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

## Documentation for package ‘RNeXML’ version 2.4.6

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

.callGeneric | Calls the given generic with the given arguments
.methodWithNext | Saves the next method in the method meta data
.sigLabel | Create a label for a method signature
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
c-ListOfmeta | Concatenate meta elements into a ListOfmeta
c-meta | Concatenate meta elements into a ListOfmeta
c-method | Concatenate meta elements into a ListOfmeta
c-method | Concatenate nexml files
charzero_as_empty | Treats zero-length character vectors as empty strings
coalesce_ | Front-end to dplyr::coalesce to deal with NULL vectors
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_item | Get the desired element from the nexml object
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_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
lcapply | Compact list then lapply
meta | Constructor function for metadata nodes
New | new with namespaced class name
nexml | Class representing a NeXML document
nexml-class | Class representing a NeXML document
nexml.cell | Constructor for the respective class
nexml.char | Constructor for the respective class
nexml.characters | Constructor for the respective class
nexml.edge | Constructor for the respective class
nexml.format | Constructor for the respective class
nexml.matrix | Constructor for the respective class
nexml.member | Constructor for the respective class
nexml.meta | Constructor function for metadata nodes
nexml.meta_ | Constructor for the respective class
nexml.node | Constructor for the respective class
nexml.otu | Constructor for the respective class
nexml.otus | Constructor for the respective class
nexml.polymorphic_states | Constructor for the respective class
nexml.row | Constructor for the respective class
nexml.seq | Constructor for the respective class
nexml.state | Constructor for the respective class
nexml.states | Constructor for the respective class
nexml.tree | Constructor for the respective class
nexml.trees | Constructor for the respective class
nexml.uncertain_state | Constructor for the respective class
nexml.uncertain_states | Constructor for the respective class
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 | Convert phylo with attached simmap to nexml object
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_to_nexml | Convert phylo with attached simmap to nexml object
slot-method | Access or set slot of S4 object
slot-ResourceMeta | Access or set slot of S4 object
slot<--method | Access or set slot of S4 object
summary-method | Summary method for nexml objects
summary.nexml | Summary method for nexml objects
taxize_nexml | taxize nexml
toPhylo | nexml to phylo
write.nexml | Write nexml files