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All functions

Annotated-class
Class of objects that have metadata as lists of meta elements
New()
new with namespaced class name
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(<meta>) c(<ListOfmeta>)
Concatenate meta elements into a ListOfmeta
c(<nexml>)
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
nexml.tree() nexml.trees() nexml.node() nexml.edge() nexml.otu() nexml.otus() nexml.char() nexml.characters() nexml.format() nexml.state() nexml.uncertain_state() nexml.states() nexml.uncertain_states() nexml.polymorphic_states() nexml.member() nexml.matrix() nexml.row() nexml.seq() nexml.cell()
Constructor for the respective class
.cacheNextMethod()
Caches next method in the calling environment
.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
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_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
nexml-class
Class representing a NeXML document
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_validate()
validate nexml using the online validator tool
nexml_write()
Write nexml files
reset_id_counter()
reset id counter
simmap_to_nexml() nexml_to_simmap()
Convert phylo with attached simmap to nexml object
slot(<ResourceMeta>) `slot<-`(<ResourceMeta>)
Access or set slot of S4 object
summary(<nexml>)
Summary method for nexml objects
taxize_nexml()
taxize nexml
toPhylo()
nexml to phylo