{
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  "Package": "MicrobiomeR",
  "Title": "Analyze Microbiome Data",
  "Version": "0.8.0",
  "Authors@R": "c(\nperson(\"Robert\", \"Gilmore\", email = \"rgilmore@umc.edu\", role = c(\"aut\", \"cre\")),\nperson(\"Shaurita\", \"Hutchins\", email = \"shaurita.hutchins@gmail.com\", role = \"aut\"))",
  "Maintainer": "Shaurita Hutchins <shaurita.hutchins@gmail.com>",
  "License": "MIT + file LICENSE",
  "biocViews": "Metagenomics, Microbiome, Sequencing, SystemsBiology",
  "Description": "An R package for microbiome analysis combining functions\nfrom phyloseq, metacodeR, and microbiome into an easy to use\nand full featured microbiome analysis package.",
  "Roxygen": "list(markdown = TRUE)",
  "Remotes": [
    "ropensci/taxa",
    "grunwaldlab/metacoder",
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  "URL": "https://github.com/vallenderlab/MicrobiomeR,\nhttps://vallenderlab.github.io/MicrobiomeR/",
  "BugReports": "https://github.com/vallenderlab/MicrobiomeR/issues",
  "VignetteBuilder": "knitr",
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  "Repository": "https://sdhutchins.r-universe.dev",
  "Date/Publication": "2026-09-05 21:37:14 UTC",
  "RemoteUrl": "https://github.com/vallenderlab/MicrobiomeR",
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  "Packaged": {
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  "Author": "Robert Gilmore [aut, cre],\nShaurita Hutchins [aut]",
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  "_created": "2026-10-05T13:02:27.000Z",
  "_published": "2026-10-06T08:00:34.621Z",
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    "author": "Shaurita D. Hutchins <ms.s.hutchins@gmail.com>",
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    "message": "Restore package compatibility and correct heat-tree plots (#114)\n\n* Fix package docs and analysis workflows\n\n* Move CI and coverage uploads to GitHub Actions\n\n* Rebuild pkgdown site for 0.6.2 release\n\n* Update GitHub Actions workflow to include 'dev-master' branch for R-CMD-check.\n\n* Update DESCRIPTION to require R version 4.1.0 and add SparseArray to Imports.\n\n* Add seed parameter to heat_tree_plots and permanova functions for reproducibility.\n\n* Add function to retrieve OTU counts for heat tree nodes and update heat_tree_plots to use these counts.\n\n* Fix heat tree rank handling.\n\n* Remove outdated lab location.\n\n* Increase documentation font sizes.\n\n* Bump package version to 0.6.3.\n\n* Rebuild package documentation site.\n\n* Fix stacked barplot axes.\n\n* Make RData test self-contained.\n\n* Reduce routine test fixtures.\n\n* Reduce executable vignette datasets.\n\n* Complete package citation support.\n\n* Bump package version to 0.8.0.\n\n* Rebuild package documentation site.\n\n* Harden R CMD check workflow.\n\n* Fix.\n\n* Fix R CMD check warnings.\n\n* Update .gitignore to exclude check and check-local directories.",
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      "name": "v0.8.0",
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    "microbiome",
    "sequencing",
    "systemsbiology",
    "alpha-diversity",
    "beta-diversity",
    "bioinformatics",
    "color-palette",
    "comprehensive",
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  "_exports": [
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    "agglomerate_taxmap",
    "alpha_diversity_measures",
    "alpha_diversity_plot",
    "as_analyzed_format",
    "as_basic_format",
    "as_custom_format",
    "as_MicrobiomeR_format",
    "as_phyloseq_format",
    "as_raw_format",
    "combination_palette",
    "correlation_data",
    "correlation_plot",
    "correlation_plots",
    "cov_filter",
    "create_phyloseq",
    "create_pub_table",
    "create_taxmap",
    "get_color_palette",
    "heat_tree_parameters",
    "heat_tree_plots",
    "is_analyzed_format",
    "is_basic_format",
    "is_phyloseq_format",
    "is_raw_format",
    "metacoder_comp_func_1",
    "order_metacoder_data",
    "ordination_plot",
    "ordination_plots",
    "otu_id_filter",
    "otu_prevalence_filter",
    "otu_proportion_filter",
    "output_dir",
    "parse_taxonomy_silva_128",
    "permanova",
    "pick_new_outgroup",
    "root_by_longest_edge",
    "root_phyloseq_tree",
