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Retrieve unique GBIF Backbone taxon keys from a species checklist

Source: R/get_nubkeys.R
get_nubkeys.Rd

This function is a wrapper around rgbif::name_usage() to retrieve the (unique) GBIF Backbone taxon keys (nubKeys) from a species checklist identified by its datasetKey. It allows to choose whether to return synonyms or accepted taxa only. When allow_synonymsis FALSE, the function makes individual API calls for each nubKey in a loop. For checklists with many taxa, this could result in a large number of sequential API requests and it can take a long time to complete.

Usage

get_nubkeys(datasetKey, allow_synonyms = TRUE)

Arguments

datasetKey

(character) Unique identifier of a GBIF species checklist.

allow_synonyms

(logical) Default: TRUE. If FALSE, the accepted taxa the synonyms refer to are returned instead of the synonyms themselves.

Value

A (unique) vector of GBIF Backbone taxon keys (nubKeys). If allow_synonyms is TRUE, the keys are retrieved from rgbif::name_usage()$data directly. If allow_synonyms is FALSE, the accepted taxa keys are retrieved by calling rgbif::name_usage() for each synonym key obtained from rgbif::name_usage()$data and extracting the accepted taxa keys from them. The final keys are returned as unique values.

Details

Synonym relationships within the checklist itself are not taken into account.

See also

Other checklist functions: gbif_get_taxa(), gbif_has_distribution(), gbif_verify_keys(), get_table_pathways(), indicator_introduction_year(), indicator_native_range_year(), indicator_total_year(), pathways_cbd(), verify_taxa(), visualize_pathways_level1(), visualize_pathways_level2(), visualize_pathways_year_level1(), visualize_pathways_year_level2()

Examples

dataset_key <- "e082b10e-476f-43c1-aa61-f8d92f33029a"
# Retrieve all GBIF Backbone taxon keys: synonyms are included
get_nubkeys(datasetKey = dataset_key)
#>  [1] 4561827 7505521 2295425 4567449 2294131 7520678 5190912 4568269 5795017
#> [10] 4598225 4598226 2296797 2296805 4565039 8014163 9291405 2294277 2296807
#> [19] 4562917 4565134 8624880 4565061 4565140 4564944 7540164 8745918 4567717
#> [28] 2295309 8045384
# Retrieve accepted taxa GBIF Backbone taxon keys
get_nubkeys(datasetKey = dataset_key, allow_synonyms = FALSE)
#>  [1] 4561827 7505521 2295425 4567449 2294131 7520678 5190912 4568269 5795017
#> [10] 4598225 4598226 9890104 2296805 4565039 8014163 2294275 2294277 2296807
#> [19] 4562917 4565134 8624880 4565061 4565140 4564944 7540164 8745918 4567717
#> [28] 2295309 8045384