treeDbalance - Computation of 3D Tree Imbalance
The main goal of the R package 'treeDbalance' is to
provide functions for the computation of several measurements
of 3D node imbalance and their respective 3D tree imbalance
indices, as well as to introduce the new 'phylo3D' format for
rooted 3D tree objects. Moreover, it encompasses an example
dataset of 3D models of 63 beans in 'phylo3D' format. Please
note that this R package was developed alongside the project
described in the manuscript 'Measuring 3D tree imbalance of
plant models using graph-theoretical approaches' by M. Fischer,
S. Kersting, and L. Kühn (2023) <arXiv:2307.14537>, which
provides precise mathematical definitions of the measurements.
Furthermore, the package contains several helpful functions,
for example, some auxiliary functions for computing the
ancestors, descendants, and depths of the nodes, which ensures
that the computations can be done in linear time. Most
functions of 'treeDbalance' require as input a rooted tree in
the 'phylo3D' format, an extended 'phylo' format (as introduced
in the R package 'ape' 1.9 in November 2006). Such a 'phylo3D'
object must have at least two new attributes next to those
required by the 'phylo' format: 'node.coord', the coordinates
of the nodes, as well as 'edge.weight', the literal weight or
volume of the edges. Optional attributes are 'edge.diam', the
diameter of the edges, and 'edge.length', the length of the
edges. For visualization purposes one can also specify
'edge.type', which ranges from normal cylinder to bud to leaf,
as well as 'edge.color' to change the color of the edge
depiction. This project was supported by the joint research
project DIG-IT! funded by the European Social Fund (ESF),
reference: ESF/14-BM-A55-0017/19, and the Ministry of
Education, Science and Culture of Mecklenburg-Western
Pomerania, Germany, as well as by the the project ArtIGROW,
which is a part of the WIR!-Alliance 'ArtIFARM – Artificial
Intelligence in Farming' funded by the German Federal Ministry
of Education and Research (FKZ: 03WIR4805).
