is_ambiguous

0th

Percentile

Find ambiguous taxon names

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

Aliases
  • is_ambiguous
Examples
# NOT RUN {
is_ambiguous(c("unknown", "uncultured", "homo sapiens", "kfdsjfdljsdf"))

# }
Documentation reproduced from package metacoder, version 0.3.3, License: GPL-2 | GPL-3

Community examples

Looks like there are no examples yet.