get_aux_classification_table()

get_aux_classification_table

R Documentation

Get auxiliary classification table

Description

Reads the manually curated auxiliary classification table from a CSV file. If the file does not yet exist, returns an empty tibble with the required columns so that the rest of the pipeline can continue and detect any missing taxa.

Usage

get_aux_classification_table(
  file_path = here::here("Data/Input/aux_classification_table.csv")
)

Arguments

file_path

A length-1 character string giving the path to the CSV file. Defaults to ‘here::here("Data/Input/aux_classification_table.csv")’. The file, if present, must contain columns ‘sel_name’, ‘family’, ‘genus’, and ‘species’.

Details

Manual classifications in this file override automatic classifications produced by ‘get_taxa_classification()’. When the file exists it is validated to confirm all required columns are present. Missing columns are filled with ‘NA_character_’ rather than raising an error, so that partial tables are accepted.

Value

A tibble with columns ‘sel_name’ (character), ‘family’ (character), ‘genus’ (character), and ‘species’ (character). Returns an empty tibble when the file does not exist.