metacoder (version 0.1.2)

subtaxa: Get all subtaxa of a taxon

Description

Return the taxon IDs or taxon_data indexes of all subtaxa in an object of type taxmap

Usage

subtaxa(obj, subset = NULL, recursive = TRUE, simplify = FALSE, include_input = FALSE, index = FALSE)

Arguments

obj

(taxmap) The taxmap object containing taxon information to be queried.

subset

(character) taxon_ids or indexes of taxon_data for which supertaxa will be returned. Default: All taxa in obj will be used.

recursive

(logical) If FALSE, only return the subtaxa one level bwlow the target taxa. If TRUE, return all the subtaxa of every subtaxa, etc.

simplify

(logical) If TRUE, then combine all the results into a single vector of unique values.

include_input

(logical) If TRUE, the input taxa are included in the output

index

(logical) If TRUE, return the indexes of supertaxa in taxon_data instead of taxon_ids

Value

If simplify = FALSE, then a list of vectors are returned corresponding to the target argument. If simplify = TRUE, then the unique values are returned in a single vector.

See Also

Other taxmap taxonomy functions: obs, roots, supertaxa

Examples

## Not run: 
# subtaxa(contaminants, subset = 1:10)## End(Not run)