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