metacoder (version 0.3.7)

branches: Get "branch" taxa

Description

Return the "branch" taxa for a [taxonomy()] or [taxmap()] object. A branch is anything that is not a root, stem, or leaf. Its the interior of the tree after the first split starting from the roots. Can also be used to get the branches of a subset of taxa.

obj$branches(subset = NULL, value = "taxon_indexes")
branches(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 used to subset the tree prior to determining branches. 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. Note that branches are determined after the filtering, so a given taxon might be a branch on the unfiltered tree, but not a branch on the filtered tree.

value

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

See Also

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

Examples

# Return indexes of branch taxa
branches(ex_taxmap)

# Return indexes for a subset of taxa
branches(ex_taxmap, subset = 2:17)
branches(ex_taxmap, subset = n_obs > 1)

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