Retrieve and organize WoRMS taxonomy for SHARK Aphia IDs

This function was deprecated and replaced by a function with more accurate name. Use add_worms_taxonomy() instead.

This function collects WoRMS (World Register of Marine Species) taxonomy information for a given set of Aphia IDs. The data is organized into a full taxonomic table that can be joined with data downloaded from SHARK.

Usage

update_worms_taxonomy(aphia_id, aphiaid = deprecated())

Arguments

aphia_id

A numeric vector containing Aphia IDs for which WoRMS taxonomy needs to be updated.

aphiaid

Use aphia_id instead.

Value

A tibble containing updated WoRMS taxonomy information.

See also

https://marinespecies.org/ for WoRMS website.

get_shark_data, update_dyntaxa_taxonomy, WoRMS API Documentation, https://CRAN.R-project.org/package=worrms

Examples

# \donttest{
# Update WoRMS taxonomy for a set of Aphia IDs
updated_taxonomy <- update_worms_taxonomy(c(149619, 149122, 11))
#> Warning: `update_worms_taxonomy()` was deprecated in SHARK4R 0.1.3.
#> ℹ Please use `add_worms_taxonomy()` instead.
#> Retrieving WoRMS classification for 3 AphiaIDs.
#> 
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print(updated_taxonomy)
#> # A tibble: 3 × 10
#>   aphia_id worms_scientific_name worms_kingdom worms_phylum     worms_class     
#>      <dbl> <chr>                 <chr>         <chr>            <chr>           
#> 1   149619 Cerataulina pelagica  Chromista     Heterokontophyta Bacillariophyce…
#> 2   149122 Chaetoceros didymus   Chromista     Heterokontophyta Bacillariophyce…
#> 3       11 Ciliophora            Chromista     Ciliophora       NA              
#> # ℹ 5 more variables: worms_order <chr>, worms_family <chr>, worms_genus <chr>,
#> #   worms_species <chr>, worms_hierarchy <chr>
# }