SiPhyNetwork: A Phylogenetic Simulator for Reticulate Evolution
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 |
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