get_tree_span: Get min and max distance of any tip to the root.

In castor: Efficient Phylogenetics on Large Trees

Get min and max distance of any tip to the root.

Description

Given a rooted phylogenetic tree, calculate the minimum and maximum phylogenetic distance (cumulative branch length) of any tip from the root.

Usage

get_tree_span(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 named list with the following elements:

min_distance	Minimum phylogenetic distance that any of the tips has to the root.
max_distance	Maximum phylogenetic distance that any of the tips has to the root.

Author(s)

Stilianos Louca

See Also

get_pairwise_distances

Examples

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

# calculate min & max tip distances from root
tree_span = get_tree_span(tree)
cat(sprintf("Tip min dist = %g, max dist = %g\n",
            tree_span$min_distance,
            tree_span$max_distance))

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