    "sample_id_filter",
    "save_alpha_diversity_plots",
    "save_correlation_plots",
    "save_heat_tree_plots",
    "save_ordination_plots",
    "save_stacked_barplots",
    "save_top_coefficients_barplot",
    "scico_palette",
    "stacked_barplot",
    "stacked_barplots",
    "taxa_prevalence_filter",
    "taxon_id_filter",
    "top_coefficients_barplot",
    "transformer",
    "transposer",
    "treatment_matrix",
    "validate_MicrobiomeR_format",
    "viridis_magma_palette",
    "viridis_palette",
    "vlookup",
    "which_format"
  ],
  "_datasets": [
    {
      "name": "phyloseq_silva_2",
      "title": "Phyloseq Data with 2 Treatment Groups",
      "object": "phyloseq_silva_2",
      "class": [
        "phyloseq"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "phyloseq_silva_3",
      "title": "Phyloseq Data with 3 Treatment Groups",
      "object": "phyloseq_silva_3",
      "class": [
        "phyloseq"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "raw_silva_2",
      "title": "\"raw_format\" Data with 2 Treatment Groups",
      "object": "raw_silva_2",
      "class": [
        "Taxmap",
        "Taxonomy",
        "R6"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "raw_silva_3",
      "title": "\"raw_format\" Data with 3 Treatment Groups",
      "object": "raw_silva_3",
      "class": [
        "Taxmap",
        "Taxonomy",
        "R6"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "agglomerate_taxmap",
      "title": "Agglomerate taxmap Objects",
      "concept": [
        "Advanced Metacoder Filters"
      ],
      "topics": [
        "agglomerate_taxmap"
      ]
    },
    {
      "page": "alpha_diversity_measures",
      "title": "Alpha Diversity Measures",
      "topics": [
        "alpha_diversity_measures"
      ]
    },
    {
      "page": "alpha_diversity_plot",
      "title": "Alpha Diversity Plot",
      "concept": [
        "Visualizations"
      ],
      "topics": [
        "alpha_diversity_plot",
        "alpha_diversity_plots"
      ]
    },
    {
      "page": "as_analyzed_format",
      "title": "As Analyzed MicrobiomeR Format",
      "concept": [
        "Formatting"
      ],
      "topics": [
        "as_analyzed_format"
      ]
    },
    {
      "page": "as_basic_format",
      "title": "As Basic MicrobiomeR Format",
      "concept": [
        "Formatting"
      ],
      "topics": [
        "as_basic_format"
      ]
    },
    {
      "page": "as_custom_format",
      "title": "As Custom MicrobiomeR Format",
      "concept": [
        "Formatting"
      ],
      "topics": [
        "as_custom_format"
      ]
    },
    {
      "page": "as_MicrobiomeR_format",
      "title": "As MicrobiomeR Format",
      "concept": [
        "Formatting"
      ],
      "topics": [
        "as_MicrobiomeR_format"
      ]
    },
    {
      "page": "as_phyloseq_format",
      "title": "As Phyloseq MicrobiomeR Format",
      "concept": [
        "Formatting"
      ],
      "topics": [
        "as_phyloseq_format"
      ]
    },
    {
      "page": "as_raw_format",
      "title": "As Raw MicrobiomeR Format",
      "concept": [
        "Formatting"
      ],
      "topics": [
        "as_raw_format"
      ]
    },
    {
      "page": "combination_palette",
      "title": "Combine Color Palettes",
      "concept": [
        "Color Palettes"
      ],
      "topics": [
        "combination_palette"
      ]
    },
    {
      "page": "convert_proportions",
      "title": "Convert Proportions",
      "concept": [
        "Data Manipulators"
      ],
      "topics": [
        "convert_proportions"
      ]
    },
    {
      "page": "correlation_data",
      "title": "Get Correlation Plot Data",
      "concept": [
        "Visualizations"
      ],
      "topics": [
        "correlation_data"
      ]
    },
    {
      "page": "correlation_plot",
      "title": "Correlation Plot",
      "concept": [
        "Visualizations"
      ],
      "topics": [
        "correlation_plot"
      ]
    },
    {
      "page": "correlation_plots",
      "title": "Get Multiple Correlation Plots",
      "concept": [
        "Visualizations"
      ],
      "topics": [
        "correlation_plots"
      ]
    },
    {
      "page": "cov_filter",
      "title": "Coefficient of Variation Filter",
      "concept": [
