extend_tree_to_height {castor}R Documentation

Extend a rooted tree up to a specific height.

Description

Given a rooted phylogenetic tree and a specific distance from the root (“new height”), elongate terminal edges (i.e. leading into tips) as needed so that all tips have a distance from the root equal to the new height. If a tip already extends beyond the specified new height, its incoming edge remains unchanged.

Usage

extend_tree_to_height(tree, new_height=NULL)

Arguments

tree

A rooted tree of class "phylo". The root is assumed to be the unique node with no incoming edge.

new_height

Numeric, specifying the phylogenetic distance from the root to which tips are to be extended. If NULL or negative, then it is set to the maximum distance of any tip from the root.

Details

The input tree may include multi-furcations (i.e. nodes with more than 2 children) as well as mono-furcations (i.e. nodes with only one child). All tip, edge and node indices remain unchanged. This function provides a quick-and-dirty way to make a tree ultrametric, or to correct small numerical inaccuracies in supposed-to-be ultrametric trees.

Value

A list with the following elements:

tree

A new rooted tree of class "phylo", representing the extended tree.

max_extension

Numeric. The largest elongation added to a terminal edge.

Author(s)

Stilianos Louca

See Also

trim_tree_at_height

Examples

# generate a random non-ultrametric tree
tree = generate_random_tree(list(birth_rate_intercept=1,death_rate_intercept=0.5),
                            max_time=1000,
                            coalescent=FALSE)$tree
                            
# print min & max distance from root
span = get_tree_span(tree)
cat(sprintf("Min & max tip height = %g & %g\n",span$min_distance,span$max_distance))

# make tree ultrametric by extending terminal edges
extended = extend_tree_to_height(tree)$tree

# print new min & max distance from root
span = get_tree_span(extended)
cat(sprintf("Min & max tip height = %g & %g\n",span$min_distance,span$max_distance))

[Package castor version 1.6.8 Index]