Package: treebalance
Title: Computation of Tree (Im)Balance Indices
Version: 1.1.0
Description: 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>.
Authors@R: c(person("Mareike", "Fischer", role = "aut"),
			person("Lina", "Herbst", role = "aut"),
			person("Sophie", "Kersting", role = "aut"),
            person("Luise", "Kuehn", role = c("aut","cre"), email = "treebalanceindices@gmail.com"),
			person("Kristina", "Wicke", role = "aut"))
Author: Mareike Fischer [aut],
  Lina Herbst [aut],
  Sophie Kersting [aut],
  Luise Kuehn [aut, cre],
  Kristina Wicke [aut]
Maintainer: Luise Kuehn <treebalanceindices@gmail.com>
Depends: R (>= 3.5.0)
Imports: ape, memoise
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2021-10-17 14:50:05 UTC; Luise
Repository: CRAN
Date/Publication: 2021-10-17 15:10:02 UTC
Built: R 4.1.0; ; 2021-10-18 11:48:36 UTC; unix
