{
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  "Package": "comparpq",
  "Type": "Package",
  "Title": "An extension to {MiscMetabar} and {phyloseq} package to compare\nphyloseq object",
  "Version": "0.1.3",
  "Authors@R": "person(\"Adrien\", \"Taudière\", email = \"adrien.taudiere@zaclys.net\",\nrole = c(\"aut\", \"cre\", \"cph\"), comment = c(ORCID = \"0000-0003-1088-1182\"))",
  "Description": "Compare phyloseq object from the R phyloseq package. This\npackage provides tools and functions to facilitate comparison\nand analysis of multiple phyloseq objects.",
  "License": "GPL (>= 3)",
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  "URL": "https://github.com/adrientaudiere/comparpq,\nhttps://adrientaudiere.github.io/comparpq/",
  "BugReports": "https://github.com/adrientaudiere/comparpq/issues",
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  "Repository": "https://adrientaudiere.r-universe.dev",
  "Date/Publication": "2026-03-13 14:23:10 UTC",
  "RemoteUrl": "https://github.com/adrientaudiere/comparpq",
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  "Packaged": {
    "Date": "2026-06-08 15:17:42 UTC",
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  "Author": "Adrien Taudière [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0003-1088-1182>)",
  "Maintainer": "Adrien Taudière <adrien.taudiere@zaclys.net>",
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  "_exports": [
    "add_external_seq_pq",
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    "add_shuffle_seq_pq",
    "adonis_lpq",
    "aldex_lpq",
    "ancombc_lpq",
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    "bubbles_pq",
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    "glmulti_lpq",
    "list_phyloseq",
    "maaslin3_pq",
    "merge_lpq",
    "midasim_pq",
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    "n_levels_lpq",
    "permute_da_pq",
    "rainplot_taxo_na",
    "remove_phyloseq",
    "rename_ranks_pq",
    "resolve_taxo_conflict",
    "select_ranks_pq",
    "shared_mod_lpq",
    "simple_venn_pq",
    "taxo2tree",
    "taxtab_replace_pattern_by_NA",
    "tc_bar",
    "tc_circle",
    "tc_congruence_metrics",
    "tc_df_pq",
    "tc_linked_trees",
    "tc_metrics_mock",
    "tc_metrics_mock_vec",
    "tc_points_matrix",
    "tc_sankey",
    "update_list_phyloseq",
    "upset_lpq"
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  "_datasets": [
    {
      "name": "Glom_otu",
      "title": "",
      "object": "Glom_otu",
      "class": [
        "phyloseq"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "add_external_seq_pq",
      "title": "Add external sequences to a phyloseq object",
      "topics": [
        "add_external_seq_pq"
      ]
    },
    {
      "page": "add_phyloseq",
      "title": "Add a phyloseq object to a list_phyloseq",
      "topics": [
        "add_phyloseq"
      ]
    },
    {
      "page": "add_shuffle_seq_pq",
      "title": "Add fake sequences by shuffling existing ones in a phyloseq object",
      "topics": [
        "add_shuffle_seq_pq"
      ]
    },
    {
      "page": "adonis_lpq",
      "title": "PERMANOVA analysis on each phyloseq object in a list_phyloseq",
      "topics": [
        "adonis_lpq"
      ]
    },
    {
      "page": "aldex_lpq",
      "title": "ALDEx2 analysis on each phyloseq object in a list_phyloseq",
      "topics": [
        "aldex_lpq"
      ]
    },
    {
      "page": "ancombc_lpq",
      "title": "ANCOM-BC analysis on each phyloseq object in a list_phyloseq",
      "topics": [
        "ancombc_lpq"
      ]
    },
    {
      "page": "apply_to_lpq",
      "title": "Apply a function to all phyloseq objects in a list_phyloseq",
      "topics": [
        "apply_to_lpq"
      ]
    },
    {
      "page": "bubbles_pq",
