<?xml version="1.0" encoding="UTF-8"?>
<oai_dc:dc xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd">
  <dc:title>A Phylogenetic Simulator for Reticulate Evolution</dc:title>
  <dc:title>R package SiPhyNetwork version 1.1.0</dc:title>
  <dc:description>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. </dc:description>
  <dc:type>Software</dc:type>
  <dc:relation>Imports: stats, ape, Rcpp, rstackdeque, lifecycle</dc:relation>
  <dc:relation>LinkingTo: Rcpp,</dc:relation>
  <dc:relation>Suggests: testthat, knitr, rmarkdown, markdown</dc:relation>
  <dc:creator>Joshua Justison &lt;justisnojo@gmail.com&gt;</dc:creator>
  <dc:publisher>Comprehensive R Archive Network (CRAN)</dc:publisher>
  <dc:contributor>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)</dc:contributor>
  <dc:rights>GPL-3</dc:rights>
  <dc:date>2023-04-14</dc:date>
  <dc:format>application/tgz</dc:format>
  <dc:identifier>https://CRAN.R-project.org/package=SiPhyNetwork</dc:identifier>
  <dc:identifier>doi:10.32614/CRAN.package.SiPhyNetwork</dc:identifier>
</oai_dc:dc>
