Semantically Rich I/O for the 'NeXML' Format
Add basic metadata
Add character data to a nexml object
Add metadata to a nexml file
Add namespaces
add_trees
Class of objects that have metadata as lists of meta elements
Concatenate meta elements into a ListOfmeta
Concatenate nexml files
Treats zero-length character vectors as empty strings
Front-end to dplyr::coalesce to deal with NULL vectors
Constructor for the respective class
Calls the given generic with the given arguments
Saves the next method in the method meta data
Create a label for a method signature
Expand namespace-prefixed string
Finds the method that callNextMethod() should chain to
Flatten a multiphylo object
Get flattened list of meta annotations
Get character data.frame from nexml
Extract the character matrix
Get citation from metadata
get_flat_trees
get_level
Get license from metadata
Extracts meta objects matching properties
get_metadata
Get the value(s) for metadata
get namespaces
Extract rdf-xml from a NeXML file
get_taxa
get_taxa_list
get_taxa_meta
get_taxa_meta_list
extract a phylogenetic tree from the nexml
extract all phylogenetic trees in ape format
Compact list then lapply
Constructor function for metadata nodes
new with namespaced class name
Class representing a NeXML document
add elements to a new or existing nexml object
publish nexml to figshare
Get the desired element from the nexml object
publish nexml files to the web and receive a DOI
Read NeXML files into various R formats
validate nexml using the online validator tool
Write nexml files
reset id counter
Convert phylo with attached simmap to nexml object
Access or set slot of S4 object
Summary method for nexml objects
taxize nexml
nexml to phylo
Provides access to phyloinformatic data in 'NeXML' format. The package should add new functionality to R such as the possibility to manipulate 'NeXML' objects in more various and refined way and compatibility with 'ape' objects.
Useful links