add_worms_taxonomy: Retrieve and Organize WoRMS Taxonomy for SHARK Aphia IDs

In sharksmhi/SHARK4R: Retrieving, Analyzing, and Validating Marine Data from SHARK and Nordic Microalgae

Retrieve and Organize WoRMS Taxonomy for SHARK Aphia IDs

Description

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

add_worms_taxonomy(aphia_id, scientific_name = NULL, verbose = TRUE)

Arguments

aphia_id	A numeric vector containing Aphia IDs for which WoRMS taxonomy needs to be updated.
scientific_name	A character vector of scientific names. If provided, Aphia IDs will be retrieved from the scientific names. The length of scientific_name must match the length of aphia_id. Defaults to NULL, in which case the function will only add taxonomy to the provided Aphia IDs.
verbose	A logical indicating whether to print progress messages. Default is TRUE.

Value

A data frame containing current WoRMS taxonomy information.

See Also

get_shark_data, update_dyntaxa_taxonomy, https://www.marinespecies.org/rest/, https://CRAN.R-project.org/package=worrms

Examples

## Not run: 
# Update WoRMS taxonomy for a set of Aphia IDs
updated_taxonomy <- add_worms_taxonomy(c(149619, 149122, 11))
print(updated_taxonomy)

# Update WoRMS with an unknown Aphia ID and scientific names
with_names <- add_worms_taxonomy(c(149619, 149122, 11, NA),
                                 c("Cerataulina pelagica",
                                   "Chaetoceros didymus",
                                   "Ciliophora",
                                   "Dinophysis"))
print(with_names)

## End(Not run)

sharksmhi/SHARK4R documentation built on Jan. 9, 2025, 5:15 p.m.