rgbif (version 0.9.7)

name_backbone: Lookup names in the GBIF backbone taxonomy.

Description

Lookup names in the GBIF backbone taxonomy.

Usage

name_backbone(name, rank = NULL, kingdom = NULL, phylum = NULL, class = NULL, order = NULL, family = NULL, genus = NULL, strict = FALSE, verbose = FALSE, start = NULL, limit = 100, ...)

Arguments

name

(character) Full scientific name potentially with authorship (required)

rank

(character) The rank given as our rank enum. (optional)

kingdom

(character) If provided default matching will also try to match against this if no direct match is found for the name alone. (optional)

phylum

(character) If provided default matching will also try to match against this if no direct match is found for the name alone. (optional)

class

(character) If provided default matching will also try to match against this if no direct match is found for the name alone. (optional)

order

(character) If provided default matching will also try to match against this if no direct match is found for the name alone. (optional)

family

(character) If provided default matching will also try to match against this if no direct match is found for the name alone. (optional)

genus

(character) If provided default matching will also try to match against this if no direct match is found for the name alone. (optional)

strict

(logical) If TRUE it (fuzzy) matches only the given name, but never a taxon in the upper classification (optional)

verbose

(logical) If TRUE show alternative matches considered which had been rejected.

start

Record number to start at. Default: 0. Use in combination with limit to page through results.

limit

Number of records to return. Default: 100. Maximum: 1000.

...

Further named parameters, such as query, path, etc, passed on to modify_url within GET call. Unnamed parameters will be combined with config.

Value

A list for a single taxon with many slots (with verbose=FALSE - default), or a list of length two, first element for the suggested taxon match, and a data.frame with alternative name suggestions resulting from fuzzy matching (with verbose=TRUE).

Details

If you don't get a match GBIF gives back a list of length 3 with slots synonym, confidence, and matchType='NONE'.

References

http://www.gbif.org/developer/species#searching

Examples

## Not run: 
# name_backbone(name='Helianthus annuus', kingdom='plants')
# name_backbone(name='Helianthus', rank='genus', kingdom='plants')
# name_backbone(name='Poa', rank='genus', family='Poaceae')
# 
# # Verbose - gives back alternatives
# name_backbone(name='Helianthus annuus', kingdom='plants', verbose=TRUE)
# 
# # Strictness
# name_backbone(name='Poa', kingdom='plants', verbose=TRUE, strict=FALSE)
# name_backbone(name='Helianthus annuus', kingdom='plants', verbose=TRUE, strict=TRUE)
# 
# # Non-existent name - returns list of lenght 3 stating no match
# name_backbone(name='Aso')
# name_backbone(name='Oenante')
# 
# # Pass on httr options
# library('httr')
# x <- name_backbone(name='Oenante', config=progress())
# ## End(Not run)