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: | 1.1.0 |
| Depends: | ape |
| Imports: | Rcpp (≥ 1.0.2), apTreeshape, graphics, methods |
| LinkingTo: | Rcpp, RcppArmadillo |
| Suggests: | knitr, rmarkdown, testthat |
| Published: | 2021-03-02 |
| 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 |
| Reference manual: | treeducken.pdf |
| Vignettes: |
Cophylogenetic simulation |
| Package source: | treeducken_1.1.0.tar.gz |
| Windows binaries: | r-devel: treeducken_1.1.0.zip, r-release: treeducken_1.1.0.zip, r-oldrel: treeducken_1.1.0.zip |
| macOS binaries: | r-release (arm64): treeducken_1.1.0.tgz, r-oldrel (arm64): treeducken_1.1.0.tgz, r-release (x86_64): treeducken_1.1.0.tgz, r-oldrel (x86_64): treeducken_1.1.0.tgz |
| Old sources: | treeducken archive |
Please use the canonical form https://CRAN.R-project.org/package=treeducken to link to this page.