tree_from_taxa: Construct a rooted tree from lists of taxa.

In castor: Efficient Phylogenetics on Large Trees

Construct a rooted tree from lists of taxa.

Description

Given a collection of taxon lists, construct a rooted taxonomic tree. Each taxon list is defined by a parent name and the names of its children (i.e., immediate descendants).

Usage

tree_from_taxa(taxa)

Arguments

taxa	Named list, whose elements are character vectors, each representing a parent and its children. The element names of taxa are parents. Each element taxa[n] is a character vector listing an arbitrary number of taxon names (the children), which immediately descend from taxon names(taxa)[n].

Details

The following rules apply:

• Each taxon must appear at most once as a parent and at most once as a child.

• Any taxa found as parents but not as children, will be assumed to descend directly from the root. If only one such taxon was found, it will become the root itself.

• Any taxa found as a child but not as a parent, will become tips.

• Any parents without children will be considered tips.

• Empty parent names (i.e., "") are not allowed.

• Taxa can be specified in any arbitrary order, including breadth-first, depth-first etc.

Since the returned tree is a taxonomy, it will contain no edge lengths.

Value

A rooted tree of class "phylo".

Author(s)

Stilianos Louca

See Also

consensus_taxonomies, place_tips_taxonomically

Examples

# define a list of taxa, with taxon "A" being the root
# Taxa G, H, I, J, K, L, M, N and O will be tips
taxa = list(A = c("B","C","D"), 
            B = c("E","I"), 
            C = c("J","F"), 
            D = c("M", "N", "O"), 
            E = c("G", "H"),
            F = c("K", "L"))
tree = castor::tree_from_taxa(taxa)

castor documentation built on June 29, 2024, 9:08 a.m.