Man pages for ropensci/RNeXML
Semantically Rich I/O for the 'NeXML' Format

add_basic_metaAdd basic metadata
add_charactersAdd character data to a nexml object
add_metaAdd metadata to a nexml file
add_namespacesAdd namespaces
add_treesadd_trees
Annotated-classClass of objects that have metadata as lists of meta elements
c-metaConcatenate meta elements into a ListOfmeta
c-nexml-methodConcatenate nexml files
coalesce_Front-end to dplyr::coalesce to deal with NULL vectors
constructorsConstructor for the respective class
dot-cacheNextMethodCaches next method in the calling environment
dot-callGenericCalls the given generic with the given arguments
dot-methodWithNextSaves the next method in the method meta data
dot-sigLabelCreate a label for a method signature
expand_prefixExpand namespace-prefixed string
findNextMethodFinds the method that callNextMethod() should chain to
flatten_multiphyloFlatten a multiphylo object
get_all_metaGet flattened list of meta annotations
get_charactersGet character data.frame from nexml
get_characters_listExtract the character matrix
get_citationGet citation from metadata
get_flat_treesget_flat_trees
get_levelget_level
get_licenseGet license from metadata
get_metaExtracts meta objects matching properties
get_metadataget_metadata
get_metadata_valuesGet the value(s) for metadata
get_namespacesget namespaces
get_rdfExtract rdf-xml from a NeXML file
get_taxaget_taxa
get_taxa_listget_taxa_list
get_taxa_metaget_taxa_meta
get_taxa_meta_listget_taxa_meta_list
get_treesextract a phylogenetic tree from the nexml
get_trees_listextract all phylogenetic trees in ape format
lcapplyCompact list then lapply
metaConstructor function for metadata nodes
Newnew with namespaced class name
nexml_addadd elements to a new or existing nexml object
nexml-classClass representing a NeXML document
nexml_figsharepublish nexml to figshare
nexml_getGet the desired element from the nexml object
nexml_publishpublish nexml files to the web and receive a DOI
nexml_readRead NeXML files into various R formats
nexml_validatevalidate nexml using the online validator tool
nexml_writeWrite nexml files
reset_id_counterreset id counter
simmap_to_nexmlConvert phylo with attached simmap to nexml object
slot-ResourceMeta-methodAccess or set slot of S4 object
taxize_nexmltaxize nexml
toPhylonexml to phylo
ropensci/RNeXML documentation built on Dec. 10, 2018, 8 a.m.