TreeDist: Distances Between Phylogenetic Trees

Implements measures of tree similarity, including information-based generalized Robinson-Foulds distances (Phylogenetic Information Distance, Clustering Information Distance, Matching Split Information Distance; Smith, 2020) <doi:10.1093/bioinformatics/btaa614>; Jaccard-Robinson-Foulds distances (Bocker et al. 2013) <doi:10.1007/978-3-642-40453-5_13>, including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>; the Matching Split Distance (Bogdanowicz & Giaro 2012) <doi:10.1109/TCBB.2011.48>; Maximum Agreement Subtree distances; the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the Nearest Neighbour Interchange (NNI) distance, approximated per Li et al. (1996) <doi:10.1007/3-540-61332-3_168>. Calculates the median of a set of trees under any distance metric.

Version:	1.1.1
Depends:	R (≥ 3.4.0), stats
Imports:	ape (≥ 5.0), colorspace, memoise, phangorn (≥ 2.2.1), TreeTools (≥ 1.1.0)
LinkingTo:	Rcpp
Suggests:	bookdown, cluster, kdensity, knitr, MASS, Quartet, rmarkdown, Rcpp, Rdpack, testthat, Ternary (≥ 1.1.2), TreeDistData (> 0.1.0), TreeSearch, vdiffr
Published:	2020-07-10
Author:	Martin R. Smith [aut, cre, cph, prg], Roy Jonker [prg, cph], Yong Yang [ctb, cph], Yi Cao [ctb, cph]
Maintainer:	Martin R. Smith <martin.smith at durham.ac.uk>
BugReports:	https://github.com/ms609/TreeDist/issues
License:	GPL (≥ 3)
Copyright:	Incorporates Jonker-Volgenant Linear Assignment Problem implementation by Roy Jonker, modified by Yong Yang after Yi Cao.
URL:	https://ms609.github.io/TreeDist, https://github.com/ms609/TreeDist
NeedsCompilation:	yes
SystemRequirements:	C++11
Language:	en-GB
Citation:	TreeDist citation info
Materials:	NEWS
CRAN checks:	TreeDist results

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