A simulator for reticulate evolution under a birth-death-hybridization process. Here the birth-death process is extended to consider reticulate Evolution by allowing hybridization events to occur. The general purpose simulator allows the modeling of three different reticulate patterns: lineage generative hybridization, lineage neutral hybridization, and lineage degenerative hybridization. Users can also specify hybridization events to be dependent on a trait value or genetic distance. We also extend some phylogenetic tree utility and plotting functions for networks. We allow two different stopping conditions: simulated to a fixed time or number of taxa. When simulating to a fixed number of taxa, the user can simulate under the Generalized Sampling Approach that properly simulates phylogenies when assuming a uniform prior on the root age.
| Version: | 1.1.0 |
| Imports: | stats, ape, Rcpp, rstackdeque, lifecycle |
| LinkingTo: | Rcpp |
| Suggests: | testthat, knitr, rmarkdown, markdown |
| Published: | 2023-04-14 |
| DOI: | 10.32614/CRAN.package.SiPhyNetwork |
| Author: | Joshua Justison [aut, cre, cph], Claudia Solis-Lemus [aut, cph], Tracy A. Heath [aut, cph], Klaus Schliep [cph] (modified code from ape in 'write.net.R' and 'read.net.R'. Crediting original copyright holder), Emmanuel Paradis [cph] (modified code from ape in 'write.net.R' and 'read.net.R'. Crediting original copyright holder), Daniel Lawson [cph] (modified code from ape in 'write.net.R' and 'read.net.R'. Crediting original copyright holder) |
| Maintainer: | Joshua Justison <justisnojo at gmail.com> |
| License: | GPL-3 |
| NeedsCompilation: | yes |
| Materials: | README, NEWS |
| CRAN checks: | SiPhyNetwork results |
| Reference manual: | SiPhyNetwork.html , SiPhyNetwork.pdf |
| Vignettes: |
Introduction (source, R code) |
| Package source: | SiPhyNetwork_1.1.0.tar.gz |
| Windows binaries: | r-devel: SiPhyNetwork_1.1.0.zip, r-release: SiPhyNetwork_1.1.0.zip, r-oldrel: SiPhyNetwork_1.1.0.zip |
| macOS binaries: | r-release (arm64): SiPhyNetwork_1.1.0.tgz, r-oldrel (arm64): SiPhyNetwork_1.1.0.tgz, r-release (x86_64): SiPhyNetwork_1.1.0.tgz, r-oldrel (x86_64): SiPhyNetwork_1.1.0.tgz |
| Old sources: | SiPhyNetwork archive |
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