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Standardize and correct species information in a datras_raw object

Source: R/clean_prune.R
correct_species.Rd

Correct selected species names, Aphia IDs, and taxonomic ranks in the CA and HL tables of a datras_raw / DATRASraw object.

Usage

correct_species(x)

Arguments

x

A datras_raw object.

Value

A datras_raw object with corrected Species, Valid_Aphia, and Rank fields in the CA and HL tables where applicable.

Details

The function is intended to harmonize species information for cases where records are better treated at genus level, where synonymous or outdated species names occur, or where taxonomic information is incomplete.

The function operates on the CA and HL components, if present and non-empty.

If the column Rank is missing, it is added and initialized as "species". Selected taxa are then reassigned to genus level by updating Species, Valid_Aphia, and Rank. In addition, a small number of species name corrections are applied.

Examples of corrections include:

  • collapsing selected taxa to genus level, for example "Dipturus" or "Gobius",

  • harmonizing alternative or inconsistent taxonomic names,

  • updating corresponding Valid_Aphia identifiers,

  • setting Rank to either "species" or "genus" as appropriate.

The function currently modifies only the CA and HL tables and leaves HH unchanged.

See also

clean_datras()

Examples

if (FALSE) { # \dontrun{
## Correct species information after reading DATRAS data
x <- correct_species(x)
} # }