taxize_nexml: taxize nexml

In RNeXML: Semantically Rich I/O for the 'NeXML' Format

taxize nexml

Description

Check taxonomic names against the specified service and add appropriate semantic metadata to the nexml OTU unit containing the corresponding identifier.

Usage

taxize_nexml(
  nexml,
  type = c("ncbi", "itis", "col", "tpl", "gbif", "wd"),
  warnings = TRUE,
  ...
)

Arguments

nexml	a nexml object
type	the name of the identifier to use
warnings	should we show warning messages if no match can be found?
...	additional arguments to [taxadb::get_ids()]

Examples

## Not run: 
data(bird.orders)
birds <- add_trees(bird.orders)
birds <- taxize_nexml(birds, "NCBI")

## End(Not run)

RNeXML documentation built on Feb. 16, 2023, 6:56 p.m.