Get taxa from checklist

Gets taxonomic information of a GBIF checklist and matching GBIF backbone taxonomy. Only source taxa are kept, denormed higher classification taxa are removed. The function rgbif::name_usage() is used under the hood.

Usage

get_taxa(datasetKey)

Arguments

datasetKey

GBIF dataset key.

Value

A tibble with taxonomic information of the dataset.

Taxa details

get_taxa() returns a tibble with 8 columns:

• taxonKey: GBIF taxon key of scientificName.

• nubKey: GBIF backbone taxon key

• taxonID: Taxon ID of scientificName, as provided in the checklist.

• scientificName: Original scientific name of the taxon in the checklist.

• taxonomicStatus: Taxonomic status of the taxon in the GBIF backbone taxonomy. It can be accepted, synonym, doubtful or NA if the taxon is not matched with the backbone.

• acceptedKey: GBIF taxon key of the accepted taxon, if the source scientificName is a synonym.

• acceptedName: Scientific name of the accepted taxon. scientificName is the accepted name in the GBIF backbone.

• acceptedKingdom: Kingdom of the accepted taxon.

• acceptedTaxonRank: Taxonomic rank of the accepted taxon.

See also

Other download functions: get_distributions()

Examples

# Global Register of Introduced and Invasive Species - Sovereign Base Areas
# of Cyprus, Cyprus
get_taxa("497fa25f-6a32-4a2a-8f42-d01d8a0b7c22")
#> # A tibble: 20 × 9
#>     taxonKey  nubKey taxonID scientificName          taxonomicStatus acceptedKey
#>        <int>   <int> <chr>   <chr>                   <chr>                 <int>
#>  1 163732873 2264597 120115  Rhopilema nomadica Gal… ACCEPTED            2264597
#>  2 163732878 2334433 120114  Pterois miles (Bennett… ACCEPTED            2334433
#>  3 163732881 2407271 120112  Torquigener flavimacul… ACCEPTED            2407271
#>  4 163732882 2407271 120117  Torquigener flavimacul… ACCEPTED            2407271
#>  5 163732885 2356802 120108  Sargocentron rubrum (F… ACCEPTED            2356802
#>  6 163732886 2356802 120116  Sargocentron rubrum (F… ACCEPTED            2356802
#>  7 163732889 2350570 120106  Gambusia holbrooki Gir… ACCEPTED            2350570
#>  8 163732892 2390262 120109  Siganus luridus (Rüpp… ACCEPTED            2390262
#>  9 163732893 2390185 120110  Siganus rivulatus Fors… ACCEPTED            2390185
#> 10 163732895 2396749 120107  Parupeneus forsskali (… ACCEPTED            2396749
#> 11 163732898      NA 120113  Fistularia commersonii… NA                       NA
#> 12 163732899      NA 120105  Fistularia commersonii… NA                       NA
#> 13 163732903 2441502 120119  Testudo marginata Scho… ACCEPTED            2441502
#> 14 163732904 2441461 120118  Testudo graeca Linnaeu… ACCEPTED            2441461
#> 15 163732911 3151764 120111  Symphyotrichum squamat… ACCEPTED            3151764
#> 16 163732914 3176197 120103  Eucalyptus camaldulens… DOUBTFUL            3176197
#> 17 163732915 3176772 120104  Eucalyptus gomphocepha… ACCEPTED            3176772
#> 18 163732918 5421144 120102  Dodonaea viscosa Jacq.  ACCEPTED            5421144
#> 19 163732921 2891932 120101  Casuarina cunninghamia… ACCEPTED            2891932
#> 20 163732924 2978552 120100  Acacia saligna (Labill… ACCEPTED            2978552
#> # ℹ 3 more variables: acceptedName <chr>, acceptedTaxonRank <chr>,
#> #   acceptedKingdom <chr>