is_ambiguous: Find ambiguous taxon names

In metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

Find ambiguous taxon names

Description

Find taxa with ambiguous names, such as "unknown" or "uncultured".

Usage

is_ambiguous(
  taxon_names,
  unknown = TRUE,
  uncultured = TRUE,
  name_regex = ".",
  ignore_case = TRUE
)

Arguments

taxon_names	A taxmap object
unknown	If TRUE, Remove taxa with names the suggest they are placeholders for unknown taxa (e.g. "unknown ...").
uncultured	If TRUE, Remove taxa with names the suggest they are assigned to uncultured organisms (e.g. "uncultured ...").
name_regex	The regex code to match a valid character in a taxon name. For example, "[a-z]" would mean taxon names can only be lower case letters.
ignore_case	If TRUE, dont consider the case of the text when determining a match.

Details

If you encounter a taxon name that represents an ambiguous taxon that is not filtered out by this function, let us know and we will add it.

Value

TRUE/FALSE vector corresponding to taxon_names

Examples

is_ambiguous(c("unknown", "uncultured", "homo sapiens", "kfdsjfdljsdf"))

metacoder documentation built on April 3, 2025, 8:39 p.m.