taxize (version 0.6.6)

gnr_resolve: Resolve names using Global Names Resolver.

Description

Uses the Global Names Index, see http://gni.globalnames.org/.

Usage

gnr_resolve(names, data_source_ids = NULL, resolve_once = FALSE,
  with_context = FALSE, canonical = FALSE, highestscore = TRUE,
  best_match_only = FALSE, preferred_data_sources = NULL,
  with_canonical_ranks = FALSE, http = "get", ...)

Arguments

names

character; taxonomic names to be resolved. Doesn't work for verncular/common names.

data_source_ids

character; IDs to specify what data source is searched. See gnr_datasources.

resolve_once

logical; Find the first available match instead of matches across all data sources with all possible renderings of a name. When TRUE, response is rapid but incomplete.

with_context

logical; Reduce the likelihood of matches to taxonomic homonyms. When TRUE a common taxonomic context is calculated for all supplied names from matches in data sources that have classification tree paths. Names out of determined context are p

canonical

logical; If FALSE (default), gives back names with taxonomic authorities. If TRUE, returns canocial names (without tax. authorities and abbreviations).

highestscore

logical; Return those names with the highest score for each searched name? Defunct

best_match_only

(logical) If TRUE, best match only returned. Default: FALSE

preferred_data_sources

(character) A vector of one or more data source IDs.

with_canonical_ranks

(logical) Returns names with infraspecific ranks, if present. If TRUE, we force canonical=TRUE, otherwise this parameter would have no effect. Default: FALSE

http

The HTTP method to use, one of "get" or "post". Default: "get". Use http="post" with large queries. Queries with > 300 records use "post" automatically because "get" would fail

...

Curl options passed on to GET

Value

• A data.frame with one attribute not_known: a character vector of taxa unknown to the Global Names Index. Acccess like attr(output, "not_known"), or attributes(output)$not_known

See Also

gnr_datasources

Examples

gnr_resolve(names = c("Helianthus annuus", "Homo sapiens"))
gnr_resolve(names = c("Asteraceae", "Plantae"))

# Using data source 12 (Encyclopedia of Life)
sources <- gnr_datasources()
sources
eol <- sources$id[sources$title == 'EOL']
gnr_resolve(names=c("Helianthos annuus","Homo sapians"), data_source_ids=eol)

# Two species in the NE Brazil catalogue
sps <- c('Justicia brasiliana','Schinopsis brasiliensis')
gnr_resolve(names = sps, data_source_ids = 145)

# Best match only, compare the two
gnr_resolve(names = "Helianthus annuus", best_match_only = FALSE)
gnr_resolve(names = "Helianthus annuus", best_match_only = TRUE)

# Preferred data source
gnr_resolve(names = "Helianthus annuus", preferred_data_sources = c(3,4))

# Return canonical names - default is canonical=FALSE
head(gnr_resolve(names = "Helianthus annuus"))
head(gnr_resolve(names = "Helianthus annuus", canonical=TRUE))

# Return canonical names with authority stripped but
# ranks still present
gnr_resolve("Scorzonera hispanica L. subsp. asphodeloides Wallr.")
## vs.
gnr_resolve("Scorzonera hispanica L. subsp. asphodeloides Wallr.",
   with_canonical_ranks = TRUE)