merge_short_edges: Eliminate short edges in a tree by merging nodes into...

In castor: Efficient Phylogenetics on Large Trees

Eliminate short edges in a tree by merging nodes into multifurcations.

Description

Given a rooted phylogenetic tree and an edge length threshold, merge nodes/tips into multifurcations when their incoming edges are shorter than the threshold.

Usage

merge_short_edges(tree, 
                  edge_length_epsilon	= 0,
                  force_keep_tips     = TRUE,
                  new_tip_prefix      = "ex.node.tip.")

Arguments

tree	A rooted tree of class "phylo". The root is assumed to be the unique node with no incoming edge.
edge_length_epsilon	Non-negative numeric, specifying the maximum edge length for an edge to be considered “short” and thus to be eliminated. Typically 0 or some small positive number.
force_keep_tips	Logical. If TRUE, then tips are always kept, even if their incoming edges are shorter than edge_length_epsilon. If FALSE, then tips with short incoming edges are removed from the tree; in that case some nodes may become tips.
new_tip_prefix	Character or NULL, specifying the prefix to use for new tip labels stemming from nodes. Only relevant if force_keep_tips==FALSE. If NULL, then labels of tips stemming from nodes will be the node labels from the original tree (in this case the original tree should include node labels).

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). Whenever a short edge is eliminated, the edges originating from its child are elongated according to the short edge's length. The corresponding grand-children become children of the short edge's parent. Short edges are eliminated in a depth-first-search manner, i.e. traversing from the root to the tips.

Note that existing monofurcations are retained. If force_keep_tips==FALSE, then new monofurcations may also be introduced due to tips being removed.

This function is conceptually similar to the function ape::di2multi.

Value

A list with the following elements:

tree	A new rooted tree of class "phylo", containing the (potentially multifurcating) tree.
new2old_clade	Integer vector of length equal to the number of tips+nodes in the new tree, with values in 1,..,Ntips+Nnodes, mapping tip/node indices of the new tree to tip/node indices in the original tree.
new2old_edge	Integer vector of length equal to the number of edges in the new tree, with values in 1,..,Nedges, mapping edge indices of the new tree to edge indices in the original tree.
Nedges_removed	Integer. Number of edges that have been eliminated.

Author(s)

Stilianos Louca

See Also

multifurcations_to_bifurcations

Examples

# generate a random tree
Ntips = 100
tree = generate_random_tree(list(birth_rate_factor=1),max_tips=Ntips)$tree

# set some edge lengths to zero
tree$edge.length[sample.int(n=Ntips, size=10, replace=FALSE)] = 0

# print number of edges
cat(sprintf("Original tree has %d edges\n",nrow(tree$edge)))

# eliminate any edges of length zero
merged = merge_short_edges(tree, edge_length_epsilon=0)$tree

# print number of edges
cat(sprintf("New tree has %d edges\n",nrow(merged$edge)))

castor documentation built on Aug. 18, 2023, 1:07 a.m.