{ "_id": "6a1033c0acfb0bcc41c98a3b", "Package": "metacoder", "Title": "Tools for Parsing, Manipulating, and Graphing Taxonomic\nAbundance Data", "Version": "0.3.9", "Authors@R": "c(person(given = \"Zachary\",\nfamily = \"Foster\",\nrole = c(\"aut\", \"cre\"),\nemail = \"zacharyfoster1989@gmail.com\"),\nperson(given = \"Niklaus\",\nfamily = \"Grunwald\",\nrole = c(\"ths\"),\nemail = \"grunwaln@science.oregonstate.edu\"),\nperson(given = \"Kamil\",\nfamily = \"Slowikowski\",\nrole = c(\"ctb\")),\nperson(given = \"Scott\",\nfamily = \"Chamberlain\",\nrole = c(\"ctb\")),\nperson(given = \"Rob\",\nfamily = \"Gilmore\",\nrole = \"ctb\"))", "Maintainer": "Zachary Foster ", "Description": "Reads, plots, and manipulates large taxonomic data sets,\nlike those generated from modern high-throughput sequencing,\nsuch as metabarcoding (i.e. amplification metagenomics, 16S\nmetagenomics, etc). It provides a tree-based visualization\ncalled \"heat trees\" used to depict statistics for every taxon\nin a taxonomy using color and size. It also provides various\nfunctions to do common tasks in microbiome bioinformatics on\ndata in the 'taxmap' format defined by the 'taxa' package. The\n'metacoder' package is described in the publication by Foster\net al. (2017) .", "License": "GPL-2 | GPL-3", "LazyData": "true", "URL": "https://grunwaldlab.github.io/metacoder_documentation/", "BugReports": "https://github.com/grunwaldlab/metacoder/issues", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "Encoding": "UTF-8", "biocViews": "", "Config/pak/sysreqs": "libglpk-dev make libicu-dev libjpeg-dev libpng-dev\nlibxml2-dev libssl-dev libx11-dev zlib1g-dev", "Repository": "https://grunwaldlab.r-universe.dev", "Date/Publication": "2026-04-10 22:42:07 UTC", "RemoteUrl": "https://github.com/grunwaldlab/metacoder", "RemoteRef": "HEAD", "RemoteSha": "aadeb4860f88108450b88ab3c3c9cc665968d5d8", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-12 08:08:07 UTC", "User": "root" }, "Author": "Zachary Foster [aut, cre],\nNiklaus Grunwald [ths],\nKamil Slowikowski [ctb],\nScott Chamberlain [ctb],\nRob Gilmore [ctb]", "MD5sum": "4becc9a97778694eb77290bb05462ee1", "_user": "grunwaldlab", "_type": "src", "_file": "metacoder_0.3.9.tar.gz", "_fileid": "f872a6aa823429332db8b866440809f494a7dad84e6fab777bd23005583414f1", "_filesize": 1383140, "_sha256": "f872a6aa823429332db8b866440809f494a7dad84e6fab777bd23005583414f1", "_created": "2026-05-12T08:08:07.000Z", "_published": "2026-05-22T10:45:20.535Z", "_distro": "noble", "_jobs": [ { "job": 77364029006, "time": 225, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "6938956284" }, { "job": 77364028298, "time": 239, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "6938962463" }, { "job": 77364029002, "time": 260, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "6938967138" }, { "job": 77364028806, "time": 248, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "6938963377" }, { "job": 77364028963, "time": 138, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "6938927895" }, { "job": 77364029005, "time": 226, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "6938956491" }, { "job": 77364028891, "time": 132, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "6938925607" }, { "job": 77364028346, "time": 257, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "6938965812" }, { "job": 77364027952, "time": 283, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6938883739" }, { "job": 77364028147, "time": 171, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7158639593" }, { "job": 77364028329, "time": 229, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "6938957019" }, { "job": 77364028567, "time": 248, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "6938963395" }, { "job": 77364028369, "time": 243, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "6938961702" } ], "_buildurl": "https://github.com/r-universe/grunwaldlab/actions/runs/25721650368", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/grunwaldlab/metacoder", "_commit": { "id": "aadeb4860f88108450b88ab3c3c9cc665968d5d8", "author": "Zachary S.L. 