is_ambiguous {metacoder}

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"))