taxize (version 0.7.9)

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", cap_first = TRUE, fields = "minimal", ...)

Arguments

names

character; taxonomic names to be resolved. Doesn't work for vernacular/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 penalized during score calculation.

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

cap_first

(logical) For each name, fix so that the first name part is capitalized, while others are not. This web service is sensitive to capitalization, so you'll get different results depending on capitalization. First name capitalized is likely what you'll want and is the default. If FALSE, names are not modified. Default: TRUE

fields

(character) One of mimimal (default) or all. Minimal gives back just four fields, whereas all gives all fields back.

...

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

## Not run: 
# 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)
# ## End(Not run)