treeducken: Nested Phylogenetic Tree Simulator

Simulates nested phylogenetic trees (gene trees in species tree, symbiont trees in host trees) using birth-death processes and transfers between lineages. Simulations of gene trees within species trees are performed using a three-tree model with species trees, locus trees, and gene trees. The cophylogenetic birth-death process is used to simulate sets of host and symbiont trees with extant associations between tips. For more information about the three-tree model see: Mallo et al. (2015) <doi:10.1093/sysbio/syv082>, Rasmussen and Kellis (2012) <doi:10.1101/gr.123901.111>.

Version: 1.0.0
Depends: ape
Imports: Rcpp (≥ 1.0.2), apTreeshape, graphics, methods
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, rmarkdown, testthat
Published: 2020-10-06
Author: Wade Dismukes [aut, cre], Tracy A. Heath [aut], Josh Justison [ctb], Damien de Vienne [ctb], Liam Revell [ctb], Emmanuel Paradis [ctb], Klaus Schliep [ctb], Ben Bolker [ctb], Luke J. Harmon [ctb], Joseph W. Brown [ctb]
Maintainer: Wade Dismukes <wade.dismukes at gmail.com>
License: GPL-3
NeedsCompilation: yes
SystemRequirements: C++11
Materials: README NEWS
CRAN checks: treeducken results

Downloads:

Reference manual: treeducken.pdf
Vignettes: Cophylogenetic simulation
Package source: treeducken_1.0.0.tar.gz
Windows binaries: r-devel: treeducken_1.0.0.zip, r-release: treeducken_1.0.0.zip, r-oldrel: treeducken_1.0.0.zip
macOS binaries: r-release: treeducken_1.0.0.tgz, r-oldrel: treeducken_1.0.0.tgz

Linking:

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