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Construct Dyntaxa Taxonomy Table From API

Source: R/dyntaxa_api_functions.R
construct_dyntaxa_table.Rd

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

[Deprecated] Use add_descendants instead.

[Deprecated] Use add_synonyms instead.

parent_ids

[Deprecated] Use taxon_ids instead. construct_dyntaxa_table now handles taxon IDs.

Value

A data frame representing the constructed taxonomy table.

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.

See also

SLU Artdatabanken API Documentation

Examples

if (FALSE) { # \dontrun{
# 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)
} # }