SHARK4R (version 1.0.2)

is_in_dyntaxa: Check if taxon names exist in Dyntaxa

Description

Checks whether the supplied scientific names exist in the Swedish taxonomic database Dyntaxa. Optionally, returns a data frame with taxon names, taxon IDs, and match status.

Usage

is_in_dyntaxa(
  taxon_names,
  subscription_key = Sys.getenv("DYNTAXA_KEY"),
  use_dwca = FALSE,
  return_df = FALSE,
  verbose = FALSE
)

Value

If return_df = FALSE (default), a logical vector indicating whether each input name was found in Dyntaxa. Returned invisibly if verbose = TRUE. If return_df = TRUE, a data frame with columns:

• taxon_name: original input names

• taxon_id: corresponding Dyntaxa taxon IDs (NA if not found)

• match: logical indicating presence in Dyntaxa

Arguments

taxon_names

Character vector of taxon names to check.

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: is_in_dyntaxa("Skeletonema marinoi", 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.

use_dwca

Logical; if TRUE, uses the DwCA version of Dyntaxa instead of querying the API.

return_df

Logical; if TRUE, returns a data frame with columns taxon_name, taxon_id, and match. Default is FALSE (returns a logical vector).

verbose

Logical; if TRUE, prints messages about unmatched taxa.

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/

Examples

if (FALSE) {
# Using an environment variable (recommended for convenience)
Sys.setenv(DYNTAXA_KEY = "your_key_here")
is_in_dyntaxa(c("Skeletonema marinoi", "Nonexistent species"))

# Return a data frame instead of logical vector
is_in_dyntaxa(c("Skeletonema marinoi", "Nonexistent species"), return_df = TRUE)

# Or pass the key directly
is_in_dyntaxa("Skeletonema marinoi", subscription_key = "your_key_here")

# Suppress messages
is_in_dyntaxa("Skeletonema marinoi", verbose = FALSE)
}