treebalance: Computation of Tree (Im)Balance Indices
The aim of the 'R' package 'treebalance' is to provide functions for the computation of
a large variety of (im)balance indices for rooted trees. The package accompanies the manuscript
”Tree balance indices: a comprehensive survey” by M. Fischer, L. Herbst, S. Kersting,
L. Kuehn and K. Wicke (2021) <arXiv:2109.12281>, which gives a precise definition for the terms
'balance index' and 'imbalance index' (Section 3) and provides an overview of the terminology in
this manual (Section 2). For further information on (im)balance indices, see also
Fischer et al. (2021) <https://treebalance.wordpress.com>.
Considering both established and new (im)balance indices, 'treebalance' provides (among
others) functions for calculating the following 18 established indices: the average leaf depth,
the B1 and B2 index, the Colijn-Plazzotta rank, the normal, corrected, quadratic and equal
weights Colless index, the family of Colless-like indices, the family of I-based indices, the
Rogers J index, the Furnas rank, the rooted quartet index, the s-shape statistic, the Sackin
index, the symmetry nodes index, the total cophenetic index and the variance of leaf depths.
Additionally, we include 5 tree shape statistics that satisfy the definition of an (im)balance
index but have not been thoroughly analyzed in terms of tree balance in the literature yet.
These are: the maximum width, the maximum difference in widths, the maximal depth, the
stairs1 and the stairs2 index.
As input, most functions of 'treebalance' require a rooted (phylogenetic) tree in 'phylo' format
(as introduced in 'ape' 1.9 in November 2006). 'phylo' is used to store (phylogenetic) trees
with no vertices of out-degree one. For further information on the format we kindly refer the
reader to E. Paradis (2012) <http://ape-package.ird.fr/misc/FormatTreeR_24Oct2012.pdf>.
| Version: |
1.1.0 |
| Depends: |
R (≥ 3.5.0) |
| Imports: |
ape, memoise |
| Published: |
2021-10-17 |
| Author: |
Mareike Fischer [aut],
Lina Herbst [aut],
Sophie Kersting [aut],
Luise Kuehn [aut, cre],
Kristina Wicke [aut] |
| Maintainer: |
Luise Kuehn <treebalanceindices at gmail.com> |
| License: |
GPL-3 |
| NeedsCompilation: |
no |
| Citation: |
treebalance citation info |
| Materials: |
NEWS |
| CRAN checks: |
treebalance results |
Documentation:
Downloads:
Linking:
Please use the canonical form
https://CRAN.R-project.org/package=treebalance
to link to this page.