SHARK4R (version 1.0.2)

get_dyntaxa_dwca: Download and read Darwin Core Archive files from Dyntaxa

Description

This function downloads a complete Darwin Core Archive (DwCA) of Dyntaxa from the SLU Artdatabanken API, extracts the archive, and reads the specified CSV file into R.

Usage

get_dyntaxa_dwca(
  subscription_key = Sys.getenv("DYNTAXA_KEY"),
  file_to_read = "Taxon.csv",
  force = FALSE,
  verbose = TRUE
)

Value

A tibble containing the data from the specified CSV file.

Arguments

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: get_dyntaxa_dwca(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.

file_to_read

A string specifying the name of the CSV file to read from the extracted archive. Allowed options are: "Reference.csv", "SpeciesDistribution.csv", "Taxon.csv", or "VernacularName.csv". Defaults to "Taxon.csv".

force

A logical value indicating whether to force a fresh download of the archive, even if a cached copy is available. Defaults to FALSE.

verbose

A logical value indicating whether to show download progress. Defaults to TRUE.

Details

By default, the archive is downloaded and cached across R sessions. On subsequent calls, the function reuses the cached copy of the extracted files to avoid repeated downloads. Use the force parameter to re-download the archive if needed. The cache is cleared automatically after 24 hours, but you can also manually clear it using clean_shark4r_cache.

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/

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

clean_shark4r_cache() to manually clear cached files.

Examples

if (FALSE) {
# Provide your Dyntaxa API subscription key
subscription_key <- "your_subscription_key"

# Download and read the Taxon.csv file
taxon_data <- get_dyntaxa_dwca(subscription_key, file_to_read = "Taxon.csv")
}