get_all_distances_to_root: Get distances of all tips and nodes to the root.

In castor: Efficient Phylogenetics on Large Trees

Get distances of all tips and nodes to the root.

Description

Given a rooted phylogenetic tree, calculate the phylogenetic distance (cumulative branch length) of the root to each tip and node.

Usage

get_all_distances_to_root(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 Ntips+Nnodes, with the i-th element being the distance (cumulative branch length) of the i-th tip or node to the root. Tips are indexed 1,..,Ntips and nodes are indexed (Ntips+1),..,(Ntips+Nnodes).

Author(s)

Stilianos Louca

See Also

get_pairwise_distances

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 distances to root
all_distances = get_all_distances_to_root(tree)

# extract distances of nodes to root
node_distances = all_distances[(Ntips+1):(Ntips+tree$Nnode)]

# plot histogram of distances (across all nodes)
hist(node_distances, xlab="distance to root", ylab="# nodes", prob=FALSE);

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