tol_resolve: Resolve names using Open Tree of Life resolver

Description

Resolve names using Open Tree of Life resolver

Usage

tol_resolve(names = NULL, context_name = NULL,
  do_approximate_matching = TRUE, ids = NULL, include_deprecated = FALSE,
  include_dubious = FALSE, ...)

Arguments

names

taxon names to be queried (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

An array 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_deprecated

A boolean indicating whether or not to include deprecated taxa in the search.

include_dubious

Whether to include so-called 'dubious' taxa--those which are not accepted by OTT.

...

Curl options passed on to POST within tnrs_match_names

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")).

References

https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-of-Life-APIs#match_names

Examples

Run this code

tol_resolve(names=c("echinodermata", "xenacoelomorpha", "chordata", "hemichordata"))
tol_resolve(c("Hyla", "Salmo", "Diadema", "Nautilus"))
tol_resolve(c("Hyla", "Salmo", "Diadema", "Nautilus"), context_name = "Animals")

turducken_spp <- c("Meleagris gallopavo", "Anas platyrhynchos", "Gallus gallus")
tnrs_match_names(turducken_spp, context="Animals")