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 |
charzero_as_empty | Treats zero-length character vectors as empty strings |
c-meta | Concatenate meta elements into a ListOfmeta |
c-nexml-method | Concatenate nexml files |
coalesce_ | Front-end to dplyr::coalesce to deal with NULL vectors |
constructors | Constructor for the respective class |
dot-cacheNextMethod | Caches next method in the calling environment |
dot-callGeneric | Calls the given generic with the given arguments |
dot-methodWithNext | Saves the next method in the method meta data |
dot-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_taxa_meta | get_taxa_meta |
get_taxa_meta_list | get_taxa_meta_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_add | add elements to a new or existing nexml object |
nexml-class | Class representing a NeXML document |
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 | Convert phylo with attached simmap to nexml object |
slot-ResourceMeta-method | Access or set slot of S4 object |
summary-nexml-method | Summary method for nexml objects |
taxize_nexml | taxize nexml |
toPhylo | nexml to phylo |
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