      "title": "Bubble plot of phyloseq object with observablehq",
      "topics": [
        "bubbles_pq"
      ]
    },
    {
      "page": "compare_refseq",
      "title": "Compare refseq slots between two phyloseq objects",
      "topics": [
        "compare_refseq"
      ]
    },
    {
      "page": "div_pq",
      "title": "Diversity indices per sample, optionally grouped by a modality",
      "topics": [
        "div_pq"
      ]
    },
    {
      "page": "estim_cor_lpq",
      "title": "Estimation statistics for numeric correlation on a list_phyloseq",
      "topics": [
        "estim_cor_lpq"
      ]
    },
    {
      "page": "estim_cor_pq",
      "title": "Estimation statistics for numeric variable correlation on a phyloseq object",
      "topics": [
        "estim_cor_pq"
      ]
    },
    {
      "page": "estim_diff_lpq",
      "title": "Estimation statistics for categorical comparisons on a list_phyloseq",
      "topics": [
        "estim_diff_lpq"
      ]
    },
    {
      "page": "estim_diff_pq",
      "title": "Estimation statistics for categorical comparisons on a phyloseq object",
      "topics": [
        "estim_diff_pq"
      ]
    },
    {
      "page": "factor_formatter",
      "title": "Format factor columns with funky colored backgrounds",
      "topics": [
        "factor_formatter"
      ]
    },
    {
      "page": "filter_common_lpq",
      "title": "Filter phyloseq objects to keep only shared samples and/or taxa",
      "topics": [
        "filter_common_lpq"
      ]
    },
    {
      "page": "formattable_lpq",
      "title": "Formattable visualization for list_phyloseq summary",
      "topics": [
        "formattable_lpq"
      ]
    },
    {
      "page": "formattable_lpq_full",
      "title": "Extended formattable for list_phyloseq with comparison info",
      "topics": [
        "formattable_lpq_full"
      ]
    },
    {
      "page": "gg_aldex_plot",
      "title": "ggplot2 version of ALDEx2 diagnostic plots",
      "topics": [
        "gg_aldex_plot"
      ]
    },
    {
      "page": "gg_bubbles_pq",
      "title": "Circle-packed bubble plot of a phyloseq object using ggplot2",
      "topics": [
        "gg_bubbles_pq"
      ]
    },
    {
      "page": "gg_hill_lpq",
      "title": "Scatter plots of Hill diversity across pairs of phyloseq objects",
      "topics": [
        "gg_hill_lpq"
      ]
    },
    {
      "page": "gg_maaslin3_plot",
      "title": "Plot MaAsLin3 results",
      "topics": [
        "gg_maaslin3_plot"
      ]
    },
    {
      "page": "glmulti_lpq",
      "title": "Automated model selection for Hill diversity on each phyloseq in a list_phyloseq",
      "topics": [
        "glmulti_lpq"
      ]
    },
    {
      "page": "list_phyloseq",
      "title": "S7 class for comparing phyloseq objects",
      "topics": [
        "list_phyloseq"
      ]
    },
    {
      "page": "maaslin3_pq",
      "title": "Run MaAsLin3 differential abundance analysis on a phyloseq object",
      "topics": [
        "maaslin3_pq"
      ]
    },
    {
      "page": "merge_lpq",
      "title": "Merge a list_phyloseq into a single phyloseq object",
      "topics": [
        "merge_lpq"
      ]
    },
    {
      "page": "midasim_pq",
      "title": "Simulate microbiome data with differential abundance using MIDASim",
      "topics": [
        "midasim_pq"
      ]
    },
    {
      "page": "multipatt_lpq",
      "title": "Indicator species analysis on each phyloseq object in a list_phyloseq",
      "topics": [
        "multipatt_lpq"
      ]
    },
    {
      "page": "multiply_counts_pq",
      "title": "Multiply OTU counts conditionally based on sample metadata",
      "topics": [
        "multiply_counts_pq"
      ]
    },
    {
      "page": "n_levels_lpq",
