Semantically Rich I/O for the 'NeXML' Format

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Documentation for package ‘RNeXML’ version 2.4.11

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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.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