CRAN/E | SiPhyNetwork

SiPhyNetwork

A Phylogenetic Simulator for Reticulate Evolution

Installation

About

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.

Key Metrics

Version 1.1.0
Published 2023-04-14 228 days ago
Needs compilation? yes
License GPL-3
CRAN checks SiPhyNetwork results

Downloads

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Maintainer

Maintainer

Joshua Justison

justisnojo@gmail.com

Authors

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)

Material

README
NEWS
Reference manual
Package source

Vignettes

Introduction

macOS

r-devel

arm64

r-release

arm64

r-oldrel

arm64

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

SiPhyNetwork archive

Imports

stats
ape
Rcpp
rstackdeque
lifecycle

Suggests

testthat
knitr
rmarkdown
markdown

LinkingTo

Rcpp