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Search AlgaeBase for information about a genus of algae

Source: R/algaebase_api_functions.R
get_algaebase_genus.Rd

[Deprecated]

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()
)

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")

  • 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

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

[Deprecated] Use subscription_key instead.

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).

Details

A valid API key is requested from the AlgaeBase team.

See also

https://www.algaebase.org/ for AlgaeBase website.

Examples

if (FALSE) { # \dontrun{
  get_algaebase_genus("Anabaena", subscription_key = "your_api_key")
} # }