construct_dyntaxa_table: Construct Dyntaxa Taxonomy Table From API

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

Construct Dyntaxa Taxonomy Table From API

Description

This function constructs a taxonomy table based on Dyntaxa taxon IDs. It queries the SLU Artdatabanken API (Dyntaxa) to fetch taxonomy information and organizes the data into a hierarchical table.

Usage

construct_dyntaxa_table(
  taxon_ids,
  subscription_key,
  shark_output = TRUE,
  add_parents = TRUE,
  add_descendants = FALSE,
  add_descendants_rank = "genus",
  add_synonyms = TRUE,
  add_missing_taxa = FALSE,
  add_hierarchy = FALSE,
  verbose = TRUE,
  add_genus_children = deprecated(),
  recommended_only = deprecated(),
  parent_ids = deprecated()
)

Arguments

taxon_ids	An integer vector containing taxon IDs for which taxonomy information is requested. These IDs should correspond to specific taxonomic entities within the Dyntaxa database.
subscription_key	A character string containing the subscription key for accessing the SLU Artdatabanken API. A key is provided to registered users at Artdatabanken.
shark_output	Logical. If TRUE, the function will return a table formatted with SHARK-compatible columns. If FALSE, all available columns are returned. Default is TRUE.
add_parents	Logical. If TRUE, the function will include parent taxa (higher ranks) for the specified taxon IDs in the output. Default is TRUE.
add_descendants	Logical. If TRUE, the output will include descendant taxa (lower ranks) for the specified taxon IDs and the rank specified in add_descendants_rank. Default is FALSE.
add_descendants_rank	Character string specifying the rank of descendant taxa to include. Allowed values are "kingdom", "phylum", "class", "order", "family", "genus", and "species". Default is "genus".
add_synonyms	Logical. If TRUE, the function will include synonyms for the accepted taxa in the output. Default is TRUE.
add_missing_taxa	Logical. If TRUE, the function will attempt to fetch missing taxa (i.e., taxa not found in the initial Dyntaxa DwC-A query, such as species complexes). Default is FALSE.
add_hierarchy	Logical. If TRUE, the function will add a hierarchy column indicating the taxonomic relationships (e.g., parent-child) among the taxa. Default is FALSE.
verbose	Logical. If TRUE, the function will print additional messages to provide feedback on its progress. Default is TRUE.
add_genus_children	Use add_descendants instead.
recommended_only	Use add_synonyms instead.
parent_ids	Use taxon_ids instead. construct_dyntaxa_table now handles taxon IDs.

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 constructed taxonomy table.

See Also

SLU Artdatabanken API Documentation

Examples

## Not run: 
# Construct Dyntaxa taxonomy table for taxon IDs 238366 and 1010380
taxon_ids <- c(238366, 1010380)
taxonomy_table <- construct_dyntaxa_table(taxon_ids, "your_subscription_key")
print(taxonomy_table)

## End(Not run)

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