{
  "_id": "6ac854b3de46216d5edd44d6",
  "Package": "rbiom",
  "Type": "Package",
  "Title": "Integrated Analysis and Visualization of Microbiome Data",
  "Version": "3.1.1",
  "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": "2026-10-08 23:45:23 UTC",
  "RemoteUrl": "https://github.com/cmmr/rbiom",
  "RemoteRef": "HEAD",
  "RemoteSha": "dd6402cc6ce7716db9bc6e7d8a4bc9e8195e19f0",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-09 02:37:31 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>",
  "_user": "cmmr",
  "_type": "src",
  "_file": "rbiom_3.1.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/37ea4fabf748120af8124712608fb38b20d30db78356b6e7468010efef8ed8b6",
  "_filesize": 1475866,
  "_sha256": "37ea4fabf748120af8124712608fb38b20d30db78356b6e7468010efef8ed8b6",
  "_expires": "2027-01-17T02:42:56.000Z",
  "_created": "2026-10-09T02:37:31.000Z",
  "_published": "2026-10-09T02:42:58.889Z",
  "_buildurl": "https://github.com/r-universe/cmmr/actions/runs/37875186618",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 113643058626,
      "time": 245,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11592064202"
    },
    {
      "job": 113643058606,
      "time": 201,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11592430965"
    },
    {
      "job": 113643058677,
      "time": 227,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11592540890"
    },
    {
      "job": 113643058649,
      "time": 182,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11592406011"
    },
    {
      "job": 113642134091,
      "time": 218,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11592540155"
    },
    {
      "job": 113643058647,
      "time": 126,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11591884401"
    },
    {
      "job": 113643058667,
      "time": 159,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11591932894"
    },
    {
      "job": 113643058736,
      "time": 224,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11592346356"
    },
    {
      "job": 113643058643,
      "time": 233,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11592790017"
    }
  ],
  "_upstream": "https://github.com/cmmr/rbiom",
  "_commit": {
    "id": "dd6402cc6ce7716db9bc6e7d8a4bc9e8195e19f0",
    "author": "Daniel Smith <dansmith@orst.edu>",
    "committer": "Daniel Smith <dansmith@orst.edu>",
    "message": "fix for \"No taxa match the criteria\"\n",
    "time": 1791503123
  },
  "_maintainer": {
    "name": "Daniel P. Smith",
    "email": "dansmith01@gmail.com",
    "login": "dansmith01",
    "orcid": "0000-0002-2479-2044",
    "description": "Bioinformatics programmer at Baylor College of Medicine, specializing in visualization of microbiome datasets.",
    "uuid": 2066273
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.3.0",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "mgcv",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "ape",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "ecodive",
      "role": "Imports"
    },
    {
      "package": "emmeans",
      "role": "Imports"
    },
    {
      "package": "fillpattern",
      "role": "Imports"
    },
    {
      "package": "ggbeeswarm",
      "role": "Imports"
    },
    {
      "package": "ggnewscale",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ggrepel",
      "role": "Imports"
    },
    {
      "package": "ggtext",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "patchwork",
      "role": "Imports"
    },
    {
      "package": "pillar",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "readr",
      "role": "Imports"
    },
    {
      "package": "readxl",
      "role": "Imports"
    },
    {
      "package": "vegan",
      "role": "Imports"
    },
    {
      "package": "cli",
      "role": "Suggests"
    },
    {
      "package": "crayon",
      "role": "Suggests"
    },
    {
      "package": "ggdensity",
      "role": "Suggests"
    },
    {
      "package": "glue",
      "role": "Suggests"
    },
    {
      "package": "h5lite",
      "role": "Suggests"
    },
    {
      "package": "labeling",
      "role": "Suggests"
    },
    {
      "package": "lifecycle",
