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Get taxonomic classification of the BOLD taxonomy database for a list of taxa

Source: R/get_bold_taxonomy.R
get_bold_taxonomy.Rd

The taxonomy functions are used to define exactly which records will be retrieved by the download functions. More precisely, only records that include the taxid/scientificName, retrieved using the taxonomy functions, as the lowest taxonomic identification will be downloaded.

For more details see the 'Searching taxonomy' vignette: vignette("Searching taxonomy", package = "barcodeMineR")

Usage

get_bold_taxonomy(ids, api_rate = NULL, ask = TRUE, descend = TRUE)

Arguments

ids

`character` A character string of species names.

api_rate

`integer` The API rate with which to iterate each separate request. If left to default `NULL`, it will be set to one request every 16 seconds approximately. Use caution when overriding the default.

ask

`logical` Should the function ask the user whether to filter the final output for taxonomic ranks. Default `TRUE`.

descend

`logical` Use the taxize package to retrieve lower level taxonomies. Default `TRUE`.

Value

`data.frame` A data.frame object with the searched taxa, the taxid and the rank.

See also

[get_ncbi_taxonomy()]

Examples

get_bold_taxonomy("Achelia assimilis", descend = FALSE)
#>           queryName  taxid             taxon    rank records
#> 1 Achelia assimilis 103191 Achelia assimilis species      25