Skip to contents

Resolve names using Open Tree of Life (OTL) resolver

Source: R/tol_resolve.R
tol_resolve.Rd

Resolve names using Open Tree of Life (OTL) resolver

Usage

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

Arguments

names

(character) taxon names to be queried

context_name

name of the taxonomic context to be searched (length-one character vector). Must match (case sensitive) one of the values returned by rotl::tnrs_contexts().

do_approximate_matching

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

ids

An array of OTL 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

(logical) 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. Default: FALSE

...

Curl options passed on to httr::POST within rotl::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/germinator/wiki/TNRS-API-v3#match_names

See also

gnr_resolve(), tnrs()

Author

Francois Michonneau francois.michonneau@gmail.com Scott Chamberlain

Examples

if (FALSE) { # \dontrun{
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")
tol_resolve(turducken_spp, context_name="Animals")
} # }