      "role": "Suggests"
    },
    {
      "package": "Matrix",
      "role": "Suggests"
    },
    {
      "package": "openxlsx",
      "role": "Suggests"
    },
    {
      "package": "optparse",
      "role": "Suggests"
    },
    {
      "package": "pkgconfig",
      "role": "Suggests"
    },
    {
      "package": "prettycode",
      "role": "Suggests"
    },
    {
      "package": "R6",
      "role": "Suggests"
    },
    {
      "package": "rlang",
      "role": "Suggests"
    },
    {
      "package": "scales",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "tibble",
      "role": "Suggests"
    },
    {
      "package": "tsne",
      "role": "Suggests"
    },
    {
      "package": "uwot",
      "role": "Suggests"
    }
  ],
  "_owner": "cmmr",
  "_selfowned": true,
  "_usedby": 3,
  "_updates": [
    {
      "week": "2026-03",
      "n": 2
    },
    {
      "week": "2026-04",
      "n": 9
    },
    {
      "week": "2026-08",
      "n": 2
    },
    {
      "week": "2026-16",
      "n": 1
    },
    {
      "week": "2026-17",
      "n": 2
    },
    {
      "week": "2026-19",
      "n": 2
    },
    {
      "week": "2026-38",
      "n": 3
    },
    {
      "week": "2026-40",
      "n": 2
    },
    {
      "week": "2026-41",
      "n": 1
    }
  ],
  "_tags": [],
  "_stars": 19,
  "_contributors": [
    {
      "user": "dansmith01",
      "count": 425,
      "uuid": 2066273
    },
    {
      "user": "tkmarkcheng",
      "count": 2,
      "uuid": 89597443
    }
  ],
  "_userbio": {
    "uuid": 7662263,
    "type": "organization",
    "name": "Alkek Center for Metagenomics and Microbiome Research",
    "followers": 23,
    "description": "CMMR researchers develop molecular and informatic tools to advance clinical microbiome research."
  },
  "_downloads": {
    "count": 1757,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/rbiom"
  },
  "_mentions": 2,
  "_devurl": "https://github.com/cmmr/rbiom",
  "_pkgdown": "https://cmmr.github.io/rbiom/",
  "_searchresults": 215,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/rbiom.html",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/cmmr/rbiom",
  "_realowner": "cmmr",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2020-05-26"
    },
    {
      "version": "1.0.2",
      "date": "2020-05-29"
    },
    {
      "version": "1.0.3",
      "date": "2021-11-05"
    },
    {
      "version": "2.0.7",
      "date": "2025-01-11"
    },
    {
      "version": "2.0.10",
      "date": "2025-01-19"
    },
    {
      "version": "2.0.13",
      "date": "2025-01-24"
    },
    {
      "version": "2.1.1",
      "date": "2025-03-10"
    },
    {
      "version": "2.1.2",
      "date": "2025-03-22"
    },
    {
      "version": "2.2.0",
      "date": "2025-04-04"
    },
    {
      "version": "2.2.1",
      "date": "2025-06-27"
    },
    {
      "version": "3.1.0",
      "date": "2026-05-08"
    }
  ],
  "_exports": [
    ".",
    "%<>%",
    "%>%",
    "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",
      "title": "Rarefy Counts to a Constant Depth",
      "concept": [
        "transformations"
      ],
      "topics": [
        "rarefy"
      ]
    },
    {
      "page": "read_biom",
      "title": "Parse counts, metadata, taxonomy, and phylogeny from a BIOM file.",
      "topics": [
        "read_biom"
      ]
    },
    {
      "page": "read_fasta",
      "title": "Parse a fasta file into a named character vector.",
      "topics": [
        "read_fasta"
      ]
    },
    {
      "page": "read_tree",
      "title": "Read a newick formatted phylogenetic tree.",
      "concept": [
        "phylogeny"
      ],
      "topics": [
        "read_tree"
      ]
    },
    {
      "page": "sample_sums",
      "title": "Summarize the taxa observations in each sample.",
      "concept": [
        "rarefaction",
        "samples",
        "taxa_abundance"
      ],
      "topics": [
        "sample_apply",
        "sample_sums"
      ]
    },
    {
      "page": "slice_metadata",
      "title": "Subset to a specific number of samples.",
      "concept": [
        "transformations"
      ],
      "topics": [
        "slice.rbiom",
        "slice_head.rbiom",
