# Semantically Rich I/O for the 'NeXML' Format

## Documentation for package ‘RNeXML’ version 2.0.7

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

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