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)
<doi:10.48550/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, or functions that convert existing
formats of 3D tree models of other software into the 'phylo3D'
format. Moreover, it comprises functions to extract the
graph-theoretical topology without vertices of in- and
out-degree 1 of rooted 3D trees as well as to adapt node
enumerations to the common 'phylo' format. 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 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).
