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Resolve names using Global Names Resolver

Source: R/gnr_resolve.R
gnr_resolve.Rd

See section Age of datasets in the Global Names Resolver

Usage

gnr_resolve(
  sci,
  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",
  names = NULL,
  ...
)

Arguments

sci

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 minimal (default) or all. Minimal gives back just four fields, whereas all gives all fields back.

names

Deprecated, see sci

...

Curl options passed on to crul::HttpClient

Value

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

Columns of the output data.frame:

  • user_supplied_name (character) - the name you passed in to the names parameter, unchanged.

  • submitted_name (character) - the actual name submitted to the GNR service

  • data_source_id (integer/numeric) - data source ID

  • data_source_title (character) - data source name

  • gni_uuid (character) - Global Names Index UUID (aka identifier)

  • matched_name (character) - the matched name in the GNR service

  • matched_name2 (character) - returned if canonical=TRUE, in which case matched_name is not returned

  • classification_path (character) - names of the taxonomic classification tree, with names separated by pipes (|)

  • classification_path_ranks (character) - ranks of the taxonomic classification tree, with names separated by pipes (|)

  • classification_path_ids (character) - identifiers of the taxonomic classification tree, with names separated by pipes (|)

  • taxon_id (character) - taxon identifier

  • edit_distance (integer/numeric) - edit distance

  • imported_at (character) - date imported

  • match_type (integer/numeric) - match type

  • match_value (character) - description of match type

  • prescore (character) - pre score

  • score (numeric) - score

  • local_id (character) - local identifier

  • url (character) - URL for taxon

  • global_id (character) - global identifier

  • current_taxon_id (character) - current taxon id

  • current_name_string (character) - current name string

Note that names (i.e. rows) are dropped that are NA, are zero length strings, are not character vectors, or are not found by the API.

Age of datasets in the Global Names Resolver

IMPORTANT: Datasets used in the Global Names Resolver vary in how recently they've been updated. See the updated_at field in the output of gnr_datasources() for dates when each dataset was last updated.

preferred_data_sources

If preferred_data_sources is used, only the preferred data is returned - if it has any results.

References

http://gnrd.globalnames.org/api http://gnrd.globalnames.org/

See also

gnr_datasources()

Author

Scott Chamberlain

Examples

if (FALSE) { # \dontrun{
gnr_resolve(sci = c("Helianthus annuus", "Homo sapiens"))
gnr_resolve(sci = 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(sci = sps, data_source_ids = 145)

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

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

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