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Add WoRMS taxonomy hierarchy to AphiaIDs or scientific names

Source: R/worms_api_functions.R
add_worms_taxonomy.Rd

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()
)

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

[Deprecated] Use aphia_ids instead.

scientific_name

[Deprecated] Use scientific_names instead.

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

Examples

# \donttest{
# Using AphiaID only
add_worms_taxonomy(c(1080, 109604), verbose = FALSE)
#> # A tibble: 2 × 10
#>   aphia_id worms_scientific_name worms_kingdom worms_phylum worms_class
#>      <dbl> <chr>                 <chr>         <chr>        <chr>      
#> 1     1080 Copepoda              Animalia      Arthropoda   Copepoda   
#> 2   109604 Dinophysis acuta      Chromista     Myzozoa      Dinophyceae
#> # ℹ 5 more variables: worms_order <chr>, worms_family <chr>, worms_genus <chr>,
#> #   worms_species <chr>, worms_hierarchy <chr>

# Using a combination of AphiaID and scientific name
add_worms_taxonomy(
  aphia_ids = c(NA, 109604),
  scientific_names = c("Calanus finmarchicus", "Oithona similis"),
  verbose = FALSE
)
#> # A tibble: 2 × 11
#>   aphia_id scientific_name      worms_scientific_name worms_kingdom worms_phylum
#>      <dbl> <chr>                <chr>                 <chr>         <chr>       
#> 1   104464 Calanus finmarchicus Calanus finmarchicus  Animalia      Arthropoda  
#> 2   109604 Oithona similis      Dinophysis acuta      Chromista     Myzozoa     
#> # ℹ 6 more variables: worms_class <chr>, worms_order <chr>, worms_family <chr>,
#> #   worms_genus <chr>, worms_species <chr>, worms_hierarchy <chr>
# }