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treespace: Statistical Exploration of Landscapes of Phylogenetic Trees

Tools for the exploration of distributions of phylogenetic trees. This package includes a 'shiny' interface which can be started from R using treespaceServer(). For further details see Jombart et al. (2017) <doi:10.1111/1755-0998.12676>.

Version: 1.1.4.3
Depends: R (≥ 3.4.0), ape, ade4
Imports: adegenet, adegraphics, combinat, compiler, distory, fields, htmlwidgets, MASS, methods, parallel, phangorn, phytools, Rcpp, rgl, RLumShiny, scatterD3, shiny, shinyBS, utils
LinkingTo: Rcpp
Suggests: ggplot2, igraph, knitr, pander, RColorBrewer, reshape2, rmarkdown, sf, testthat
Published: 2023-09-07
DOI: 10.32614/CRAN.package.treespace
Author: Thibaut Jombart ORCID iD [aut], Michelle Kendall ORCID iD [aut, cre], Jacob Almagro-Garcia ORCID iD [aut], Caroline Colijn ORCID iD [aut]
Maintainer: Michelle Kendall <michelle.kendall at warwick.ac.uk>
BugReports: https://github.com/thibautjombart/treespace/issues
License: MIT + file LICENSE
URL: https://cran.r-project.org/package=treespace, https://github.com/thibautjombart/treespace
NeedsCompilation: yes
Citation: treespace citation info
Materials: README, NEWS
In views: Phylogenetics
CRAN checks: treespace results [issues need fixing before 2025-09-03]

Documentation:

Reference manual: treespace.html , treespace.pdf
Vignettes: treespace worked example: Dengue trees (source)
treespace worked example: Transmission trees (source)
Exploration of landscapes of phylogenetic trees (source)
Comparing trees by tip label categories (source)

Downloads:

Package source: treespace_1.1.4.3.tar.gz
Windows binaries: r-devel: treespace_1.1.4.3.zip, r-release: treespace_1.1.4.3.zip, r-oldrel: treespace_1.1.4.3.zip
macOS binaries: r-release (arm64): treespace_1.1.4.3.tgz, r-oldrel (arm64): treespace_1.1.4.3.tgz, r-release (x86_64): treespace_1.1.4.3.tgz, r-oldrel (x86_64): treespace_1.1.4.3.tgz
Old sources: treespace archive

Reverse dependencies:

Reverse imports: mixtree

Linking:

Please use the canonical form https://CRAN.R-project.org/package=treespace to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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