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Find taxa with ambiguous names, such as "unknown" or "uncultured".
is_ambiguous( taxon_names, unknown = TRUE, uncultured = TRUE, name_regex = ".", ignore_case = TRUE )
TRUE/FALSE vector corresponding to taxon_names
taxon_names
A taxmap object
taxmap
If TRUE, Remove taxa with names the suggest they are placeholders for unknown taxa (e.g. "unknown ...").
TRUE
If 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.
If TRUE, dont consider the case of the text when determining a match.
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.
is_ambiguous(c("unknown", "uncultured", "homo sapiens", "kfdsjfdljsdf"))
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