Get patterns for ambiguous taxa
This function stores the regex patterns for ambiguous taxa.
ambiguous_patterns(unknown = TRUE, uncultured = TRUE, whole_match = FALSE, name_regex = ".")
TRUE, Remove taxa with names the suggest they are placeholders for unknown taxa (e.g. "unknown ...").
TRUE, Remove taxa with names the suggest they are assigned to uncultured organisms (e.g. "uncultured ...").
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.
TRUE, add "^" to front and "$" to the back of each pattern to indicate they are to match whole words.