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Match names to the Open Tree Taxonomy

Source: R/tnrs.R
tnrs_match_names.Rd

Match taxonomic names to the Open Tree Taxonomy.

Usage

tnrs_match_names(
  names = NULL,
  context_name = "All life",
  do_approximate_matching = TRUE,
  ids = NULL,
  include_suppressed = FALSE,
  ...
)

Arguments

names

taxon names to be queried. Currently limited to 10,000 names for exact matches and 2,500 names for approximate matches (character vector)

context_name

name of the taxonomic context to be searched (length-one character vector or NULL). Must match (case sensitive) one of the values returned by tnrs_contexts. Default to "All life".

do_approximate_matching

A logical indicating whether or not to perform approximate string (a.k.a. “fuzzy”) matching. Using FALSE will greatly improve speed. Default, however, is TRUE.

ids

A vector of ids to use for identifying names. These will be assigned to each name in the names array. If ids is provided, then ids and names must be identical in length.

include_suppressed

Ordinarily, some quasi-taxa, such as incertae sedis buckets and other non-OTUs, are suppressed from TNRS results. If this parameter is true, these quasi-taxa are allowed as possible TNRS results.

...

additional arguments to customize the API request (see rotl package documentation).

Value

A data frame summarizing the results of the query. The original query output is appended as an attribute to the returned object (and can be obtained using attr(object, "original_response")).

Details

Accepts one or more taxonomic names and returns information about potential matches for these names to known taxa in the Open Tree Taxonomy.

This service uses taxonomic contexts to disambiguate homonyms and misspelled names; a context may be specified using the context_name argument. The default value for context_name is "All life". If no context is specified (i.e., context_name is set to NULL), then the context will be inferred (i.e., the shallowest taxonomic context that contains all unambiguous names in the input). Taxonomic contexts are uncontested higher taxa that have been selected to allow limits to be applied to the scope of TNRS searches (e.g. 'match names only within flowering plants'). Once a context has been identified (either user-specified or inferred), all taxon name matches will performed only against taxa within that context. For a list of available taxonomic contexts, see tnrs_contexts.

A name is considered unambiguous if it is not a synonym and has only one exact match to any taxon name in the entire taxonomy.

When the name search returns multiple matches, the taxon with the highest match score is returned. If the name returned is not the one you intended, you can use the inspect function to check the other taxa returned by your search. The Getting Started vignette has more information on how to do this.

Several functions listed in the ‘See also’ section can be used to inspect and manipulate the object generated by this function.

See also

inspect.match_names, update.match_names, synonyms.match_names.

Examples

if (FALSE) { # \dontrun{
 deuterostomes <- tnrs_match_names(names=c("echinodermata", "xenacoelomorpha",
                                            "chordata", "hemichordata"))
} # }