inspect.match_names: Inspect and Update alternative matches for a name returned by tnrs_match_names

Description

Taxonomic names may have different meanings in different taxonomic contexts, as the same genus name can be applied to animals and plants for instance. Additionally, the meaning of a taxonomic name may have change throughout its history, and may have referred to a different taxon in the past. In such cases, a given names might have multiple matches in the Open Tree Taxonomy. These functions allow users to inspect (and update) alternative meaning of a given name and its current taxonomic status according to the Open Tree Taxonomy.

Usage

# S3 method for match_names
inspect(response, row_number, taxon_name, ott_id, ...)
inspect(response, ...)
# S3 method for match_names
update(object, row_number, taxon_name, ott_id, new_row_number, new_ott_id, ...)

Value

a data frame

Arguments

response: an object generated by the tnrs_match_names function
row_number: the row number corresponding to the name to inspect
taxon_name: the taxon name corresponding to the name to inspect
ott_id: the ott id corresponding to the name to inspect
...: currently ignored
object: an object created by tnrs_match_names
new_row_number: the row number in the output of inspect to replace the taxa specified by row_number, taxon_name, or ott_id.
new_ott_id: the ott id of the taxon to replace the taxa specified by row_number, taxon_name, or ott_id.

Details

To inspect alternative taxonomic meanings of a given name, you need to provide the object resulting from a call to the tnrs_match_names function, as well as one of either the row number corresponding to the name in this object, the name itself (as used in the original query), or the ott_id listed for this name.

To update one of the name, you also need to provide the row number in which the name to be replaced appear or its ott id.

Examples

Run this code

  if (FALSE) {
   matched_names <- tnrs_match_names(c("holothuria", "diadema", "boletus"))
   inspect(matched_names, taxon_name="diadema")
   new_matched_names <- update(matched_names, taxon_name="diadema",
                               new_ott_id = 631176)
   new_matched_names
   }