alpha_div",
      "title": "Alpha Diversity Wrapper Function",
      "topics": [
        "alpha_div"
      ]
    },
    {
      "page": "berger",
      "title": "Berger-Parker Index",
      "concept": [
        "Dominance metrics"
      ],
      "topics": [
        "berger"
      ]
    },
    {
      "page": "beta_div",
      "title": "Beta Diversity Wrapper Function",
      "topics": [
        "beta_div"
      ]
    },
    {
      "page": "bhattacharyya",
      "title": "Bhattacharyya distance",
      "concept": [
        "Abundance metrics"
      ],
      "topics": [
        "bhattacharyya"
      ]
    },
    {
      "page": "bray",
      "title": "Bray-Curtis dissimilarity",
      "concept": [
        "Abundance metrics"
      ],
      "topics": [
        "bray"
      ]
    },
    {
      "page": "brillouin",
      "title": "Brillouin Index",
      "concept": [
        "Diversity metrics"
      ],
      "topics": [
        "brillouin"
      ]
    },
    {
      "page": "canberra",
      "title": "Canberra distance",
      "concept": [
        "Abundance metrics"
      ],
      "topics": [
        "canberra"
      ]
    },
    {
      "page": "chao1",
      "title": "Chao1 Richness Estimator",
      "concept": [
        "Richness metrics"
      ],
      "topics": [
        "chao1"
      ]
    },
    {
      "page": "chebyshev",
      "title": "Chebyshev distance",
      "concept": [
        "Abundance metrics"
      ],
      "topics": [
        "chebyshev"
      ]
    },
    {
      "page": "chord",
      "title": "Chord distance",
      "concept": [
        "Abundance metrics"
      ],
      "topics": [
        "chord"
      ]
    },
    {
      "page": "clark",
      "title": "Clark's divergence distance",
      "concept": [
        "Abundance metrics"
      ],
      "topics": [
        "clark"
      ]
    },
    {
      "page": "divergence",
      "title": "Divergence",
      "concept": [
        "Abundance metrics"
      ],
      "topics": [
        "divergence"
      ]
    },
    {
      "page": "euclidean",
      "title": "Euclidean distance",
      "concept": [
        "Abundance metrics"
      ],
      "topics": [
        "euclidean"
      ]
    },
    {
      "page": "ex_counts",
      "title": "Example counts matrix",
      "topics": [
        "ex_counts"
      ]
    },
    {
      "page": "ex_tree",
      "title": "Example phylogenetic tree",
      "topics": [
        "ex_tree"
      ]
    },
    {
      "page": "faith",
      "title": "Faith's Phylogenetic Diversity (PD)",
      "concept": [
        "Phylogenetic metrics"
      ],
      "topics": [
        "faith"
      ]
    },
    {
      "page": "fisher",
      "title": "Fisher's Alpha",
      "concept": [
        "Diversity metrics"
      ],
      "topics": [
        "fisher"
      ]
    },
    {
      "page": "generalized_unifrac",
      "title": "Generalized UniFrac (GUniFrac)",
      "concept": [
        "Phylogenetic metrics"
      ],
      "topics": [
        "generalized_unifrac"
      ]
    },
    {
      "page": "gower",
      "title": "Gower distance",
      "concept": [
        "Abundance metrics"
      ],
      "topics": [
        "gower"
      ]
    },
    {
      "page": "hamming",
      "title": "Hamming distance",
      "concept": [
        "Presence/Absence metrics"
      ],
      "topics": [
        "hamming"
      ]
    },
    {
      "page": "hellinger",
      "title": "Hellinger distance",
      "concept": [
        "Abundance metrics"
      ],
      "topics": [
        "hellinger"
      ]
    },
    {
      "page": "horn",
      "title": "Horn-Morisita dissimilarity",
      "concept": [
        "Abundance metrics"
      ],
      "topics": [
        "horn"
      ]
    },
    {
      "page": "inv_simpson",
      "title": "Inverse Simpson Index",
      "concept": [
        "Diversity metrics"
