match_algaebase_genus: Search AlgaeBase for information about a genus of algae

Description

This function searches the AlgaeBase API for genus information and returns detailed taxonomic data, including higher taxonomy, taxonomic status, scientific names, and other related metadata.

Usage

match_algaebase_genus(
  genus,
  subscription_key = Sys.getenv("ALGAEBASE_KEY"),
  higher = TRUE,
  unparsed = FALSE,
  newest_only = TRUE,
  exact_matches_only = TRUE,
  apikey = deprecated()
)

Value

A data frame with the following columns:

id — AlgaeBase identifier.
accepted_name — Accepted scientific name (if different from the input).
input_name — The genus name supplied by the user.
input_match — Indicator of exact match (1 = exact, 0 = not exact).
currently_accepted — Indicator if the taxon is currently accepted (1 = TRUE, 0 = FALSE).
genus_only — Indicator if the search was for a genus only (1 = genus, 0 = genus + species).
kingdom, phylum, class, order, family — Higher taxonomy (returned if higher = TRUE).
taxonomic_status — Status of the taxon (e.g., currently accepted, synonym, unverified).
taxon_rank — Taxonomic rank of the accepted name (e.g., genus, species).
mod_date — Date when the entry was last modified.
long_name — Full scientific name including author and date (if available).
authorship — Author information (if available).

Arguments

genus

The genus name to search for (character string). This parameter is required.

subscription_key

A character string containing the API key for accessing the AlgaeBase API. By default, the key is read from the environment variable ALGAEBASE_KEY.

You can provide the key in three ways:

Directly as a parameter: match_algaebase_genus("Skeletonema", subscription_key = "your_key_here").
Temporarily for the session: Sys.setenv(ALGAEBASE_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: ALGAEBASE_KEY=your_key_here. After this, you do not need to pass subscription_key to the function.

higher

A boolean flag indicating whether to include higher taxonomy in the output (default is TRUE).

unparsed

A boolean flag indicating whether to return the raw JSON output from the API (default is FALSE).

newest_only

A boolean flag to return only the most recent entry (default is TRUE).

exact_matches_only

A boolean flag to limit results to exact matches (default is TRUE).

apikey

Use subscription_key instead.

Details

A valid API key is requested from the AlgaeBase team.

Examples

Run this code

if (FALSE) {
  match_algaebase_genus("Anabaena", subscription_key = "your_api_key")
}