R/tol_resolve.R

In taxize: Taxonomic Information from Around the Web

#' Resolve names using Open Tree of Life (OTL) resolver
#'
#' @export
#' @param names (character) taxon names to be queried
#' @param 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()].
#' @param do_approximate_matching (logical) A logical indicating whether or not
#' to perform approximate string (a.k.a. \dQuote{fuzzy}) matching. Using `FALSE`
#' will greatly improve speed. Default: `TRUE`
#' @param 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.
#' @param 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`
#'
#' @return 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")`).
#'
#' @param ... Curl options passed on to `httr::POST` within
#' [rotl::tnrs_match_names()]
#' @author Francois Michonneau \email{francois.michonneau@@gmail.com}
#' Scott Chamberlain
#' @seealso [gnr_resolve()], [tnrs()]
#' @references
#' https://github.com/OpenTreeOfLife/germinator/wiki/TNRS-API-v3#match_names
#' @keywords resolve names taxonomy
#' @examples \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")
#' }
tol_resolve <- function(names = NULL, context_name = NULL,
  do_approximate_matching = TRUE, ids = NULL, include_suppressed = FALSE, ...) {

  rotl::tnrs_match_names(names = names, context_name = context_name,
    do_approximate_matching = do_approximate_matching, ids = ids, 
    include_suppressed = include_suppressed, ...)
}