set_scientific_name: Set, create or modify columns with scientific name &...

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

Set, create or modify columns with scientific name & authorship information

Description

Format the field scientificName, the lowest identified taxonomic name of an occurrence, along with the rank and authorship of the provided name to a tibble using Darwin Core Standard.

Usage

set_scientific_name(
  .df,
  scientificName = NULL,
  scientificNameAuthorship = NULL,
  taxonRank = NULL,
  .keep = "unused"
)

Arguments

.df	A data.frame or tibble that the column should be appended to.
scientificName	The full scientific name in the lower level taxonomic rank that can be determined.
scientificNameAuthorship	The authorship information for scientificName.
taxonRank	The taxonomic rank of scientificName.
.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

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

Examples of scientificName values (we specify the rank in parentheses, but users should not include this information):

• Coleoptera (order)

• Vespertilionidae (family)

• Manis (genus)

• ⁠Ctenomys sociabilis⁠ (genus + specificEpithet)

• ⁠Ambystoma tigrinum diaboli⁠ (genus + specificEpithet + infraspecificEpithet)

Examples of scientificNameAuthorship:

• ⁠(Györfi, 1952)⁠

• ⁠R. A. Graham⁠

• ⁠(Martinovský) Tzvelev⁠

Examples of taxonRank:

• order

• genus

• subspecies

• infraspecies

Value

A tibble with the requested columns added/reformatted.

See Also

set_taxonomy() for taxonomic name information.

Examples

df <- tibble::tibble(
  name = c("Crinia Signifera", "Crinia Signifera", "Litoria peronii"),
  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 Standard terms
df |>
  set_scientific_name(
    scientificName = name
    )

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