R: Match names to the Open Tree Taxonomy

tnrs_match_names {rotl} | R Documentation

## Match names to the Open Tree Taxonomy

### Description

Match taxonomic names to the Open Tree Taxonomy.

### Usage

    tnrs_match_names(names = NULL, context_name = NULL,
      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). Must match (case sensitive) one of the values returned by `tnrs_contexts`.
`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).

### 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. If no context is specified, 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.

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

### 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")`).

### See Also

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

### Examples

    ## Not run:
     deuterostomes <- tnrs_match_names(names=c("echinodermata", "xenacoelomorpha",
                                                "chordata", "hemichordata"))

    ## End(Not run)

[Package rotl version 3.0.4 Index]