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"_datasets": [ { "name": "ex_taxmap", "title": "An example taxmap object", "object": "ex_taxmap", "class": [ "Taxmap", "Taxonomy", "R6" ], "fields": [], "table": false, "tojson": false }, { "name": "hmp_otus", "title": "A HMP subset", "object": "hmp_otus", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "otu_id", "lineage", "700035949", "700097855", "700100489", "700111314", "700033744", "700109581", "700111044", "700101365", "700100431", "700016050", "700032425", "700024855", "700103488", "700096869", "700107379", "700096422", "700102417", "700114168", "700037540", "700106397", "700113498", "700033743", "700105205", "700024238", "700034183", "700038390", "700015973", "700038124", "700107206", "700037403", "700098429", "700101224", "700114615", "700024234", "700108596", "700101076", "700105882", "700016902", "700102242", "700038231", "700109394", "700102530", "700108229", "700099013", "700098680", "700106938", "700014916", "700095535", "700102367", "700101358" ], "rows": 1000, "table": true, "tojson": true }, { "name": "hmp_samples", "title": "Sample information for HMP subset", "object": "hmp_samples", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "sample_id", "sex", "body_site" ], "rows": 50, "table": true, "tojson": true }, { "name": "ranks_ref", "title": "Lookup-table for IDs of taxonomic ranks", "object": "ranks_ref", "class": [ "data.frame" ], "fields": [ "rankid", "ranks" ], "rows": 34, "table": true, "tojson": true } ], "_help": [ { "page": "all_names", "title": "Return names of data in [taxonomy()] or [taxmap()]", "concept": [ "NSE helpers" ], "topics": [ "all_names" ] }, { "page": "ambiguous_synonyms", "title": "Get patterns for ambiguous taxa", "topics": [ "ambiguous_synonyms" ] }, { "page": "arrange_obs", "title": "Sort user data in [taxmap()] objects", "concept": [ "taxmap manipulation functions" ], "topics": [ "arrange_obs" ] }, { "page": "arrange_taxa", "title": "Sort the edge list of [taxmap()] objects", "concept": [ "taxmap manipulation functions" ], "topics": [ "arrange_taxa" ] }, { "page": "as_phyloseq", "title": "Convert taxmap to phyloseq", "topics": [ "as_phyloseq" ] }, { "page": "branches", "title": "Get \"branch\" taxa", "concept": [ "taxonomy indexing functions" ], "topics": [ "branches" ] }, { "page": "calc_diff_abund_deseq2", "title": "Differential abundance with DESeq2", "concept": [ "calculations" ], "topics": [ "calc_diff_abund_deseq2" ] }, { "page": "calc_group_mean", "title": "Calculate means of groups of columns", "concept": [ "calculations" ], "topics": [ "calc_group_mean" ] }, { "page": "calc_group_median", "title": "Calculate medians of groups of columns", "concept": [ "calculations" ], "topics": [ "calc_group_median" ] }, { "page": "calc_group_rsd", "title": "Relative standard deviations of groups of columns", "concept": [ "calculations" ], "topics": [ "calc_group_rsd" ] }, { "page": "calc_group_stat", "title": "Apply a function to groups of columns", "concept": [ "calculations" ], "topics": [ "calc_group_stat" ] }, { "page": "calc_n_samples", "title": "Count the number of samples", "concept": [ "calculations" ], "topics": [ "calc_n_samples" ] }, { "page": "calc_obs_props", "title": "Calculate proportions from observation counts", "concept": [ "calculations" ], "topics": [ "calc_obs_props" ] }, { "page": "calc_prop_samples", "title": "Calculate the proportion of samples", "concept": [ "calculations" ], "topics": [ "calc_prop_samples" ] }, { "page": "classifications", "title": "Get classifications of taxa", "concept": [ "taxonomy data functions" ], "topics": [ "classifications" ] }, { "page": "compare_groups", "title": "Compare groups of samples", "concept": [ "calculations" ], "topics": [ "compare_groups" ] }, { "page": "complement", "title": "Find complement of sequences", "concept": [ "sequence transformations" ], "topics": [ "complement" ] }, { "page": "counts_to_presence", "title": "Apply a function to groups of columns", "concept": [ "calculations" ], "topics": [ "counts_to_presence" ] }, { "page": "database_list", "title": "Database list", "topics": [ "database_list" ] }, { "page": "diverging_palette", "title": "The default diverging color palette", "topics": [ "diverging_palette" ] }, { "page": "ex_hierarchies", "title": "An example hierarchies object", "concept": [ "taxa-datasets" ], "topics": [ "ex_hierarchies" ] }, { "page": "ex_hierarchy1", "title": "An example Hierarchy object", "concept": [ "taxa-datasets" ], "topics": [ "ex_hierarchy1" ] }, { "page": "ex_hierarchy2", "title": "An example Hierarchy object", "concept": [ "taxa-datasets" ], "topics": [ "ex_hierarchy2" ] }, { "page": "ex_hierarchy3", "title": "An example Hierarchy object", "concept": [ "taxa-datasets" ], "topics": [ "ex_hierarchy3" ] }, { "page": "ex_taxmap", "title": "An example taxmap object", "concept": [ "taxa-datasets" ], "topics": [ "ex_taxmap" ] }, { "page": "extract_tax_data", "title": "Extracts taxonomy info from vectors with regex", "concept": [ "parsers" ], "topics": [ "extract_tax_data" ] }, { "page": "filter_ambiguous_taxa", "title": "Filter ambiguous taxon names", "topics": [ "filter_ambiguous_taxa" ] }, { "page": "filter_obs", "title": "Filter observations with a list of conditions", "concept": [ "taxmap manipulation functions" ], "topics": [ "filter_obs" ] }, { "page": "filter_taxa", "title": "Filter taxa with a list of conditions", "concept": [ "taxmap manipulation functions" ], "topics": [ "filter_taxa" ] }, { "page": "filtering-helpers", "title": "Taxonomic filtering helpers", "topics": [ "filtering-helpers", "ids", "nms", "ranks" ] }, { "page": "get_data", "title": "Get data in a taxmap object by name", "concept": [ "NSE helpers" ], "topics": [ "get_data" ] }, { "page": "get_data_frame", "title": "Get data in a taxonomy or taxmap object by name", "concept": [ "accessors" ], "topics": [ "get_data_frame" ] }, { "page": "get_dataset", "title": "Get a data set from a taxmap object", "topics": [ "get_dataset" ] }, { "page": "heat_tree", "title": "Plot a taxonomic tree", "topics": [ "heat_tree", "heat_tree.default", "heat_tree.Taxmap" ] }, { "page": "heat_tree_matrix", "title": "Plot a matrix of heat trees", "topics": [ "heat_tree_matrix" ] }, { "page": "hierarchies", "title": "Make a set of many [hierarchy()] class objects", "concept": [ "classes" ], "topics": [ "hierarchies" ] }, { "page": "hierarchy", "title": "The Hierarchy class", "concept": [ "classes" ], "topics": [ "hierarchy" ] }, { "page": "highlight_taxon_ids", "title": "Highlight taxon ID column", "topics": [ "highlight_taxon_ids" ] }, { "page": "hmp_otus", "title": "A HMP subset", "concept": [ "hmp_data" ], "topics": [ "hmp_otus" ] }, { "page": "hmp_samples", "title": "Sample information for HMP subset", "concept": [ "hmp_data" ], "topics": [ "hmp_samples" ] }, { "page": "id_classifications", "title": "Get ID classifications of taxa", "concept": [ "taxonomy data functions" ], "topics": [ "id_classifications" ] }, { "page": "internodes", "title": "Get \"internode\" taxa", "concept": [ "taxonomy indexing functions" ], "topics": [ "internodes" ] }, { "page": "is_ambiguous", "title": "Find ambiguous taxon names", "topics": [ "is_ambiguous" ] }, { "page": "is_branch", "title": "Test if taxa are branches", "concept": [ "taxonomy data functions" ], "topics": [ "is_branch" ] }, { "page": "is_internode", "title": "Test if taxa are \"internodes\"", "concept": [ "taxonomy data functions" ], "topics": [ "is_internode" ] }, { "page": "is_leaf", "title": "Test if taxa are leaves", "concept": [ "taxonomy data functions" ], "topics": [ "is_leaf" ] }, { "page": "is_root", "title": "Test if taxa are roots", "concept": [ "taxonomy data functions" ], "topics": [ "is_root" ] }, { "page": "is_stem", "title": "Test if taxa are stems", "concept": [ "taxonomy data functions" ], "topics": [ "is_stem" ] }, { "page": "layout_functions", "title": "Layout functions", "topics": [ "layout_functions" ] }, { "page": "leaves", "title": "Get leaf taxa", "concept": [ "taxonomy indexing functions" ], "topics": [ "leaves" ] }, { "page": "leaves_apply", "title": "Apply function to leaves of each taxon", "topics": [ "leaves_apply" ] }, { "page": "lookup_tax_data", "title": "Convert one or more data sets to taxmap", "concept": [ "parsers" ], "topics": [ "lookup_tax_data" ] }, { "page": "make_dada2_asv_table", "title": "Make a imitation of the dada2 ASV abundance matrix", "concept": [ "writers" ], "topics": [ "make_dada2_asv_table" ] }, { "page": "make_dada2_tax_table", "title": "Make a imitation of the dada2 taxonomy matrix", "concept": [ "writers" ], "topics": [ "make_dada2_tax_table" ] }, { "page": "map_data", "title": "Create a mapping between two variables", "concept": [ "taxonomy data functions" ], "topics": [ "map_data" ] }, { "page": "map_data_", "title": "Create a mapping without NSE", "concept": [ "taxonomy data functions" ], "topics": [ "map_data_" ] }, { "page": "metacoder", "title": "Metacoder", "topics": [ "metacoder" ] }, { "page": "mutate_obs", "title": "Add columns to [taxmap()] objects", "concept": [ "taxmap manipulation functions" ], "topics": [ "mutate_obs" ] }, { "page": "n_leaves", "title": "Get number of leaves", "concept": [ "taxonomy data functions" ], "topics": [ "n_leaves" ] }, { "page": "n_leaves_1", "title": "Get number of leaves", "concept": [ "taxonomy data functions" ], "topics": [ "n_leaves_1" ] }, { "page": "n_obs", "title": "Count observations in [taxmap()]", "concept": [ "taxmap data functions" ], "topics": [ "n_obs" ] }, { "page": "n_obs_1", "title": "Count observation assigned in [taxmap()]", "concept": [ "taxmap data functions" ], "topics": [ "n_obs_1" ] }, { "page": "n_subtaxa", "title": "Get number of subtaxa", "concept": [ "taxonomy data functions" ], "topics": [ "n_subtaxa" ] }, { "page": "n_subtaxa_1", "title": "Get number of subtaxa", "concept": [ "taxonomy data functions" ], "topics": [ "n_subtaxa_1" ] }, { "page": "n_supertaxa", "title": "Get number of 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