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DESCRIPTION
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DESCRIPTION
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Package: TreeTools
Title: Create, Modify and Analyse Phylogenetic Trees
Version: 1.12.0.9000
Authors@R: c(
person("Martin R.", 'Smith', role = c("aut", "cre", "cph"),
email = "martin.smith@durham.ac.uk",
comment = c(ORCID = "0000-0001-5660-1727")),
person(given = "Emmanuel", family = "Paradis", role = c("cph"),
comment = c(ORCID = "0000-0003-3092-2199")),
person(given = "Robert", family = "Noble", role = c("cph"),
comment = c(ORCID = "0000-0002-8057-4252"))
)
License: GPL (>= 3)
Copyright: Incorporates C/C++ code from 'ape' by Emmanuel Paradis
<doi:10.1093/bioinformatics/bty633> and 'RUtreebalance' by Robert Noble
<doi:10.5281/zenodo.5873857>.
Description: Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
tree rearrangement;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of split support;
plotting the position of rogue taxa (Klopfstein & Spasojevic 2019)
<doi:10.1371/journal.pone.0212942>;
calculation of ancestor-descendant relationships,
of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>,
and of tree balance (Mir et al. 2013, Lemant et al. 2022)
<doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>;
artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.
URL: https://ms609.github.io/TreeTools/, https://github.com/ms609/TreeTools/
BugReports: https://github.com/ms609/TreeTools/issues/
SystemRequirements: C++17
Depends:
R (>= 3.4.0),
ape (>= 5.6),
Imports:
bit64,
lifecycle,
colorspace,
fastmatch (>= 1.1.3),
methods,
PlotTools,
RCurl,
R.cache,
Rdpack (>= 2.3),
Suggests:
spelling,
knitr,
phangorn (>= 2.2.1),
purrr,
Rcpp (>= 1.0.8),
rlang,
rmarkdown,
testthat (>= 3.0),
vdiffr (>= 1.0.0),
Config/Needs/check: rcmdcheck
Config/Needs/coverage: covr
Config/Needs/memcheck: devtools
Config/Needs/metadata: codemeta
Config/Needs/revdeps: revdepcheck
Config/Needs/website: pkgdown
Config/testthat/parallel: false
Config/testthat/edition: 3
LinkingTo: Rcpp
RdMacros: Rdpack
LazyData: true
ByteCompile: true
Encoding: UTF-8
Language: en-GB
VignetteBuilder: knitr
RoxygenNote: 7.3.2
Roxygen: list(markdown = TRUE)