Resolve names using Global Names Resolver
See section Age of datasets in the Global Names Resolver
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, ... )
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 |
resolve_once |
logical; Find the first available match instead of
matches across all data sources with all possible renderings of a name.
When |
with_context |
logical; Reduce the likelihood of matches to taxonomic
homonyms. When |
canonical |
logical; If |
highestscore |
logical; Return those names with the highest score for each searched name? Defunct |
best_match_only |
(logical) If |
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 |
http |
The HTTP method to use, one of "get" or "post". Default: "get".
Use |
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 |
fields |
(character) One of minimal (default) or all. Minimal gives back just four fields, whereas all gives all fields back. |
names |
Deprecated, see |
... |
Curl options passed on to crul::HttpClient |
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.
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.
If preferred_data_sources is used, only the preferred data
is returned - if it has any results.
Scott Chamberlain
http://gnrd.globalnames.org/api http://gnrd.globalnames.org/
## Not run:
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)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.