set_taxonomy: Set, create or modify columns with taxonomic information

In corella: Prepare, Manipulate and Check Data to Comply with Darwin Core Standard

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"
)

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.

Value

A tibble with the requested columns added/reformatted.

See Also

set_scientific_name() for adding scientificName and authorship information.

Examples

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
    )

corella documentation built on April 4, 2025, 12:20 a.m.