Split a binomial name column into genus and epithet

Splits a binomial scientific name column into separate genus and epithet columns, appended to the data frame. The inverse of this operation is taxon_combine. Only values matching strict binomial format ("Genus epithet") are split; non-conforming values produce NA in both output columns.

Usage

taxon_split(data, column, genus = NULL, epithet = NULL, drop_na = FALSE)

Arguments

data

A data frame.

column

Column name of the binomial name column to split, supplied either unquoted (scientific_name) or quoted ("scientific_name").

genus

Optional. Name for the genus output column. Default is <column>_genus.

epithet

Optional. Name for the epithet output column. Default is <column>_epithet.

drop_na

Logical. If TRUE, rows where splitting produces NA — including non-conforming names — are dropped. Default is FALSE.

Value

The input data frame with two additional character columns appended, named according to genus and epithet. The original column is retained. Values that do not match the expected binomial format produce NA in both output columns.

Details

Splitting is performed by splitting on the first space. A value is considered a valid binomial if it matches the pattern "^[A-Z][a-z]+ [a-z]+$" — an initial-capitalised genus followed by a single lowercase epithet, separated by one space. Values with authorship, infraspecific ranks, uncertainty markers (cf., sp.), or extra whitespace will not match and produce NA. Use taxon_cleaner to standardise formatting before splitting.

See also

taxon_combine for merging separate genus and epithet columns into a binomial name,

taxon_cleaner for standardising binomial name formatting before splitting,

taxon_validate for validating split columns against ITIS and GBIF,

taxon_add for appending higher taxonomic rank columns after splitting.

Examples

df <- data.frame(
  scientific_name = c("Homo sapiens", "Panthera leo", "Canis lupus")
)

# Split with default output column names
taxon_split(df, column = scientific_name)
#>   scientific_name scientific_name_genus scientific_name_epithet
#> 1    Homo sapiens                  Homo                 sapiens
#> 2    Panthera leo              Panthera                     leo
#> 3     Canis lupus                 Canis                   lupus

# Use custom output column names
taxon_split(df, column = scientific_name,
            genus = "gen", epithet = "sp")
#>   scientific_name      gen      sp
#> 1    Homo sapiens     Homo sapiens
#> 2    Panthera leo Panthera     leo
#> 3     Canis lupus    Canis   lupus

# Non-conforming values produce NA in both output columns
df_mixed <- data.frame(
  scientific_name = c("Homo sapiens", "Canis cf. lupus",
                      "Ursus sp.", "panthera leo")
)
taxon_split(df_mixed, column = scientific_name)
#>   scientific_name scientific_name_genus scientific_name_epithet
#> 1    Homo sapiens                  Homo                 sapiens
#> 2 Canis cf. lupus                  <NA>                    <NA>
#> 3       Ursus sp.                  <NA>                    <NA>
#> 4    panthera leo                  <NA>                    <NA>

# Drop rows that fail to split
taxon_split(df_mixed, column = scientific_name, drop_na = TRUE)
#>   scientific_name scientific_name_genus scientific_name_epithet
#> 1    Homo sapiens                  Homo                 sapiens