get_all_node_depths: Get the phylogenetic depth of each node in a tree.

In castor: Efficient Phylogenetics on Large Trees

Get the phylogenetic depth of each node in a tree.

Description

Given a rooted phylogenetic tree, calculate the phylogenetic depth of each node (mean distance to its descending tips).

Usage

get_all_node_depths(tree, as_edge_count=FALSE)

Arguments

tree	A rooted tree of class "phylo". The root is assumed to be the unique node with no incoming edge.
as_edge_count	Logical, specifying whether distances should be counted in number of edges, rather than cumulative edge length. This is the same as if all edges had length 1.

Details

If tree$edge.length is missing, then every edge in the tree is assumed to be of length 1. The tree may include multi-furcations as well as mono-furcations (i.e. nodes with only one child). The asymptotic average time complexity of this function is O(Nedges), where Nedges is the number of edges in the tree.

Value

A numeric vector of size Nnodes, with the i-th element being the mean distance of the i-th node to all of its tips.

Author(s)

Stilianos Louca

See Also

get_all_distances_to_root

Examples

# generate a random tree
Ntips = 1000
tree = generate_random_tree(list(birth_rate_intercept=1, 
                            	 death_rate_intercept=0.5),
                            max_tips=Ntips)$tree

# calculate node phylogenetic depths
node_depths = get_all_node_depths(tree)

# plot histogram of node depths
hist(node_depths, xlab="phylogenetic depth", ylab="# nodes", prob=FALSE);

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