name_backbone: Lookup names in the GBIF backbone taxonomy.

Description Usage Arguments Details Value References Examples

View source: R/name_backbone.r

Description

Lookup names in the GBIF backbone taxonomy.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
name_backbone(
  name,
  rank = NULL,
  kingdom = NULL,
  phylum = NULL,
  class = NULL,
  order = NULL,
  family = NULL,
  genus = NULL,
  strict = FALSE,
  verbose = NULL,
  start = NULL,
  limit = 100,
  curlopts = list()
)

name_backbone_verbose(
  name,
  rank = NULL,
  kingdom = NULL,
  phylum = NULL,
  class = NULL,
  order = NULL,
  family = NULL,
  genus = NULL,
  strict = FALSE,
  start = NULL,
  limit = 100,
  curlopts = list()
)

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) Defunct. See function name_backbone_verbose()

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.

curlopts

list of named curl options passed on to HttpClient. see curl::curl_options for curl options

Details

If you don't get a match, GBIF gives back a data.frame with columns synonym, confidence, and matchType='NONE'.

Value

For name_backbone, a data.frame for a single taxon with many columns. For name_backbone_verbose a list of length two (data and alternatives), first data.frame for the suggested taxon match, and a data.frame with alternative name suggestions resulting from fuzzy matching

References

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

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
## 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
## Strictness
name_backbone_verbose(name='Poa', kingdom='plants',
  strict=FALSE)
name_backbone_verbose(name='Helianthus annuus', kingdom='plants',
  strict=TRUE)

# Non-existent name - returns list of lenght 3 stating no match
name_backbone(name='Aso')
name_backbone(name='Oenante')

# Pass on curl options
name_backbone(name='Oenante', curlopts = list(verbose=TRUE))

## End(Not run)

rgbif documentation built on June 2, 2021, 9:07 a.m.