metacoder (version 0.3.7)

ambiguous_synonyms: Get patterns for ambiguous taxa

Description

This function stores the regex patterns for ambiguous taxa.

Usage

ambiguous_synonyms(
  unknown = TRUE,
  uncultured = TRUE,
  regex = TRUE,
  case_variations = FALSE
)

Arguments

unknown

If TRUE, include names that suggest they are placeholders for unknown taxa (e.g. "unknown ...").

uncultured

If TRUE, include names that suggest they are assigned to uncultured organisms (e.g. "uncultured ...").

regex

If TRUE, includes regex syntax to make matching things like spaces more robust.

case_variations

If TRUE, include variations of letter case.