{
  "_id": "6a1f375db401979e73428bf7",
  "Package": "breakaway",
  "Title": "Species Richness Estimation and Modeling",
  "Version": "4.8.5",
  "Date": "2022-11-17",
  "Authors@R": "c(\nperson(\"Amy D\", \"Willis\", email = \"adwillis@uw.edu\", role = c(\"aut\", \"cre\")),\nperson(\"Bryan D\", \"Martin\", role = \"aut\"),\nperson(\"Pauline\", \"Trinh\", role = \"aut\"),\nperson(\"Sarah\", \"Teichman\", role = \"aut\"),\nperson(\"David\", \"Clausen\", role = \"aut\"),\nperson(\"Kathryn\", \"Barger\", role = \"aut\"),\nperson(\"John\", \"Bunge\", role = \"aut\")\n)",
  "Description": "Understanding the drivers of microbial diversity is an\nimportant frontier of microbial ecology, and investigating the\ndiversity of samples from microbial ecosystems is a common step\nin any microbiome analysis. 'breakaway' is the premier package\nfor statistical analysis of microbial diversity. 'breakaway'\nimplements the latest and greatest estimates of species\nrichness, described in Willis and Bunge (2015)\n<doi:10.1111/biom.12332>, Willis et al. (2017)\n<doi:10.1111/rssc.12206>, and Willis (2016) <arXiv:1604.02598>,\nas well as the most commonly used estimates, including the\nobjective Bayes approach described in Barger and Bunge (2010)\n<doi:10.1214/10-BA527>.",
  "License": "GPL-2",
  "BugReports": "https://github.com/adw96/breakaway/issues",
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  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
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  "Encoding": "UTF-8",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libxml2-dev\nzlib1g-dev",
  "Repository": "https://adw96.r-universe.dev",
  "Date/Publication": "2026-04-14 23:28:13 UTC",
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  "RemoteRef": "HEAD",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-15 05:41:07 UTC",
    "User": "root"
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  "Author": "Amy D Willis [aut, cre],\nBryan D Martin [aut],\nPauline Trinh [aut],\nSarah Teichman [aut],\nDavid Clausen [aut],\nKathryn Barger [aut],\nJohn Bunge [aut]",
  "Maintainer": "Amy D Willis <adwillis@uw.edu>",
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  "_created": "2026-05-15T05:41:07.000Z",
  "_published": "2026-06-02T20:04:45.476Z",
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    "name": "AmyW",
    "description": "statistician, biodiversity enthusiast, associate professor"
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    "extra/citation.html",
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    "extra/contents.json",
    "extra/readme.html",
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  "_realowner": "adw96",
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  "_releases": [
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      "date": "2014-08-04"
    },
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      "date": "2015-10-01"
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    "alpha_estimate",
    "alpha_estimates",
    "betta",
    "betta_lincom",
    "betta_pic",
    "betta_random",
    "breakaway",
    "breakaway_nof1",
    "build_frequency_count_tables",
    "chao_bunge",
    "chao_shen",
    "chao1",
    "chao1_bc",
    "convert",
    "F_test",
    "good_turing",
    "kemp",
    "make_design_matrix",
    "make_frequency_count_table",
    "objective_bayes_geometric",
    "objective_bayes_mixedgeo",
    "objective_bayes_negbin",
    "objective_bayes_poisson",
    "poisson_model",
    "poisson_model_nof1",
    "proportions_instead",
    "rnbinomtable",
    "rztnbinomtable",
    "sample_inverse_simpson",
    "sample_richness",
    "sample_shannon",
    "sample_shannon_e",
    "sample_simpson",
    "sample_size_estimate",
    "sample_size_figure",
    "test_submodel",
    "true_gini",
    "true_hill",
    "true_inverse_simpson",
    "true_shannon",
    "true_shannon_e",
    "true_simpson",
    "wlrm_transformed",
    "wlrm_untransformed"
  ],
  "_datasets": [
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      "name": "apples",
      "title": "(Data) Frequency count table of soil microbes in an apples orchard.",
      "object": "apples",
      "class": [
        "data.frame"
      ],
      "fields": [
        "index",
        "frequency"
      ],
