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).
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
[aut],
Sophie Kersting