Package: treeDbalance
Title: Computation of 3D Tree Imbalance
Version: 1.2.0
Authors@R: c(
    person("Mareike", "Fischer", , "email@mareikefischer.de", role = "aut",
    comment = c(ORCID = "0000-0002-9429-0859")),
    person("Sophie", "Kersting", , "sophie.kersting@uni-greifswald.de", role = c("aut", "cre"),
    comment = c(ORCID = "0000-0002-1038-9246")),
    person("Luise", "Kühn", , "luise.kuehn@uni-greifswald.de", role = "aut",
    comment = c(ORCID = "0000-0002-0158-8286")),
    person("Jule", "Möller", role = "ctr")
  )
Maintainer: Sophie Kersting <sophie.kersting@uni-greifswald.de>
Description: 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).
License: GPL-3
Depends: R (>= 3.5.0)
Imports: rgl, R.matlab
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
RoxygenNote: 7.3.3
Packaged: 2026-02-24 15:49:29 UTC; AGFischer
Author: Mareike Fischer [aut] (ORCID: <https://orcid.org/0000-0002-9429-0859>),
  Sophie Kersting [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-1038-9246>),
  Luise Kühn [aut] (ORCID: <https://orcid.org/0000-0002-0158-8286>),
  Jule Möller [ctr]
Repository: CRAN
Date/Publication: 2026-02-24 18:40:02 UTC
Built: R 4.6.0; ; 2026-04-25 21:04:20 UTC; unix
