.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 |
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 |
c-ListOfmeta |
Concatenate meta elements into a ListOfmeta |
c-meta |
Concatenate meta elements into a ListOfmeta |
c-method |
Concatenate meta elements into a ListOfmeta |
c-method |
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 |
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_item |
Get the desired element from the nexml object |
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_otu |
get_taxa |
get_otus_list |
get_taxa_list |
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 |
New |
new with namespaced class name |
nexml |
Class representing a NeXML document |
nexml-class |
Class representing a NeXML document |
nexml.cell |
Constructor for the respective class |
nexml.char |
Constructor for the respective class |
nexml.characters |
Constructor for the respective class |
nexml.edge |
Constructor for the respective class |
nexml.format |
Constructor for the respective class |
nexml.matrix |
Constructor for the respective class |
nexml.member |
Constructor for the respective class |
nexml.meta |
Constructor function for metadata nodes |
nexml.meta_ |
Constructor for the respective class |
nexml.node |
Constructor for the respective class |
nexml.otu |
Constructor for the respective class |
nexml.otus |
Constructor for the respective class |
nexml.polymorphic_states |
Constructor for the respective class |
nexml.row |
Constructor for the respective class |
nexml.seq |
Constructor for the respective class |
nexml.state |
Constructor for the respective class |
nexml.states |
Constructor for the respective class |
nexml.tree |
Constructor for the respective class |
nexml.trees |
Constructor for the respective class |
nexml.uncertain_state |
Constructor for the respective class |
nexml.uncertain_states |
Constructor for the respective class |
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_read.character |
Read NeXML files into various R formats |
nexml_read.XMLInternalDocument |
Read NeXML files into various R formats |
nexml_read.XMLInternalNode |
Read NeXML files into various R formats |
nexml_to_simmap |
Convert phylo with attached simmap to nexml object |
nexml_validate |
validate nexml using the online validator tool |
nexml_write |
Write nexml files |
read.nexml |
Read NeXML files into various R formats |
reset_id_counter |
reset id counter |
simmap_to_nexml |
Convert phylo with attached simmap to nexml object |
slot-method |
Access or set slot of S4 object |
slot-ResourceMeta |
Access or set slot of S4 object |
slot<--method |
Access or set slot of S4 object |
summary-method |
Summary method for nexml objects |
summary.nexml |
Summary method for nexml objects |
taxize_nexml |
taxize nexml |
toPhylo |
nexml to phylo |
write.nexml |
Write nexml files |