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: 1.0.0
Imports: stats, ape, Rcpp, rstackdeque
LinkingTo: Rcpp
Suggests: testthat, knitr, rmarkdown, markdown
Published: 2022-09-20
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_1.0.0.tar.gz
Windows binaries: r-devel: SiPhyNetwork_1.0.0.zip, r-release: SiPhyNetwork_1.0.0.zip, r-oldrel: SiPhyNetwork_1.0.0.zip
macOS binaries: r-release (arm64): SiPhyNetwork_1.0.0.tgz, r-oldrel (arm64): SiPhyNetwork_1.0.0.tgz, r-release (x86_64): SiPhyNetwork_1.0.0.tgz, r-oldrel (x86_64): SiPhyNetwork_1.0.0.tgz

Linking:

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