inherit_taxonomies: Inherit ancestral taxonomies from a phylogeny.

In castor: Efficient Phylogenetics on Large Trees

Inherit ancestral taxonomies from a phylogeny.

Description

Given a rooted tree and taxon names associated with some nodes and/or tips, infer the inherited taxonomic paths for all tips and/or nodes by concatenating the ancestral taxon names. Tip/node taxon names can be specified as separate vectors or taken from the tip/node labels stored in the tree itself.

Usage

inherit_taxonomies(tree,
                   tip_taxa      = NULL,
                   node_taxa     = NULL,
                   delimiter     = ";",
                   only_proper   = FALSE,
                   halt          = "last",
                   strict_proper = TRUE,
                   focal_tips    = NULL,
                   focal_nodes   = NULL)

Arguments

tree	A rooted tree of class "phylo".
tip_taxa	Optional character vector of length Ntips, listing taxon names for the tips. These will be appended to the inherited taxonomies of the tips. If NULL, then tip labels are used as taxon names. If you don't want any taxon names associated with tips, pass an empty vector. Some elements in tip_taxa may be ""/NULL/NA.
node_taxa	Optional character vector of length Nnodes, listing taxon names for the nodes. If NULL, then node labels are assumed to be taxon names. Some elements in node_taxa may be ""/NULL/NA.
delimiter	Character, the delimiter to use between taxonomic levels (e.g., ";" for SILVA taxonomies)
only_proper	Logical, whether to only include proper taxa in the inferred taxonomies. See option strict_proper on how proper taxa are defined.
halt	Character, specifying when to halt accumulating taxon levels, moving from root to tips. Options are "last" (halt after the last non-empty taxon, i.e., don't skip any levels), "last_proper" (halt at the last properly name taxon, including the latter), "first_improper" (halt at the first improperly named non-empty taxon, not including the latter) and "first_empty" (halt at the first empty taxon).
strict_proper	Logical, specifying whether to define taxa as proper in the strict sense, i.e., only if the taxon name is a properly encoded taxon name (i.e., contains no numeric digits, dashes or "candidatus"). If FALSE, then a taxon is considered proper as long as any of the descendants are proper in the strict sense; for example, the taxon "WOR-3" would be considered proper if one of its descending clades has taxon name "Hydrothermia".
focal_tips	Optional specification of tips to focus on. Either a character vector listing tip names, or an integer vector listing tip indices. If NULL, inherited taxonomies will be returned for all tips.
focal_nodes	Optional specification of nodes to focus on. Either a character vector listing node names, or an integer vector listing node indices. If NULL, inherited taxonomies will be returned for all nodes.

Details

This function may be used for example to infer taxonomic paths of new genomes placed on a phylogeny/taxonomy such as the GTDB. Some taxa may be empty (""), i.e., not all tips/nodes are expected to have taxon names; empty taxa are never included in the returned taxonomies, not even as placeholders.

Value

A named list with the following elements:

• tip_taxonomies: Character vector of length Ntips (if focal_tips=NULL) or of the same length as focal_tips, listing the inferred "inheritted" taxonomies at the tips.

• node_taxonomies: Character vector of length Nnodes (if focal_nodes=NULL) or of the same length as focal_nodes, listing the inferred "inheritted" taxonomies at each node.

• tip_levels: Integer vector of the same length as tip_taxonomies, listing the number of concatenated taxonomic levels for each inferred tip taxonomy. Note that each taxon name is counted once, even if it consists of multiple levels; for example, if a node has taxon name "WOR-3; Hydrothermia" then any descending taxonomies will count this taxon as one level.

• node_levels: Integer vector of the same length as node_taxonomies, listing the number of concatenated taxonomic levels for each inferred node taxonomy, similarly to tip_taxonomies.

Author(s)

Stilianos Louca

See Also

place_tips_taxonomically, consensus_taxonomies

Examples

# generate a random tree
tree = generate_random_tree(list(birth_rate_factor=0.1), max_tips=7)$tree

# define a character vector storing hypothetical node taxa
node_taxa = paste("taxon.",seq_len(tree$Nnode),sep="")

# infer inheritted taxonomies for all tips
inheritted = castor::inherit_taxonomies(tree, node_taxa = node_taxa)
print(inheritted$tip_taxonomies)

castor documentation built on Aug. 5, 2026, 1:08 a.m.