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

Source: R/set_scientific_name.R
set_scientific_name.Rd

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.

Value

A tibble with the requested columns added/reformatted.

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

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
    )
#> ⠙ Checking 1 column: scientificName
#> ✔ Checking 1 column: scientificName [310ms]
#> 
#> # A tibble: 3 × 4
#>   latitude longitude eventDate  scientificName  
#>      <dbl>     <dbl> <chr>      <chr>           
#> 1    -35.3      149. 2010-10-14 Crinia Signifera
#> 2    -35.2      149. 2010-10-14 Crinia Signifera
#> 3    -35.8      149. 2010-10-14 Litoria peronii