{
  "_id": "6a20bedecd65a98ecbd1a2d6",
  "Package": "rbiom",
  "Type": "Package",
  "Title": "Integrated Analysis and Visualization of Microbiome Data",
  "Version": "3.1.0",
  "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\"Alkek Center for Metagenomics and Microbiome Research\",\nrole = c(\"cph\", \"fnd\") ))",
  "Description": "A toolkit for working with Biological Observation Matrix\n('BIOM') files. Read/write all 'BIOM' formats. Compute\nrarefaction, alpha diversity, and beta diversity (including\n'UniFrac'). Summarize counts by taxonomic level. Subset based\non metadata. Generate visualizations and statistical analyses.",
  "URL": "https://cmmr.github.io/rbiom/, https://github.com/cmmr/rbiom",
  "BugReports": "https://github.com/cmmr/rbiom/issues",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "Config/Needs/website": "rmarkdown, phyloseq, npregfast, withr",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "libicu-dev libjpeg-dev libpng-dev libxml2-dev\nlibssl-dev libx11-dev",
  "Repository": "https://cmmr.r-universe.dev",
  "Date/Publication": "2026-05-07 16:41:36 UTC",
  "RemoteUrl": "https://github.com/cmmr/rbiom",
  "RemoteRef": "HEAD",
  "RemoteSha": "8a9bb35967c85af290cf79cc68eda8a070bb082c",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-03 23:49:09 UTC",
    "User": "root"
  },
  "Author": "Daniel P. Smith [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-2479-2044>),\nAlkek Center for Metagenomics and Microbiome Research [cph, fnd]",
  "Maintainer": "Daniel P. Smith <dansmith01@gmail.com>",
  "MD5sum": "25ff7551b5c9d0e3da9488c585997efa",
  "_user": "cmmr",
  "_type": "src",
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  "_created": "2026-06-03T23:49:09.000Z",
  "_published": "2026-06-03T23:55:10.149Z",
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    "name": "Alkek Center for Metagenomics and Microbiome Research",
    "description": "CMMR researchers develop molecular and informatic tools to advance clinical microbiome research."
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  "_rbuild": "4.6.0",
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    "extra/citation.json",
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    "extra/contents.json",
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    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
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  "_homeurl": "https://github.com/cmmr/rbiom",
  "_realowner": "cmmr",
  "_cranurl": true,
  "_releases": [
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      "date": "2020-05-26"
    },
    {
      "version": "1.0.2",
      "date": "2020-05-29"
    },
    {
      "version": "1.0.3",
      "date": "2021-11-05"
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    ".",
    "%<>%",
    "%>%",
    "adiv_boxplot",
    "adiv_corrplot",
    "adiv_matrix",
    "adiv_stats",
    "adiv_table",
    "adiv_vector",
    "as_rbiom",
    "babies",
    "bdiv_boxplot",
    "bdiv_clusters",
    "bdiv_corrplot",
    "bdiv_distmat",
    "bdiv_heatmap",
    "bdiv_matrix",
    "bdiv_ord_plot",
    "bdiv_ord_table",
    "bdiv_stats",
    "bdiv_table",
    "bdply",
    "biom_inflate",
    "biom_merge",
    "biom_relativize",
    "biom_rescale",
    "blply",
    "convert_to_animalcules",
    "convert_to_biomformat",
    "convert_to_phyloseq",
    "convert_to_SE",
    "convert_to_TSE",
    "ddply",
    "distmat_ord_table",
    "distmat_stats",
    "gems",
    "ggsave",
    "glimpse",
    "hmp50",
    "ldply",
    "left_join",
    "list_metrics",
    "llply",
    "match_metric",
    "mtx_percent",
    "mtx_rarefy",
    "mtx_rescale",
    "mutate",
    "n_cpus",
    "na.omit",
    "plot_heatmap",
    "pull",
    "rare_corrplot",
    "rare_multiplot",
    "rare_stacked",
    "rarefy",
    "rarefy_cols",
    "read_biom",
    "read_fasta",
    "read_tree",
    "relocate",
    "rename",
    "rescale_cols",
    "rescale_rows",
    "sample_apply",
    "sample_sums",
    "select",
    "slice",
    "slice_head",
    "slice_max",
    "slice_min",
    "slice_sample",
    "slice_tail",
    "stats_boxplot",
    "stats_corrplot",
    "stats_table",
    "subset_taxa",
    "suggest_inflate_depths",
    "suggest_rarefy_depth",
