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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

Documentation:

Reference manual: SiPhyNetwork.pdf
Vignettes: Introduction

Downloads:

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

Linking:

Please use the canonical form https://CRAN.R-project.org/package=SiPhyNetwork 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.