{
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  "Title": "Semantically Rich I/O for the 'NeXML' Format",
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  "Description": "Provides access to phyloinformatic data in 'NeXML' format.\nThe package should add new functionality to R such as the\npossibility to manipulate 'NeXML' objects in more various and\nrefined way and compatibility with 'ape' objects.",
  "URL": "https://docs.ropensci.org/RNeXML/,\nhttps://github.com/ropensci/RNeXML",
  "BugReports": "https://github.com/ropensci/RNeXML/issues",
  "License": "BSD_3_clause + file LICENSE",
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  "Repository": "https://ropensci.r-universe.dev",
  "Date/Publication": "2024-05-06 19:06:44 UTC",
  "RemoteUrl": "https://github.com/ropensci/RNeXML",
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    "add_basic_meta",
    "add_characters",
    "add_meta",
    "add_namespaces",
    "add_trees",
    "expand_prefix",
    "flatten_multiphylo",
    "get_all_meta",
    "get_characters",
    "get_characters_list",
    "get_citation",
    "get_flat_trees",
    "get_level",
    "get_license",
    "get_meta",
    "get_metadata",
    "get_metadata_values",
    "get_namespaces",
    "get_otu",
    "get_otus_list",
    "get_rdf",
    "get_taxa",
    "get_taxa_list",
    "get_trees",
    "get_trees_list",
    "meta",
    "nexml",
    "nexml_add",
    "nexml_figshare",
    "nexml_get",
    "nexml_publish",
    "nexml_read",
    "nexml_to_simmap",
    "nexml_validate",
    "nexml_write",
    "nexml.cell",
    "nexml.char",
    "nexml.characters",
    "nexml.edge",
    "nexml.format",
    "nexml.matrix",
    "nexml.member",
    "nexml.node",
    "nexml.otu",
    "nexml.otus",
    "nexml.polymorphic_states",
    "nexml.row",
    "nexml.seq",
    "nexml.state",
    "nexml.states",
    "nexml.tree",
    "nexml.trees",
    "nexml.uncertain_state",
    "nexml.uncertain_states",
    "read.nexml",
    "reset_id_counter",
    "simmap_to_nexml",
    "slot",
    "slot<-",
    "summary",
    "taxize_nexml",
    "write.nexml"
  ],
  "_help": [
    {
      "page": "dot-callGeneric",
      "title": "Calls the given generic with the given arguments",
      "topics": [
        ".callGeneric"
      ]
    },
    {
      "page": "dot-methodWithNext",
      "title": "Saves the next method in the method meta data",
      "topics": [
        ".methodWithNext"
      ]
    },
    {
      "page": "dot-sigLabel",
      "title": "Create a label for a method signature",
      "topics": [
        ".sigLabel"
      ]
    },
    {
      "page": "add_basic_meta",
      "title": "Add basic metadata",
      "topics": [
        "add_basic_meta"
      ]
    },
    {
      "page": "add_characters",
      "title": "Add character data to a nexml object",
      "topics": [
        "add_characters"
      ]
    },
    {
      "page": "add_meta",
      "title": "Add metadata to a nexml file",
      "topics": [
        "add_meta"
      ]
    },
    {
      "page": "add_namespaces",
      "title": "Add namespaces",
      "topics": [
        "add_namespaces"
      ]
    },
    {
      "page": "add_trees",
      "title": "add_trees",
      "topics": [
        "add_trees"
      ]
    },
    {
      "page": "Annotated-class",
      "title": "Class of objects that have metadata as lists of meta elements",
      "topics": [
        "Annotated-class"
      ]
    },
    {
      "page": "c-meta",
      "title": "Concatenate meta elements into a ListOfmeta",
      "topics": [
        "c,ListOfmeta-method",
        "c,meta-method",
        "c-ListOfmeta",
        "c-meta"
      ]
    },
    {
      "page": "c-nexml-method",
      "title": "Concatenate nexml files",
      "topics": [
        "c,nexml-method"
      ]
    },
    {
      "page": "charzero_as_empty",
      "title": "Treats zero-length character vectors as empty strings",
