SHARK4R (version 1.1.0)

add_worms_taxonomy: Add WoRMS taxonomy hierarchy to AphiaIDs or scientific names

Description

This function enhances a dataset of AphiaIDs (and optionally scientific names) with their complete hierarchical taxonomy from the World Register of Marine Species (WoRMS). Missing AphiaIDs can be resolved from scientific names automatically.

Usage

add_worms_taxonomy(
  aphia_ids,
  scientific_names = NULL,
  add_rank_to_hierarchy = FALSE,
  verbose = TRUE,
  aphia_id = deprecated(),
  scientific_name = deprecated()
)

Value

A tibble with taxonomy columns added, including:

• aphia_id, scientific_name

• worms_kingdom, worms_phylum, worms_class, worms_order, worms_family, worms_genus, worms_species

• worms_scientific_name, worms_hierarchy

Arguments

aphia_ids

Numeric vector of AphiaIDs.

scientific_names

Optional character vector of scientific names (same length as aphia_id).

add_rank_to_hierarchy

Logical (default FALSE). If TRUE, includes rank labels in the concatenated hierarchy string.

verbose

Logical (default TRUE). If TRUE, prints progress updates.

aphia_id

Use aphia_ids instead.

scientific_name

Use scientific_names instead.

Examples

# \donttest{
# Using AphiaID only
try(add_worms_taxonomy(c(1080, 109604), verbose = FALSE))

# Using a combination of AphiaID and scientific name
try(add_worms_taxonomy(
  aphia_ids = c(NA, 109604),
  scientific_names = c("Calanus finmarchicus", "Oithona similis"),
  verbose = FALSE
))
# }