Detect the taxonomic rank of a column

Infers the taxonomic rank (e.g. species, genus, family) of one or more columns based on column name pattern matching. Returns a named character vector of detected ranks, one per input column. Useful for verifying rank assignments before calling taxon_sort or taxon_add.

Usage

taxon_rank(data, columns)

Arguments

data

A data frame.

columns

Column name or c() of column names to check, supplied either unquoted (genus) or quoted ("genus").

Value

A named character vector the same length as columns, where names are the input column names and values are the detected rank as a lowercase string (e.g. "family", "genus"). Returns NA for any column whose name does not match a recognised taxonomic rank pattern.

Details

Detection uses a two-tier approach applied to the lowercased column name:

1. Strong match — the column name contains a full taxonomic keyword: scientificname, species, genus, family, order, class, phylum, kingdom, or taxon. Strong patterns are checked first and take priority.

2. Weak match — for columns not assigned by a strong match, substrings of length 3–5 derived from the strong keywords are checked. The first matching keyword is assigned.

Detection is based on column names only — column values are not inspected. For content-based detection across all columns in a data frame, use taxon_column instead.

See also

taxon_column for detecting taxonomic columns across an entire data frame using both name and content patterns,

taxon_sort for sorting columns into standard taxonomic rank order,

taxon_add for appending higher taxonomic rank columns,

taxon_validate for validation, which uses this function internally to detect column rank.

Examples

df <- data.frame(
  genus       = character(),
  family_name = character(),
  my_order    = character(),
  site        = character()
)

# Detect rank of a single column
taxon_rank(df, genus)
#>   genus 
#> "genus" 

# Detect ranks of multiple columns
taxon_rank(df, c(genus, family_name, my_order))
#>       genus family_name    my_order 
#>     "genus"    "family"     "order" 

# NA returned for columns with no recognisable rank pattern
taxon_rank(df, c(genus, site))
#>   genus    site 
#> "genus"      NA