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Set, create or modify columns with taxonomic information

Source: R/set_taxonomy.R
set_taxonomy.Rd

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.

Value

A tibble with the requested columns added/reformatted.

Details

Examples of specificEphithet:

  • If scientificName is Abies concolor, the specificEpithet is concolor.

  • If scientificName is Semisulcospira gottschei, the specificEpithet is gottschei.

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
    )
#> ⠙ Checking 1 column: scientificName
#> ✔ Checking 1 column: scientificName [310ms]
#> 
#> ⠙ Checking 2 columns: family and order
#> ✔ Checking 2 columns: family and order [617ms]
#> 
#> # A tibble: 3 × 6
#>   scientificName   latitude longitude eventDate  family         order
#>   <chr>               <dbl>     <dbl> <chr>      <chr>          <chr>
#> 1 Crinia Signifera    -35.3      149. 2010-10-14 Myobatrachidae Anura
#> 2 Crinia Signifera    -35.2      149. 2010-10-14 Myobatrachidae Anura
#> 3 Litoria peronii     -35.8      149. 2010-10-14 Hylidae        Anura