extractTopology

<code>extractTopology</code> - Extracts the topology of a rooted tree in phylo or
phylo3D format by ignoring edge subdivisions, i.e. nodes with both in- and
out-degree of 1. The nodes have to be enumerated from 1 to \(|V|\)
(otherwise use enum2_1toV()). 
The function works for trees in phylo as well as phylo3D format as existing
information on the coordinates or edge weights is dropped anyway. 
Edge lengths in the topology are based on the sum of the edge lengths of
the corresponding paths in the original tree.

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).

Sophie Kersting

treeDbalance

Computation of 3D Tree Imbalance

Mareike Fischer

Luise Kühn

Jule Möller

extractTopology function

<dl><dt>tree</dt>
<dd>A rooted tree in (extended) phylo(3D) 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.</dd></dl>

Arguments

Author

<code>extractTopology</code> - Extracts the topology of a rooted tree in phylo or
phylo3D format by ignoring edge subdivisions, i.e. nodes with both in- and
out-degree of 1. The nodes have to be enumerated from 1 to \(|V|\)
(otherwise use enum2_1toV()). 
The function works for trees in phylo as well as phylo3D format as existing
information on the coordinates or edge weights is dropped anyway. 
Edge lengths in the topology are based on the sum of the edge lengths of
the corresponding paths in the original tree.

Extract the non-3D topology of trees in phylo(3D) format — extractTopology

<dl>

<dt>tree</dt>
<dd>A rooted tree in (extended) phylo(3D) 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.</dd>

</dl>

extractTopology: Extract the non-3D topology of trees in phylo(3D) format

Description

Usage

Value

Arguments

Author

Examples