get_algaebase_genus: Search AlgaeBase for information about a genus of algae

Description

This function has been deprecated. Users are encouraged to use match_algaebase_species instead.

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

get_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: get_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) {
  get_algaebase_genus("Anabaena", subscription_key = "your_api_key")
}