Normalize a kingdom string to the coarse kingdom-group vocabulary

Case-insensitive; also folds the NCBI clade and OTT kingdom names (Pseudomonadati, Archaeplastida, ...). Unrecognised, empty, or explicitly unknown values return NA, so an unknown kingdom is never a reason to reject a row. The coarse vocabulary is animalia, plantae, fungi, bacteria, archaea, chromista, protozoa and viruses; taxifydb uses it to check enrichment name expansion against a source's declared kingdoms.

Usage

normalize_kingdom_group(x)

Arguments

x

Character vector.

Value

Character vector of coarse kingdom groups (or NA).

Examples

normalize_kingdom_group(c("Animalia", "Viridiplantae", "plants", "unknown"))