    "taxa_apply",
    "taxa_boxplot",
    "taxa_clusters",
    "taxa_corrplot",
    "taxa_heatmap",
    "taxa_map",
    "taxa_matrix",
    "taxa_means",
    "taxa_stacked",
    "taxa_stats",
    "taxa_sums",
    "taxa_table",
    "tree_subset",
    "write_biom",
    "write_counts",
    "write_fasta",
    "write_metadata",
    "write_mothur",
    "write_qiime2",
    "write_taxonomy",
    "write_tree",
    "write_xlsx"
  ],
  "_help": [
    {
      "page": "adiv_boxplot",
      "title": "Visualize alpha diversity with boxplots.",
      "concept": [
        "alpha_diversity",
        "visualization"
      ],
      "topics": [
        "adiv_boxplot"
      ]
    },
    {
      "page": "adiv_corrplot",
      "title": "Visualize alpha diversity with scatterplots and trendlines.",
      "concept": [
        "alpha_diversity",
        "visualization"
      ],
      "topics": [
        "adiv_corrplot"
      ]
    },
    {
      "page": "adiv_stats",
      "title": "Test alpha diversity for associations with metadata.",
      "concept": [
        "alpha_diversity",
        "stats_tables"
      ],
      "topics": [
        "adiv_stats"
      ]
    },
    {
      "page": "adiv_table",
      "title": "Calculate the alpha diversity of each sample.",
      "concept": [
        "alpha_diversity"
      ],
      "topics": [
        "adiv_matrix",
        "adiv_table",
        "adiv_vector"
      ]
    },
    {
      "page": "as_rbiom",
      "title": "Convert a variety of data types to an rbiom object.",
      "topics": [
        "as_rbiom"
      ]
    },
    {
      "page": "as.list.rbiom",
      "title": "Convert an rbiom object to a base R list.",
      "concept": [
        "conversion"
      ],
      "topics": [
        "as.list.rbiom"
      ]
    },
    {
      "page": "as.matrix.rbiom",
      "title": "Convert an rbiom object to a simple count matrix.",
      "concept": [
        "conversion"
      ],
      "topics": [
        "as.matrix.rbiom"
      ]
    },
    {
      "page": "babies",
      "title": "Longitudinal Stool Samples from Infants (n = 2,684)",
      "concept": [
        "Built-In Datasets"
      ],
      "topics": [
        "babies"
      ]
    },
    {
      "page": "bdiv_boxplot",
      "title": "Visualize BIOM data with boxplots.",
      "concept": [
        "beta_diversity",
        "visualization"
      ],
      "topics": [
        "bdiv_boxplot"
      ]
    },
    {
      "page": "bdiv_clusters",
      "title": "Cluster samples by beta diversity k-means.",
      "concept": [
        "beta_diversity",
        "clustering"
      ],
      "topics": [
        "bdiv_clusters"
      ]
    },
    {
      "page": "bdiv_corrplot",
      "title": "Visualize beta diversity with scatterplots and trendlines.",
      "concept": [
        "beta_diversity",
        "visualization"
      ],
      "topics": [
        "bdiv_corrplot"
      ]
    },
    {
      "page": "bdiv_heatmap",
      "title": "Display beta diversities in an all vs all grid.",
      "concept": [
        "beta_diversity",
        "visualization"
      ],
      "topics": [
        "bdiv_heatmap"
      ]
    },
    {
      "page": "bdiv_ord_plot",
      "title": "Ordinate samples and taxa on a 2D plane based on beta diversity distances.",
      "concept": [
        "beta_diversity",
        "ordination",
        "visualization"
      ],
      "topics": [
        "bdiv_ord_plot"
      ]
    },
    {
      "page": "bdiv_ord_table",
      "title": "Calculate PCoA and other ordinations, including taxa biplots and statistics.",
      "concept": [
        "beta_diversity",
        "ordination"
      ],
      "topics": [
        "bdiv_ord_table"
      ]
    },
    {
      "page": "bdiv_stats",
      "title": "Test beta diversity for associations with metadata.",
      "concept": [
        "beta_diversity",
        "stats_tables"
      ],
      "topics": [
        "bdiv_stats"
      ]
    },
    {
      "page": "bdiv_table",
      "title": "Distance / dissimilarity between samples.",
      "concept": [
        "beta_diversity"
      ],
      "topics": [
        "bdiv_distmat",
        "bdiv_matrix",
        "bdiv_table"
      ]
    },
    {
      "page": "bdply",
      "title": "Apply a function to each subset of an rbiom object.",