      "rows": 88,
      "table": true,
      "tojson": true
    },
    {
      "name": "hawaii",
      "title": "(Data) Frequency count table of soil microbes in Hawaii.",
      "object": "hawaii",
      "class": [
        "data.frame"
      ],
      "fields": [
        "index",
        "frequency"
      ],
      "rows": 198,
      "table": true,
      "tojson": true
    },
    {
      "name": "pasolli_et_al",
      "title": "(Data) Data frame of covariate information about pasolli_et_al.",
      "object": "pasolli_et_al",
      "class": [
        "data.frame"
      ],
      "fields": [
        "SGB.ID",
        "AverageAbundance",
        "std",
        "q1",
        "MedianAbundance",
        "q3",
        "min",
        "max",
        "#.Samples"
      ],
      "rows": 4930,
      "table": true,
      "tojson": true
    },
    {
      "name": "soil_phylo",
      "title": "(Data) Data frame of soil data from whitman_et_al.",
      "object": "soil_phylo",
      "class": [
        "phyloseq"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "toy_metadata",
      "title": "(Data) Data frame of covariate information about toy_otu_table.",
      "object": "toy_metadata",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Years",
        "bloom2",
        "Period",
        "Site"
      ],
      "rows": 143,
      "table": true,
      "tojson": true
    },
    {
      "name": "toy_otu_table",
      "title": "(Data) A toy OTU table.",
      "object": "toy_otu_table",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Sample1",
        "Sample2",
        "Sample3",
        "Sample4",
        "Sample5",
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      ],
      "rows": 448,
      "table": true,
      "tojson": true
    },
    {
      "name": "toy_taxonomy",
      "title": "(Data) The taxonomy of the OTUs in 'toy_otu_table'.",
      "object": "toy_taxonomy",
      "class": [
        "factor"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
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    {
      "page": "alpha_estimate",
      "title": "alpha_estimate",
      "topics": [
        "alpha_estimate"
      ]
    },
    {
      "page": "alpha_estimates",
      "title": "alpha_estimates",
      "topics": [
        "alpha_estimates"
      ]
    },
    {
      "page": "apples",
      "title": "(Data) Frequency count table of soil microbes in an apples orchard.",
      "topics": [
        "apples"
      ]
    },
    {
      "page": "betta",
      "title": "Modelling total diversity with betta",
      "topics": [
        "betta"
      ]
    },
    {
      "page": "betta_lincom",
      "title": "Confidence intervals and testing for linear combinations of fixed effects estimated via betta() or betta_random()",
      "topics": [
        "betta_lincom"
      ]
    },
    {
      "page": "betta_pic",
      "title": "function for plotting total diversity",
      "topics": [
        "betta_pic"
      ]
    },
    {
      "page": "betta_random",
      "title": "modelling total diversity with random effects",
      "topics": [
        "betta_random"
      ]
    },
    {
      "page": "breakaway",
      "title": "Species richness estimation with breakaway",
      "topics": [
        "breakaway"
      ]
    },
    {
      "page": "breakaway_nof1",
      "title": "species richness estimation without singletons",
      "topics": [
        "breakaway_nof1"
      ]
    },
    {
      "page": "build_frequency_count_tables",
      "title": "Build frequency count tables from an OTU table",
      "topics": [
        "build_frequency_count_tables"
      ]
    },
    {
      "page": "chao_bunge",
      "title": "Chao-Bunge species richness estimator",
      "topics": [
        "chao_bunge"
      ]
    },
    {
      "page": "chao_shen",
      "title": "The Chao-Shen estimate of Shannon diversity",
      "topics": [
        "chao_shen"
      ]
    },
    {
      "page": "chao1",
      "title": "Chao1 species richness estimator",
      "topics": [
        "chao1"
      ]
    },
    {
      "page": "chao1_bc",
      "title": "Bias-corrected Chao1 species richness estimator",
      "topics": [
        "chao1_bc"
      ]
    },
    {
      "page": "check_format",
      "title": "Run some basic checks on a possible frequency count table",