      "topics": [
        "charzero_as_empty"
      ]
    },
    {
      "page": "coalesce_",
      "title": "Front-end to dplyr::coalesce to deal with NULL vectors",
      "topics": [
        "coalesce_"
      ]
    },
    {
      "page": "expand_prefix",
      "title": "Expand namespace-prefixed string",
      "topics": [
        "expand_prefix"
      ]
    },
    {
      "page": "findNextMethod",
      "title": "Finds the method that callNextMethod() should chain to",
      "topics": [
        "findNextMethod"
      ]
    },
    {
      "page": "flatten_multiphylo",
      "title": "Flatten a multiphylo object",
      "topics": [
        "flatten_multiphylo"
      ]
    },
    {
      "page": "get_all_meta",
      "title": "Get flattened list of meta annotations",
      "topics": [
        "get_all_meta"
      ]
    },
    {
      "page": "get_characters",
      "title": "Get character data.frame from nexml",
      "topics": [
        "get_characters"
      ]
    },
    {
      "page": "get_characters_list",
      "title": "Extract the character matrix",
      "topics": [
        "get_characters_list"
      ]
    },
    {
      "page": "get_citation",
      "title": "Get citation from metadata",
      "topics": [
        "get_citation"
      ]
    },
    {
      "page": "get_flat_trees",
      "title": "get_flat_trees",
      "topics": [
        "get_flat_trees"
      ]
    },
    {
      "page": "get_level",
      "title": "get_level",
      "topics": [
        "get_level"
      ]
    },
    {
      "page": "get_license",
      "title": "Get license from metadata",
      "topics": [
        "get_license"
      ]
    },
    {
      "page": "get_meta",
      "title": "Extracts meta objects matching properties",
      "topics": [
        "get_meta"
      ]
    },
    {
      "page": "get_metadata",
      "title": "get_metadata",
      "topics": [
        "get_metadata"
      ]
    },
    {
      "page": "get_metadata_values",
      "title": "Get the value(s) for metadata",
      "topics": [
        "get_metadata_values"
      ]
    },
    {
      "page": "get_namespaces",
      "title": "get namespaces",
      "topics": [
        "get_namespaces"
      ]
    },
    {
      "page": "get_rdf",
      "title": "Extract rdf-xml from a NeXML file",
      "topics": [
        "get_rdf"
      ]
    },
    {
      "page": "get_taxa",
      "title": "get_taxa",
      "topics": [
        "get_otu",
        "get_taxa"
      ]
    },
    {
      "page": "get_taxa_list",
      "title": "get_taxa_list",
      "topics": [
        "get_otus_list",
        "get_taxa_list"
      ]
    },
    {
      "page": "get_trees",
      "title": "extract a phylogenetic tree from the nexml",
      "topics": [
        "get_trees"
      ]
    },
    {
      "page": "get_trees_list",
      "title": "extract all phylogenetic trees in ape format",
      "topics": [
        "get_trees_list"
      ]
    },
    {
      "page": "lcapply",
      "title": "Compact list then lapply",
      "topics": [
        "lcapply"
      ]
    },
    {
      "page": "meta",
      "title": "Constructor function for metadata nodes",
      "topics": [
        "meta",
        "nexml.meta"
      ]
    },
    {
      "page": "New",
      "title": "new with namespaced class name",
      "topics": [
        "New"
      ]
    },
    {
      "page": "nexml_add",
      "title": "add elements to a new or existing nexml object",
      "topics": [
        "nexml_add"
      ]
    },
    {
      "page": "nexml_figshare",
      "title": "publish nexml to figshare",
      "topics": [
        "nexml_figshare"
      ]
    },
    {
      "page": "nexml_get",
      "title": "Get the desired element from the nexml object",
      "topics": [
        "get_item",
        "nexml_get"
      ]
    },
    {
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