imbalProfile {treeDbalance}

Calculation of 3D imbalance profiles

Description

imbalProfile - Calculates the database for a 3D imbalance profile of a 3D tree in phylo3D format for any of the four node imbalance approaches: relative centroid distance, expanded relative centroid distance, centroid angle, or minimal centroid angle. It is also used as a basis to visualize the imbalance in a 3D plot, i.e., functions plotImbalPhylo3D and addImbalPhylo3D.
The profile is computed with regards to the z-coordinate (height), path length to the root, and path length to the nearest descendant leaf of the nodes.
The accuracy can be determined by defining the maximal section length max.seclen, which means that an edge with length l will be subdivided ceiling(l/max.seclen)-1 times into parts of equal length and all subdividing nodes will be analyzed for their node imbalance. For example, an edge (p,v) of length 3 with a maximal section length of 1 would be subdivided twice and would then be evaluated for three points in total: for v itself and for the two subdivisions at 1/3 and 2/3 of the edge length.

Usage

imbalProfile(tree, imbal_type, max.seclen)

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.

imbal_type

Specifies which node imbalance measurement should be used. Available are:
"A" - centroid angle
"alpha" - minimal centroid angle
"M" - expanded relative centroid distance
"mu" - relative centroid distance

max.seclen

Numeric value >0 that specifies the maximal section length.

Value

imbalProfile Numeric matrix with five columns. The rows each represent the values of a single tree node or edge subdivision. The first column contains the z-coordinate (height), the second the root path length, the third the (nearest) descendant leaf path length, and the fourth the imbalance value. The fifth column stores the number of the corresponding edge.

Author(s)

Sophie Kersting

Examples

tree <- treeDbalance::extendPhylo(treeDbalance::example3Dtrees$bean09)
imbalProfile(tree, imbal_type="mu", max.seclen=1)