      "topics": [
        "check_format"
      ]
    },
    {
      "page": "convert",
      "title": "convert between different inputs for alpha-diversity estimates",
      "topics": [
        "convert"
      ]
    },
    {
      "page": "cutoff_wrap",
      "title": "Find a cut-off for estimates relying on contiguous counts",
      "topics": [
        "cutoff_wrap"
      ]
    },
    {
      "page": "F_test",
      "title": "Conduct F test of null hypothesis LB = 0 using output from betta() or betta_random()",
      "topics": [
        "F_test"
      ]
    },
    {
      "page": "get_F_stat",
      "title": "Calculate F statistic under null hypothesis LB = 0 using output from betta() or betta_random()",
      "topics": [
        "get_F_stat"
      ]
    },
    {
      "page": "good_turing",
      "title": "The Good-Turing estimate of species richness",
      "topics": [
        "good_turing"
      ]
    },
    {
      "page": "hawaii",
      "title": "(Data) Frequency count table of soil microbes in Hawaii.",
      "topics": [
        "hawaii"
      ]
    },
    {
      "page": "kemp",
      "title": "Species richness estimation with Kemp-type models",
      "topics": [
        "kemp"
      ]
    },
    {
      "page": "make_design_matrix",
      "title": "Make design matrix",
      "topics": [
        "make_design_matrix"
      ]
    },
    {
      "page": "make_frequency_count_table",
      "title": "Draw frequency count subtables from an OTU table",
      "topics": [
        "make_frequency_count_table"
      ]
    },
    {
      "page": "objective_bayes_geometric",
      "title": "Estimate species richness with an objective Bayes method using a geometric model",
      "topics": [
        "objective_bayes_geometric"
      ]
    },
    {
      "page": "objective_bayes_mixedgeo",
      "title": "Objective Bayes species richness estimate with the mixed-geometric model",
      "topics": [
        "objective_bayes_mixedgeo"
      ]
    },
    {
      "page": "objective_bayes_negbin",
      "title": "Objective Bayes species richness estimate with the Negative Binomial model",
      "topics": [
        "objective_bayes_negbin"
      ]
    },
    {
      "page": "objective_bayes_poisson",
      "title": "Objective Bayes species richness estimate with the Poisson model",
      "topics": [
        "objective_bayes_poisson"
      ]
    },
    {
      "page": "pasolli_et_al",
      "title": "(Data) Data frame of covariate information about pasolli_et_al.",
      "topics": [
        "pasolli_et_al"
      ]
    },
    {
      "page": "physeq_wrap",
      "title": "Wrapper for phyloseq objects",
      "topics": [
        "physeq_wrap"
      ]
    },
    {
      "page": "plot.alpha_estimates",
      "title": "Plot function for alpha_estimates class",
      "topics": [
        "plot.alpha_estimates"
      ]
    },
    {
      "page": "poisson_model",
      "title": "PoissonModel",
      "topics": [
        "poisson_model"
      ]
    },
    {
      "page": "poisson_model_nof1",
      "title": "PoissonModelNof1",
      "topics": [
        "poisson_model_nof1"
      ]
    },
    {
      "page": "proportions_instead",
      "title": "OTU table to relative abundances",
      "topics": [
        "proportions_instead"
      ]
    },
    {
      "page": "rnbinomtable",
      "title": "Negative binomially distributed frequency count tables.",
      "topics": [
        "rnbinomtable"
      ]
    },
    {
      "page": "rztnbinomtable",
      "title": "beta version: Zero-truncated negative binomially distributed frequency count tables.",
      "topics": [
        "rztnbinomtable"
      ]
    },
    {
      "page": "sample_inverse_simpson",
      "title": "Plug-in Inverse Simpson diversity",
      "topics": [
        "sample_inverse_simpson"
      ]
    },
    {
      "page": "sample_richness",
      "title": "Sample richness estimator",
      "topics": [
        "sample_richness"
      ]
    },
    {
      "page": "sample_shannon",
      "title": "Plug-in Shannon diversity",
      "topics": [
        "sample_shannon"
      ]
    },
    {
      "page": "sample_shannon_e",
      "title": "Plug-in Shannon's E (\"Equitability\")",
      "topics": [
        "sample_shannon_e"
      ]
    },
    {
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