        "slice_max.rbiom",
        "slice_metadata",
        "slice_min.rbiom",
        "slice_sample.rbiom",
        "slice_tail.rbiom"
      ]
    },
    {
      "page": "stats_boxplot",
      "title": "Visualize categorical metadata effects on numeric values.",
      "concept": [
        "visualization"
      ],
      "topics": [
        "stats_boxplot"
      ]
    },
    {
      "page": "stats_corrplot",
      "title": "Visualize regression with scatterplots and trendlines.",
      "concept": [
        "visualization"
      ],
      "topics": [
        "stats_corrplot"
      ]
    },
    {
      "page": "stats_table",
      "title": "Run non-parametric statistics on a data.frame.",
      "concept": [
        "stats_tables"
      ],
      "topics": [
        "stats_table"
      ]
    },
    {
      "page": "subset",
      "title": "Subset an rbiom object by sample names, OTU names, metadata, or taxonomy.",
      "concept": [
        "transformations"
      ],
      "topics": [
        "na.omit.rbiom",
        "subset",
        "subset.rbiom",
        "subset_taxa",
        "[.rbiom"
      ]
    },
    {
      "page": "suggest_inflate_depths",
      "title": "Suggest Inflation Depths",
      "topics": [
        "suggest_inflate_depths"
      ]
    },
    {
      "page": "suggest_rarefy_depth",
      "title": "Suggest Rarefaction Depth",
      "topics": [
        "suggest_rarefy_depth"
      ]
    },
    {
      "page": "taxa_boxplot",
      "title": "Visualize BIOM data with boxplots.",
      "concept": [
        "taxa_abundance",
        "visualization"
      ],
      "topics": [
        "taxa_boxplot"
      ]
    },
    {
      "page": "taxa_clusters",
      "title": "Cluster samples by taxa abundances k-means.",
      "concept": [
        "clustering",
        "taxa_abundance"
      ],
      "topics": [
        "taxa_clusters"
      ]
    },
    {
      "page": "taxa_corrplot",
      "title": "Visualize taxa abundance with scatterplots and trendlines.",
      "concept": [
        "taxa_abundance",
        "visualization"
      ],
      "topics": [
        "taxa_corrplot"
      ]
    },
    {
      "page": "taxa_heatmap",
      "title": "Display taxa abundances as a heatmap.",
      "concept": [
        "taxa_abundance",
        "visualization"
      ],
      "topics": [
        "taxa_heatmap"
      ]
    },
    {
      "page": "taxa_map",
      "title": "Map OTUs names to taxa names at a given rank.",
      "concept": [
        "taxonomy"
      ],
      "topics": [
        "taxa_map"
      ]
    },
    {
      "page": "taxa_stacked",
      "title": "Display taxa abundances as a stacked bar graph.",
      "concept": [
        "taxa_abundance",
        "visualization"
      ],
      "topics": [
        "taxa_stacked"
      ]
    },
    {
      "page": "taxa_stats",
      "title": "Test taxa abundances for associations with metadata.",
      "concept": [
        "stats_tables",
        "taxa_abundance"
      ],
      "topics": [
        "taxa_stats"
      ]
    },
    {
      "page": "taxa_sums",
      "title": "Get summary taxa abundances.",
      "concept": [
        "taxa_abundance"
      ],
      "topics": [
        "taxa_apply",
        "taxa_means",
        "taxa_sums"
      ]
    },
    {
      "page": "taxa_matrix",
      "title": "Taxa abundances per sample.",
      "concept": [
        "taxa_abundance"
      ],
      "topics": [
        "taxa_matrix",
        "taxa_table"
      ]
    },
    {
      "page": "tree_subset",
      "title": "Create a subtree by specifying tips to keep.",
      "concept": [
        "phylogeny"
      ],
      "topics": [
        "tree_subset"
      ]
    },
    {
      "page": "with",
      "title": "Evaluate expressions on metadata.",
      "concept": [
        "transformations"
      ],
      "topics": [
        "with",
        "with.rbiom",
        "within.rbiom"
      ]
    },
    {
      "page": "write_biom",
      "title": "Save an rbiom object to a file.",
      "topics": [
        "write_biom",
        "write_counts",
        "write_fasta",
        "write_metadata",
        "write_taxonomy",
        "write_tree",
        "write_xlsx"
      ]
    }
