Function reference • RNeXML

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 nexml: 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