is_stem: Test if taxa are stems

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

Test if taxa are stems

Description

Test if taxa are stems in a [taxonomy()] or [taxmap()] object. Stems are taxa from the [roots()] taxa to the first taxon with more than one subtaxon. These can usually be filtered out of the taxonomy without removing any information on how the remaining taxa are related.

obj$is_stem()
is_stem(obj)

Arguments

obj	The [taxonomy()] or [taxmap()] object.

Value

A 'logical' of length equal to the number of taxa.

See Also

Other taxonomy data functions: classifications(), id_classifications(), is_branch(), is_internode(), is_leaf(), is_root(), map_data_(), map_data(), n_leaves_1(), n_leaves(), n_subtaxa_1(), n_subtaxa(), n_supertaxa_1(), n_supertaxa(), taxon_ids(), taxon_indexes(), taxon_names(), taxon_ranks()

Examples

# Test which taxon IDs correspond to stems
is_stem(ex_taxmap)

# Filter out stems
filter_taxa(ex_taxmap, ! is_stem)

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