Skip to contents

taxize nexml

Source: R/taxize_nexml.R
taxize_nexml.Rd

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

if (FALSE) { # \dontrun{
data(bird.orders)
birds <- add_trees(bird.orders)
birds <- taxize_nexml(birds, "NCBI")
} # }