roots: Get root taxa

In metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

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")

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.

Value

'character'

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")

metacoder documentation built on April 4, 2023, 9:08 a.m.