Man pages for RNeXML
Semantically Rich I/O for the 'NeXML' Format
| add_basic_meta | Add basic metadata |
| add_characters | Add character data to a nexml object |
| add_meta | Add metadata to a nexml file |
| add_namespaces | Add namespaces |
| add_trees | add_trees |
| Annotated-class | Class of objects that have metadata as lists of meta elements |
| charzero_as_empty | Treats zero-length character vectors as empty strings |
| c-meta | Concatenate meta elements into a ListOfmeta |
| c-nexml-method | Concatenate nexml files |
| coalesce_ | Front-end to dplyr::coalesce to deal with NULL vectors |
| constructors | Constructor for the respective class |
| dot-callGeneric | Calls the given generic with the given arguments |
| dot-methodWithNext | Saves the next method in the method meta data |
| dot-sigLabel | Create a label for a method signature |
| expand_prefix | Expand namespace-prefixed string |
| findNextMethod | Finds the method that callNextMethod() should chain to |
| flatten_multiphylo | Flatten a multiphylo object |
| get_all_meta | Get flattened list of meta annotations |
| get_characters | Get character data.frame from nexml |
| get_characters_list | Extract the character matrix |
| get_citation | Get citation from metadata |
| get_flat_trees | get_flat_trees |
| get_level | get_level |
| get_license | Get license from metadata |
| get_meta | Extracts meta objects matching properties |
| get_metadata | get_metadata |
| get_metadata_values | Get the value(s) for metadata |
| get_namespaces | get namespaces |
| get_rdf | Extract rdf-xml from a NeXML file |
| get_taxa | get_taxa |
| get_taxa_list | get_taxa_list |
| get_taxa_meta | get_taxa_meta |
| get_taxa_meta_list | get_taxa_meta_list |
| get_trees | extract a phylogenetic tree from the nexml |
| get_trees_list | extract all phylogenetic trees in ape format |
| lcapply | Compact list then lapply |
| meta | Constructor function for metadata nodes |
| New | new with namespaced class name |
| nexml_add | add elements to a new or existing nexml object |
| nexml-class | Class representing a NeXML document |
| nexml_figshare | publish nexml to figshare |
| nexml_get | Get the desired element from the nexml object |
| nexml_publish | publish nexml files to the web and receive a DOI |
| nexml_read | Read NeXML files into various R formats |
| nexml_validate | validate nexml using the online validator tool |
| nexml_write | Write nexml files |
| reset_id_counter | reset id counter |
| simmap_to_nexml | Convert phylo with attached simmap to nexml object |
| slot-ResourceMeta-method | Access or set slot of S4 object |
| summary-nexml-method | Summary method for nexml objects |
| taxize_nexml | taxize nexml |
| toPhylo | nexml to phylo |
