metacoder (version 0.3.7)

roots: Get root taxa

Description

Return the root taxa for a [taxonomy()] or [taxmap()] object. Can also be used to get the roots of a subset of taxa.

obj$roots(subset = NULL, value = "taxon_indexes")
roots(obj, subset = NULL, value = "taxon_indexes")

Value

`character`

Arguments

obj

The [taxonomy()] or [taxmap()] object containing taxon information to be queried.

subset

Taxon IDs, TRUE/FALSE vector, or taxon indexes to find roots for. Default: All taxa in `obj` will be used. Any variable name that appears in [all_names()] can be used as if it was a vector on its own.

value

What data to return. This is usually the name of column in a table in `obj$data`. Any result of `all_names(obj)` can be used, but it usually only makes sense to data that corresponds to taxa 1:1, such as [taxon_ranks()]. By default, taxon indexes are returned.

See Also

Other taxonomy indexing functions: branches(), internodes(), leaves(), stems(), subtaxa(), supertaxa()

Examples

# Return indexes of root taxa
roots(ex_taxmap)

# Return indexes for a subset of taxa
roots(ex_taxmap, subset = 2:17)

# Return something besides taxon indexes
roots(ex_taxmap, value = "taxon_names")