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Check if taxon names exist in Dyntaxa

Source: R/dyntaxa_api_functions.R
is_in_dyntaxa.Rd

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
)

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.

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

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) { # \dontrun{
# 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)
} # }