makePhylo3DBalanced {treeDbalance}

Turn a rooted 3D tree into one of its balanced versions

Description

makePhylo3DBalanced - Creates a balanced version of a rooted 3D tree in phylo3D format. From the leaves of lowest depth to the root, each node is turned into a balanced node by rotating its pending subtree such that it is in line with its incoming edge. The edge and subtree lengths and weights as well as the angles between the outgoing edges of a single node (the sister edges) are left intact.
Note that this function yields only one of many possible balanced version of the given rooted 3D tree (most often the minimal tree under the aforementioned requirements is not unique).

rotate3dVec - Rotates a vector in 3D space for a given angle and rotation axis.

Usage

makePhylo3DBalanced(tree)

rotate3dVec(angle, axis, vec)

Arguments

tree

A rooted tree in phylo3D format (no special node enumeration required, except that nodes are numbered from 1 to |V| = the total number of nodes). There must be at least 2 nodes, i.e., one edge. The attributes 'node.coord' and 'edge.weight' are strictly required.

angle

Angle for the rotation.

axis

Rotation axis.

vec

Numeric vector of size 3 (3D coordinates of the vector that shall be rotated).

Value

makePhylo3DBalanced Tree in phylo3D format which is balanced with regards to all four node imbalance measurements and their corresponding imbalance indices.

rotate3dVec Numeric vector of size 3 (3D coordinates of the rotated vector).

Author(s)

Sophie Kersting, Luise Kühn

Examples

tree <- treeDbalance::extendPhylo(treeDbalance::example3Dtrees$bean22)
tree_bal <- makePhylo3DBalanced(tree)
rotate3dVec(angle = pi/2, axis = c(0,-1,0), vec = c(5,0,0)) # approx. (0,0,5)
round(rotate3dVec(angle = pi/2, axis = c(0,-1,0), vec = c(5,0,0)),15)