update_dyntaxa_taxonomy: Update taxonomy from SHARK via SLU Artdatabanken API...

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

Update taxonomy from SHARK via SLU Artdatabanken API (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,
  add_missing_taxa = FALSE,
  verbose = TRUE
)

Arguments

dyntaxa_ids	A vector of Dyntaxa taxon IDs to update.
subscription_key	A character string containing the subscription key for accessing the SLU Artdatabanken API for Dyntaxa. A key is provided for registered users at SLU Artdatabanken.
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

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.

Value

A data frame representing the updated Dyntaxa taxonomy table.

See Also

get_shark_data, update_worms_taxonomy, SLU Artdatabanken API Documentation

Examples

## Not run: 
# Update Dyntaxa taxonomy for taxon IDs 238366 and 1010380
updated_taxonomy <- update_dyntaxa_taxonomy(c(238366, 1010380), "your_subscription_key")
print(updated_taxonomy)

## End(Not run)

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