update_dyntaxa_taxonomy: Update SHARK taxonomy records using Dyntaxa

Description

This function updates Dyntaxa taxonomy records based on a list of Dyntaxa taxon IDs. It collects parent IDs from SLU Artdatabanken API (Dyntaxa), retrieves full taxonomy records, and organizes the data into a full taxonomic table that can be joined with data downloaded from SHARK

Usage

update_dyntaxa_taxonomy(
  dyntaxa_ids,
  subscription_key = Sys.getenv("DYNTAXA_KEY"),
  add_missing_taxa = FALSE,
  verbose = TRUE
)

Value

A data frame representing the updated Dyntaxa taxonomy table.

Arguments

dyntaxa_ids

A vector of Dyntaxa taxon IDs to update.

subscription_key

A Dyntaxa API subscription key. By default, the key is read from the environment variable DYNTAXA_KEY.

You can provide the key in three ways:

Directly as a parameter: update_dyntaxa_taxonomy(238366, subscription_key = "your_key_here").
Temporarily for the session: Sys.setenv(DYNTAXA_KEY = "your_key_here"). After this, you do not need to pass subscription_key to the function.
Permanently across sessions by adding it to your ~/.Renviron file. Use usethis::edit_r_environ() to open the file, then add: DYNTAXA_KEY=your_key_here. After this, you do not need to pass subscription_key to the function.

add_missing_taxa

Logical. If TRUE, the function will attempt to fetch missing taxa (i.e., taxon_ids not found in the initial Dyntaxa DwC-A query). Default is FALSE.

verbose

Logical. Print progress messages. Default is TRUE.

Details

A valid Dyntaxa API subscription key is required. You can request a free key for the "Taxonomy" service from the ArtDatabanken API portal: https://api-portal.artdatabanken.se/

Note: Please review the API conditions and register for access before using the API. Data collected through the API is stored at SLU Artdatabanken. Please also note that the authors of SHARK4R are not affiliated with SLU Artdatabanken.

Examples

Run this code

if (FALSE) {
# Update Dyntaxa taxonomy for taxon IDs 238366 and 1010380
updated_taxonomy <- update_dyntaxa_taxonomy(c(238366, 1010380), "your_subscription_key")
print(updated_taxonomy)
}