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Add the full higher classification to a taxify result

Source: R/browse.R
add_classification.Rd

Attaches the Linnaean ranks above family (kingdom, phylum, class, order) to a taxify() result by joining each matched row back to its backbone. The core taxify() output already carries family and genus; this fills the ranks above them, for whichever ranks the matched backbone stores. Rows matched by different backbones are each joined against their own backbone.

Usage

add_classification(
  x,
  ranks = c("kingdom", "phylum", "class", "order"),
  verbose = TRUE
)

Arguments

x

A data.frame returned by taxify().

ranks

Character vector of ranks to attach. Default c("kingdom", "phylum", "class", "order").

verbose

Logical. Default TRUE.

Value

x with the requested rank columns added. A rank a backbone does not store is left NA (WFO, for example, carries no ranks above family).

See also

add_col_info(), add_gbif_info() for backbone-specific extras.

Examples

# Runs offline against the bundled example database.
old <- options(taxify.data_dir = taxify_example_data())

taxify("Naja naja", backbone = "reptiledb") |>
  add_classification()

options(old)