  ],
  "_readme": "https://github.com/cmmr/rbiom/raw/HEAD/README.md",
  "_rundeps": [
    "ape",
    "beeswarm",
    "bit",
    "bit64",
    "cellranger",
    "cli",
    "clipr",
    "cluster",
    "commonmark",
    "cpp11",
    "crayon",
    "curl",
    "digest",
    "dplyr",
    "ecodive",
    "emmeans",
    "estimability",
    "farver",
    "fillpattern",
    "generics",
    "ggbeeswarm",
    "ggnewscale",
    "ggplot2",
    "ggrepel",
    "ggtext",
    "glue",
    "gridtext",
    "gtable",
    "hms",
    "isoband",
    "jpeg",
    "jsonlite",
    "labeling",
    "lattice",
    "lifecycle",
    "litedown",
    "magrittr",
    "markdown",
    "MASS",
    "Matrix",
    "mgcv",
    "mvtnorm",
    "nlme",
    "numDeriv",
    "patchwork",
    "permute",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "prettyunits",
    "progress",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "readr",
    "readxl",
    "rematch",
    "rlang",
    "S7",
    "scales",
    "stringi",
    "stringr",
    "tibble",
    "tidyselect",
    "tzdb",
    "utf8",
    "vctrs",
    "vegan",
    "vipor",
    "viridisLite",
    "vroom",
    "withr",
    "xfun",
    "xml2"
  ],
  "_score": 7.7644488412423796,
  "_indexed": true,
  "_nocasepkg": "rbiom",
  "_universes": [
    "cmmr",
    "dansmith01"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "3.1.1",
      "date": "2026-10-09T02:40:19.000Z",
      "distro": "resolute",
      "commit": "dd6402cc6ce7716db9bc6e7d8a4bc9e8195e19f0",
      "fileid": "https://r2.ropensci.org/9dad453e477df5a9e72ae90c180a0d754dbecac1b0bffd326c4cbb63fa21e1cf",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cmmr/actions/runs/37875186618"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "3.1.1",
      "date": "2026-10-09T02:40:03.000Z",
      "distro": "resolute",
      "commit": "dd6402cc6ce7716db9bc6e7d8a4bc9e8195e19f0",
      "fileid": "https://r2.ropensci.org/721b536299224f39c816e03b7742f48b329e629b1dc52f543f6c02687590a6b6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cmmr/actions/runs/37875186618"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "3.1.1",
      "date": "2026-10-09T02:40:22.000Z",
      "commit": "dd6402cc6ce7716db9bc6e7d8a4bc9e8195e19f0",
      "fileid": "https://r2.ropensci.org/434b42358e7e3ec0dfe16cb298e5b361e027c3109b66caa808da213edb9c1aa7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cmmr/actions/runs/37875186618"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "3.1.1",
      "date": "2026-10-09T02:39:30.000Z",
      "commit": "dd6402cc6ce7716db9bc6e7d8a4bc9e8195e19f0",
      "fileid": "https://r2.ropensci.org/fe6f1082c23075bc330765ff213f8cc2160e106a3cc92dec60b342aa8cd599ae",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cmmr/actions/runs/37875186618"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "3.1.1",
      "date": "2026-10-09T02:40:12.000Z",
      "commit": "dd6402cc6ce7716db9bc6e7d8a4bc9e8195e19f0",
      "fileid": "https://r2.ropensci.org/f387434591778156f83afae39f4c07d908879a21067507db6747515de26a5cdd",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cmmr/actions/runs/37875186618"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "3.1.1",
      "date": "2026-10-09T02:39:04.000Z",
      "commit": "dd6402cc6ce7716db9bc6e7d8a4bc9e8195e19f0",
      "fileid": "https://r2.ropensci.org/67ed3fd16773eeb004515da10a963d44b8448fcebd4e72dd945758a2a588b5dc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cmmr/actions/runs/37875186618"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "3.1.1",
      "date": "2026-10-09T02:39:22.000Z",
      "commit": "dd6402cc6ce7716db9bc6e7d8a4bc9e8195e19f0",
      "fileid": "https://r2.ropensci.org/f295d47cd54621308f3c5d58da798330cd0f61429b48371421f06a93de87d969",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cmmr/actions/runs/37875186618"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "3.1.1",
      "date": "2026-10-09T02:39:24.000Z",
      "commit": "dd6402cc6ce7716db9bc6e7d8a4bc9e8195e19f0",
      "fileid": "https://r2.ropensci.org/70711e36525a60050f741fcdd1449decdc156518afeb03de7fcecdd7768f4afb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cmmr/actions/runs/37875186618"
    }
  ]
}