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Combine genus and epithet columns into a binomial name

Source: R/taxon_combine.R
taxon_combine.Rd

Merges separate genus and epithet columns into a single binomial scientific name column, appended to the data frame. Both columns are coerced to character and joined with a single space, following standard binomial nomenclature formatting. The inverse of this operation is taxon_split.

Usage

taxon_combine(data, genus, epithet, new_column = NULL)

Arguments

data

A data frame.

genus

Column name of the genus column, supplied either unquoted (genus) or quoted ("genus").

epithet

Column name of the specific epithet column, supplied either unquoted (epithet) or quoted ("epithet").

new_column

Optional. Unquoted or quoted name for the combined output column. Default is "scientific_name".

Value

The input data frame with one additional character column appended, named according to new_column, containing values of the form "<genus> <epithet>". The original genus and epithet columns are retained. Rows where either input column is NA will produce "NA <epithet>" or "<genus> NA" in the output column.

Details

No validation of genus or epithet values is performed. Use taxon_cleaner to standardize formatting and remove uncertain names before combining. The resulting binomial column can be passed directly to taxon_add for higher rank look-ups or to italicize for formatted ggplot2 labels.

See also

taxon_split for splitting a binomial name column back into separate genus and epithet columns,

taxon_cleaner for standardising genus and epithet columns before combining,

taxon_validate for validating the combined binomial name against ITIS and GBIF,

taxon_add for looking up higher taxonomic ranks from the combined binomial name,

italicize for formatting the combined name for ggplot2 display.

Examples

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

# Combine with default output column name
taxon_combine(df, genus = genus, epithet = epithet)
#>      genus epithet scientific_name
#> 1     Homo sapiens    Homo sapiens
#> 2 Panthera     leo    Panthera leo
#> 3    Canis   lupus     Canis lupus

# Use a custom output column name
taxon_combine(df, genus = genus, epithet = epithet,
              new_column = "binomial")
#>      genus epithet     binomial
#> 1     Homo sapiens Homo sapiens
#> 2 Panthera     leo Panthera leo
#> 3    Canis   lupus  Canis lupus

# NA in either column is propagated as a string
df_na <- data.frame(
  genus   = c("Homo", NA, "Canis"),
  epithet = c("sapiens", "leo", NA)
)
taxon_combine(df_na, genus = genus, epithet = epithet)
#>   genus epithet scientific_name
#> 1  Homo sapiens    Homo sapiens
#> 2  <NA>     leo          NA leo
#> 3 Canis    <NA>        Canis NA