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| 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 |
| c-method | Concatenate ListOfmeta elements into a ListOfmeta |
| c-method | Concatenate meta elements into a ListOfmeta |
| c-method | Concatenate nexml files |
| flatten_multiphylo | Flatten a multiphylo object |
| get_characters | Get character data.frame from nexml |
| get_characters_list | Extract the character matrix |
| get_citation | get_citation |
| get_flat_trees | get_flat_trees |
| get_item | Get the desired element from the nexml object |
| get_level | get_level |
| get_license | get_license |
| get_metadata | get_metadata |
| get_namespaces | get namespaces |
| get_otu | get_taxa |
| get_otus_list | get_taxa_list |
| get_rdf | Extract rdf-xml from a NeXML file |
| get_taxa | get_taxa |
| get_taxa_list | get_taxa_list |
| get_trees | extract a phylogenetic tree from the nexml |
| get_trees_list | extract all phylogenetic trees in ape format |
| meta | Constructor function for metadata nodes |
| nexml_add | add elements to a new or existing nexml object |
| 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_read.character | Read NeXML files into various R formats |
| nexml_read.XMLInternalDocument | Read NeXML files into various R formats |
| nexml_read.XMLInternalNode | Read NeXML files into various R formats |
| nexml_to_simmap | nexml_to_simmap |
| nexml_validate | validate nexml using the online validator tool |
| nexml_write | Write nexml files |
| read.nexml | Read NeXML files into various R formats |
| reset_id_counter | reset id counter |
| simmap_ex | A nexml class R object that includes simmap annotations |
| simmap_to_nexml | simmap_to_nexml |
| taxize_nexml | taxize nexml |
| toPhylo | nexml to phylo |
| write.nexml | Write nexml files |