reorder_tree_edges: Reorder tree edges in preorder or postorder.

In castor: Efficient Phylogenetics on Large Trees

Reorder tree edges in preorder or postorder.

Description

Given a rooted tree, this function reorders the rows in tree$edge so that they are listed in preorder (root–>tips) or postorder (tips–>root) traversal.

Usage

reorder_tree_edges(tree, root_to_tips=TRUE, 
                   depth_first_search=TRUE,
                   index_only=FALSE)

Arguments

tree	A rooted tree of class "phylo". The root is assumed to be the unique node with no incoming edge.
root_to_tips	Logical, specifying whether to sort edges in preorder traversal (root–>tips), rather than in postorder traversal (tips–>roots).
depth_first_search	Logical, specifying whether the traversal (or the reversed traversal, if root_to_tips is FALSE) should be in depth-first-search format rather than breadth-first-search format.
index_only	Whether the function should only return a vector listing the reordered row indices of the edge matrix, rather than a modified tree.

Details

This function does not change the tree structure, nor does it affect tip/node indices and names. It merely changes the order in which edges are listed in the matrix tree$edge, so that edges are listed in preorder or postorder traversal. Preorder traversal guarantees that each edge is listed before any of its descending edges. Likewise, postorder guarantees that each edge is listed after any of its descending edges.

With options root_to_tips=TRUE and depth_first_search=TRUE, this function is analogous to the function reorder in the ape package with option order="cladewise".

The tree can include multifurcations (nodes with more than 2 children) as well as monofurcations (nodes with 1 child). This function has asymptotic time complexity O(Nedges).

Value

If index_only==FALSE, a tree object of class "phylo", with the rows in edge reordered such that they are listed in direction root–>tips (if root_to_tips==TRUE) or tips–>root. The vector tree$edge.length will also be updated in correspondence. Tip and node indices and names remain unchanged.

If index_only=TRUE, an integer vector (X) of size Nedges, listing the reordered row indices of tree$edge, i.e. such that tree$edge[X,] would be the reordered edge matrix.

Author(s)

Stilianos Louca

See Also

get_tree_traversal_root_to_tips

Examples

## Not run: 
# generate a random tree
tree = generate_random_tree(list(birth_rate_factor=1), max_tips=100)$tree

# get new tree with reordered edges
postorder_tree = reorder_tree_edges(tree, root_to_tips=FALSE)

## End(Not run)

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