join_rooted_trees {castor}R Documentation

Join two rooted trees.

Description

Given two rooted phylogenetic trees, place one tree (tree2) onto an edge of the other tree (tree1), so that tree2 becomes a monophyletic group of the final joined tree. As a special case, this function can join two trees at their roots, i.e. so that both are disjoint monophyletic clades of the final tree, splitting at the new root.

Usage

join_rooted_trees(  tree1, 
                    tree2,
                    target_edge1,
                    target_edge_length1,
                    root_edge_length2)

Arguments

tree1

A rooted tree of class "phylo".

tree2

A rooted tree of class "phylo". This tree will become a monophyletic subclade of the final joined tree.

target_edge1

Integer, edge index in tree1 onto which tree2 is to be joined. If <=0, then this refers to the hypothetical edge leading into the root of tree1, in which case both trees will become disjoint monophyletic subclades of the final joined tree.

target_edge_length1

Numeric, length of the edge segment in tree1 from the joining-point to the next child node, i.e. how far from the child of target_edge1 should the joining occur. If target_edge1<=0, then target_edge_length1 is the distance of the root of tree1 from the final joined tree's root.

root_edge_length2

Numeric, length of the edge leading into the root of tree2, i.e. the distance from the joining point to the root of tree2.

Details

The input trees may include multi-furcations (i.e. nodes with more than 2 children) as well as mono-furcations (i.e. nodes with only one child). If any of the input trees does not have edge lengths (i.e., edge.length is NULL), then its edge lengths are assumed to all be 1.

The tips of the two input trees will become the tips of the final joined tree. The nodes of the two input trees will become nodes of the final joined tree, however one additional node will be added at the joining point. Tip labels and node labels (if available) of the joined tree are inheritted from the two input trees.

Value

A list with the following elements:

tree

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

clade1_to_clade

Integer vector of length Ntips1+Nnodes1, mapping tip/node indices of the input tree1 to tip/node indices in the final joined tree.

clade2_to_clade

Integer vector of length Ntips2+Nnodes2, mapping tip/node indices of the input tree2 to tip/node indices in the final joined tree.

Author(s)

Stilianos Louca

See Also

split_tree_at_height

Examples

# generate two random trees, include tip & node names
tree1 = generate_random_tree(list(birth_rate_intercept=1),
                             max_tips=10,
                             tip_basename="tip1.",
                             node_basename="node1.")$tree
tree2 = generate_random_tree(list(birth_rate_intercept=1),
                             max_tips=5,
                             tip_basename="tip2.",
                             node_basename="node2.")$tree

# join trees at their roots
# each subtree's root should have distance 1 from the new root
joined_tree = join_rooted_trees(tree1, 
                                tree2,
                                target_edge1=0,
                                target_edge_length1=1,
                                root_edge_length2=1)$tree

[Package castor version 1.7.0 Index]