extract_taxon: Extract a taxon by name from a 'phylotax' object

In brendanf/phylotax: Refine taxonomic assignment of environmental sequences using a taxonomic tree

Description

For a phylotax object with a tree, the taxon is extracted based on node annotations. If more than one node is annotated as belonging to the given taxon (i.e., it seems to be para/polyphyletic in the tree) then the "correct" clade can be chosen by providing "true members"; the result will only include the clade(s) which contain the "true members".

Usage

extract_taxon(phylotax, taxon, true_members = NULL)

Arguments

phylotax	(phylotax object) The object to extract from.
taxon	(character string) The name of the taxon to extract.
true_members	(character) (optional) Labels of sequences known to belong in the taxon.

Details

If no tree is present (meaning the phylotax object was generated using lca_consensus()), and also for sequences which are not present in the tree, then the chosen taxon is simply extracted using the assigned taxonomy.

Value

A phylotax object containing only the specified taxon.

brendanf/phylotax documentation built on March 3, 2021, 2:21 p.m.