ambiguous_patterns: Get patterns for ambiguous taxa

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

Get patterns for ambiguous taxa

Description

This function stores the regex patterns for ambiguous taxa.

Usage

ambiguous_patterns(
  unknown = TRUE,
  uncultured = TRUE,
  case_variations = FALSE,
  whole_match = FALSE,
  name_regex = "."
)

Arguments

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 ...").
case_variations	If TRUE, include variations of letter case.
whole_match	If TRUE, add "^" to front and "$" to the back of each pattern to indicate they are to match whole words.
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.

metacoder documentation built on April 4, 2023, 9:08 a.m.