      "title": "Count unique taxonomic levels across phyloseq objects",
      "topics": [
        "n_levels_lpq"
      ]
    },
    {
      "page": "permute_da_pq",
      "title": "Simulate differential abundance by redistributing OTU counts",
      "topics": [
        "permute_da_pq"
      ]
    },
    {
      "page": "rainplot_taxo_na",
      "title": "Rainplot of the nb taxa assigned (not NA)",
      "topics": [
        "rainplot_taxo_na"
      ]
    },
    {
      "page": "remove_phyloseq",
      "title": "Remove a phyloseq object from a list_phyloseq",
      "topics": [
        "remove_phyloseq"
      ]
    },
    {
      "page": "rename_ranks_pq",
      "title": "Rename names of ranks in the tax_table slot of a phyloseq object",
      "topics": [
        "rename_ranks_pq"
      ]
    },
    {
      "page": "resolve_taxo_conflict",
      "title": "Resolve taxonomic conflict in the tax_table of a phyloseq object",
      "topics": [
        "resolve_taxo_conflict"
      ]
    },
    {
      "page": "select_ranks_pq",
      "title": "Select taxonomic ranks in a phyloseq object",
      "topics": [
        "select_ranks_pq"
      ]
    },
    {
      "page": "shared_mod_lpq",
      "title": "Display shared sample_data modalities",
      "topics": [
        "shared_mod_lpq"
      ]
    },
    {
      "page": "simple_venn_pq",
      "title": "Venn diagram of shared taxa across sample groups",
      "topics": [
        "simple_venn_pq"
      ]
    },
    {
      "page": "taxo2tree",
      "title": "Convert taxonomy dataframe to phylogenetic tree",
      "topics": [
        "taxo2tree"
      ]
    },
    {
      "page": "taxtab_replace_pattern_by_NA",
      "title": "Replace taxonomic value with a given pattern by NA",
      "topics": [
        "taxtab_replace_pattern_by_NA"
      ]
    },
    {
      "page": "tc_bar",
      "title": "Barchart of ratio to compare 2 taxonomic ranks",
      "topics": [
        "tc_bar"
      ]
    },
    {
      "page": "tc_circle",
      "title": "Circle of correspondence between two taxonomic levels",
      "topics": [
        "tc_circle"
      ]
    },
    {
      "page": "tc_congruence_metrics",
      "title": "Compute congruence metrics between two taxonomic assignments",
      "topics": [
        "tc_congruence_metrics"
      ]
    },
    {
      "page": "tc_df_pq",
      "title": "Contingency table of two taxonomic ranks",
      "topics": [
        "tc_df_pq"
      ]
    },
    {
      "page": "tc_linked_trees",
      "title": "Plot two taxonomy trees with linked correspondences",
      "topics": [
        "tc_linked_trees"
      ]
    },
    {
      "page": "tc_metrics_mock",
      "title": "Compute accuracy metrics of multiple taxonomic assignations method using mock for multi-rank and multi assignation methods",
      "topics": [
        "tc_metrics_mock"
      ]
    },
    {
      "page": "tc_metrics_mock_vec",
      "title": "Compute accuracy metrics of taxonomic assignation using a mock (known) community for one rank",
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        "tc_metrics_mock_vec"
      ]
    },
    {
      "page": "tc_points_matrix",
      "title": "Matrix of point to compare two taxonomic ranks",
      "topics": [
        "tc_points_matrix"
      ]
    },
    {
      "page": "tc_sankey",
      "title": "Sankey diagram to compare two taxonomic ranks",
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        "tc_sankey"
      ]
    },
    {
      "page": "update_list_phyloseq",
      "title": "Update the summary table and comparison characteristics",
      "topics": [
        "update_list_phyloseq"
      ]
    },
    {
      "page": "upset_lpq",
      "title": "UpSet or Venn plot of shared taxonomic values across phyloseq objects",
      "topics": [
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