      ],
      "topics": [
        "inv_simpson"
      ]
    },
    {
      "page": "jaccard",
      "title": "Jaccard distance",
      "concept": [
        "Presence/Absence metrics"
      ],
      "topics": [
        "jaccard"
      ]
    },
    {
      "page": "jensen",
      "title": "Jensen-Shannon distance",
      "concept": [
        "Abundance metrics"
      ],
      "topics": [
        "jensen"
      ]
    },
    {
      "page": "jsd",
      "title": "Jensen-Shannon divergence (JSD)",
      "concept": [
        "Abundance metrics"
      ],
      "topics": [
        "jsd"
      ]
    },
    {
      "page": "metrics",
      "title": "Find and Browse Available Metrics",
      "topics": [
        "list_metrics",
        "match_metric"
      ]
    },
    {
      "page": "lorentzian",
      "title": "Lorentzian distance",
      "concept": [
        "Abundance metrics"
      ],
      "topics": [
        "lorentzian"
      ]
    },
    {
      "page": "manhattan",
      "title": "Manhattan distance",
      "concept": [
        "Abundance metrics"
      ],
      "topics": [
        "manhattan"
      ]
    },
    {
      "page": "margalef",
      "title": "Margalef's Richness Index",
      "concept": [
        "Richness metrics"
      ],
      "topics": [
        "margalef"
      ]
    },
    {
      "page": "matusita",
      "title": "Matusita distance",
      "concept": [
        "Abundance metrics"
      ],
      "topics": [
        "matusita"
      ]
    },
    {
      "page": "mcintosh",
      "title": "McIntosh Index",
      "concept": [
        "Dominance metrics"
      ],
      "topics": [
        "mcintosh"
      ]
    },
    {
      "page": "menhinick",
      "title": "Menhinick's Richness Index",
      "concept": [
        "Richness metrics"
      ],
      "topics": [
        "menhinick"
      ]
    },
    {
      "page": "minkowski",
      "title": "Minkowski distance",
      "concept": [
        "Abundance metrics"
      ],
      "topics": [
        "minkowski"
      ]
    },
    {
      "page": "morisita",
      "title": "Morisita dissimilarity",
      "concept": [
        "Abundance metrics"
      ],
      "topics": [
        "morisita"
      ]
    },
    {
      "page": "motyka",
      "title": "Motyka dissimilarity",
      "concept": [
        "Abundance metrics"
      ],
      "topics": [
        "motyka"
      ]
    },
    {
      "page": "n_cpus",
      "title": "Number of CPU Cores",
      "topics": [
        "n_cpus"
      ]
    },
    {
      "page": "normalized_unifrac",
      "title": "Normalized Weighted UniFrac",
      "concept": [
        "Phylogenetic metrics"
      ],
      "topics": [
        "normalized_unifrac"
      ]
    },
    {
      "page": "observed",
      "title": "Observed Features",
      "concept": [
        "Richness metrics"
      ],
      "topics": [
        "observed"
      ]
    },
    {
      "page": "ochiai",
      "title": "Otsuka-Ochiai dissimilarity",
      "concept": [
        "Presence/Absence metrics"
      ],
      "topics": [
        "ochiai"
      ]
    },
    {
      "page": "psym_chisq",
      "title": "Probabilistic Symmetric Chi-Squared distance",
      "concept": [
        "Abundance metrics"
      ],
      "topics": [
        "psym_chisq"
      ]
    },
    {
      "page": "rarefy",
      "title": "Rarefy Observation Counts",
      "topics": [
        "rarefy"
      ]
    },
    {
      "page": "read_tree",
      "title": "Read a newick formatted phylogenetic tree.",
      "topics": [
        "read_tree"
      ]
    },
    {
      "page": "robust_aitchison",
      "title": "Robust Aitchison distance",
      "concept": [
        "Abundance metrics"
      ],
      "topics": [
        "robust_aitchison"
      ]
    },
    {
      "page": "shannon",
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