set_taxonomy: Set, create or modify columns with taxonomic information

Description

Format fields that contain taxonomic name information from kingdom to species, as well as the common/vernacular name, to a tibble using Darwin Core Standard.

In practice this is no different from using mutate(), but gives some informative errors, and serves as a useful lookup for accepted column names in the Darwin Core Standard.

Usage

set_taxonomy(
  .df,
  kingdom = NULL,
  phylum = NULL,
  class = NULL,
  order = NULL,
  family = NULL,
  genus = NULL,
  specificEpithet = NULL,
  vernacularName = NULL,
  .keep = "unused"
)

Value

A tibble with the requested columns added/reformatted.

Arguments

.df: A data.frame or tibble that the column should be appended to.
kingdom: The kingdom name of identified taxon.
phylum: The phylum name of identified taxon.
class: The class name of identified taxon.
order: The order name of identified taxon.
family: The family name of identified taxon.
genus: The genus name of the identified taxon.
specificEpithet: The name of the first species or species epithet of the scientificName. See documentation
vernacularName: The common or vernacular name of the identified taxon.
.keep: Control which columns from .data are retained in the output. Note that unlike dplyr::mutate(), which defaults to "all" this defaults to "unused"; i.e. only keeps Darwin Core columns, and not those columns used to generate them.

Details

Examples of specificEphithet:

If scientificName is Abies concolor, the specificEpithet is concolor.
If scientificName is Semisulcospira gottschei, the specificEpithet is gottschei.

Examples

Run this code

df <- tibble::tibble(
  scientificName = c("Crinia Signifera", "Crinia Signifera", "Litoria peronii"),
  fam = c("Myobatrachidae", "Myobatrachidae", "Hylidae"),
  ord = c("Anura", "Anura", "Anura"),
  latitude = c(-35.27, -35.24, -35.83),
  longitude = c(149.33, 149.34, 149.34),
  eventDate = c("2010-10-14", "2010-10-14", "2010-10-14")
  )

# Reformat columns to Darwin Core terms
df |>
  set_scientific_name(
    scientificName = scientificName
    ) |>
  set_taxonomy(
    family = fam,
    order = ord
    )