      "concept": [
        "biom",
        "metadata"
      ],
      "topics": [
        "bdply",
        "blply"
      ]
    },
    {
      "page": "biom_inflate",
      "title": "Inflate Relative Abundances to Integer Counts",
      "concept": [
        "transformations"
      ],
      "topics": [
        "biom_inflate"
      ]
    },
    {
      "page": "biom_merge",
      "title": "Combine several rbiom objects into one.",
      "concept": [
        "biom"
      ],
      "topics": [
        "biom_merge"
      ]
    },
    {
      "page": "biom_relativize",
      "title": "Relativize Counts to Proportions",
      "concept": [
        "transformations"
      ],
      "topics": [
        "biom_relativize"
      ]
    },
    {
      "page": "biom_rescale",
      "title": "Rescale Counts to a Specific Range",
      "concept": [
        "transformations"
      ],
      "topics": [
        "biom_rescale"
      ]
    },
    {
      "page": "convert_to",
      "title": "Convert biom data to an external package class",
      "topics": [
        "convert_to",
        "convert_to_animalcules",
        "convert_to_biomformat",
        "convert_to_phyloseq",
        "convert_to_SE",
        "convert_to_TSE"
      ]
    },
    {
      "page": "distmat_ord_table",
      "title": "Run ordinations on a distance matrix.",
      "concept": [
        "ordination"
      ],
      "topics": [
        "distmat_ord_table"
      ]
    },
    {
      "page": "distmat_stats",
      "title": "Run statistics on a distance matrix vs a categorical or numeric variable.",
      "concept": [
        "beta_diversity",
        "stats_tables"
      ],
      "topics": [
        "distmat_stats"
      ]
    },
    {
      "page": "export",
      "title": "Export data to QIIME 2 or mothur.",
      "topics": [
        "export",
        "write_mothur",
        "write_qiime2"
      ]
    },
    {
      "page": "gems",
      "title": "Global Enteric Multicenter Study (n = 1,006)",
      "concept": [
        "Built-In Datasets"
      ],
      "topics": [
        "gems"
      ]
    },
    {
      "page": "glimpse.rbiom",
      "title": "Get a glimpse of your metadata.",
      "concept": [
        "metadata"
      ],
      "topics": [
        "glimpse.rbiom"
      ]
    },
    {
      "page": "hmp50",
      "title": "Human Microbiome Project - demo dataset (n = 50)",
      "concept": [
        "Built-In Datasets"
      ],
      "topics": [
        "hmp50"
      ]
    },
    {
      "page": "matrix_ops",
      "title": "Deprecated matrix transformations",
      "topics": [
        "matrix_ops",
        "mtx_percent",
        "mtx_rarefy",
        "mtx_rescale",
        "rarefy_cols",
        "rescale_cols",
        "rescale_rows"
      ]
    },
    {
      "page": "modify_metadata",
      "title": "Create, modify, and delete metadata fields.",
      "concept": [
        "transformations"
      ],
      "topics": [
        "modify_metadata",
        "mutate.rbiom",
        "rename.rbiom"
      ]
    },
    {
      "page": "plot_heatmap",
      "title": "Create a heatmap with tracks and dendrograms from any matrix.",
      "concept": [
        "visualization"
      ],
      "topics": [
        "plot_heatmap"
      ]
    },
    {
      "page": "pull.rbiom",
      "title": "Map sample names to metadata field values.",
      "concept": [
        "samples"
      ],
      "topics": [
        "pull.rbiom"
      ]
    },
    {
      "page": "rare_corrplot",
      "title": "Visualize rarefaction curves with scatterplots and trendlines.",
      "concept": [
        "rarefaction",
        "visualization"
      ],
      "topics": [
        "rare_corrplot"
      ]
    },
    {
      "page": "rare_multiplot",
      "title": "Combines rare_corrplot and rare_stacked into a single figure.",
      "concept": [
        "rarefaction",
        "visualization"
      ],
      "topics": [
        "rare_multiplot"
      ]
    },
    {
      "page": "rare_stacked",
      "title": "Visualize the number of observations per sample.",
      "concept": [
        "rarefaction",
        "visualization"
      ],
      "topics": [
        "rare_stacked"
      ]
    },
    {
      "page": "rarefy",
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