        "Advanced Metacoder Filters"
      ],
      "topics": [
        "cov_filter"
      ]
    },
    {
      "page": "create_phyloseq",
      "title": "Get Phyloseq Object",
      "concept": [
        "Data Importers"
      ],
      "topics": [
        "create_phyloseq"
      ]
    },
    {
      "page": "create_pub_table",
      "title": "Create Publication Table",
      "topics": [
        "create_pub_table"
      ]
    },
    {
      "page": "create_taxmap",
      "title": "Get Taxmap Object",
      "concept": [
        "Data Importers"
      ],
      "topics": [
        "create_taxmap"
      ]
    },
    {
      "page": "get_color_palette",
      "title": "Get a Color Palette",
      "concept": [
        "Color Palettes"
      ],
      "topics": [
        "get_color_palette"
      ]
    },
    {
      "page": "heat_tree_parameters",
      "title": "Get Heat Tree Parameters",
      "concept": [
        "Visualizations"
      ],
      "topics": [
        "heat_tree_parameters"
      ]
    },
    {
      "page": "heat_tree_plots",
      "title": "Get Heat Tree Plots",
      "concept": [
        "Visualizations"
      ],
      "topics": [
        "heat_tree_plots"
      ]
    },
    {
      "page": "is_analyzed_format",
      "title": "Is Analyzed MicrobiomeR Format",
      "concept": [
        "Validation"
      ],
      "topics": [
        "is_analyzed_format"
      ]
    },
    {
      "page": "is_basic_format",
      "title": "Is Basic MicrobiomeR Format",
      "concept": [
        "Validation"
      ],
      "topics": [
        "is_basic_format"
      ]
    },
    {
      "page": "is_phyloseq_format",
      "title": "Is Phyloseq MicrobiomeR Format",
      "concept": [
        "Validation"
      ],
      "topics": [
        "is_phyloseq_format"
      ]
    },
    {
      "page": "is_raw_format",
      "title": "Is Raw MicrobiomeR Format",
      "concept": [
        "Validation"
      ],
      "topics": [
        "is_raw_format"
      ]
    },
    {
      "page": "melt_taxmap",
      "title": "Melt Taxmap",
      "concept": [
        "Formatting"
      ],
      "topics": [
        "melt_taxmap"
      ]
    },
    {
      "page": "metacoder_comp_func_1",
      "title": "Metacoder Comparison Function #1",
      "concept": [
        "Data Manipulators"
      ],
      "topics": [
        "metacoder_comp_func_1"
      ]
    },
    {
      "page": "MicrobiomeR_Formats",
      "title": "The MicrobiomeR Formats",
      "concept": [
        "Formatting"
      ],
      "topics": [
        "MicrobiomeR_Formats"
      ]
    },
    {
      "page": "MicrobiomeR_Workflow",
      "title": "The MicrobiomeR Workflow",
      "topics": [
        "MicrobiomeR_Workflow"
      ]
    },
    {
      "page": "order_metacoder_data",
      "title": "Order Metacoder Observation Data",
      "concept": [
        "Validation"
      ],
      "topics": [
        "order_metacoder_data"
      ]
    },
    {
      "page": "ordination_plot",
      "title": "Ordination Plot",
      "concept": [
        "Visualizations"
      ],
      "topics": [
        "ordination_plot",
        "ordination_plots"
      ]
    },
    {
      "page": "otu_id_filter",
      "title": "Filter OTU Ids from Taxmap Objects",
      "concept": [
        "Basic Metacoder Filters"
      ],
      "topics": [
        "otu_id_filter"
      ]
    },
    {
      "page": "otu_prevalence_filter",
      "title": "OTU Prevalence Filter",
      "concept": [
        "Advanced Metacoder Filters"
      ],
      "topics": [
        "otu_prevalence_filter"
      ]
    },
    {
      "page": "otu_proportion_filter",
      "title": "OTU Proportion Filter",
      "concept": [
        "Advanced Metacoder Filters"
      ],
      "topics": [
        "otu_proportion_filter"
      ]
    },
    {
      "page": "output_dir",
      "title": "Create an Output Directory",
      "concept": [
        "Project Management"
      ],
      "topics": [
        "output_dir"
      ]
    },
    {
      "page": "parse_taxonomy_silva_128",
      "title": "Parse elements of a taxonomy vector",
      "topics": [
        "parse_taxonomy_silva_128"
      ]
    },
    {
      "page": "permanova",
      "title": "PERMANOVA",
      "topics": [
        "permanova"
      ]
    },
    {
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