Package: SiPhyNetwork
Title: A Phylogenetic Simulator for Reticulate Evolution
Version: 1.1.0
Authors@R: 
    c(person("Joshua", "Justison", email = "justisnojo@gmail.com", role = c("aut", "cre","cph")),
    		person(c("Claudia","Solis-Lemus"), role=c("aut","cph")),
		person(c("Tracy","A."), "Heath", role=c("aut","cph")),
		person("Klaus", "Schliep", role = c("cph"), comment = c("modified code from ape in 'write.net.R' and 'read.net.R'. Crediting original copyright holder")),
		person("Emmanuel", "Paradis", role = c("cph"), comment = c("modified code from ape in 'write.net.R' and 'read.net.R'. Crediting original copyright holder")),
		person("Daniel", "Lawson", role = c("cph"), comment = c("modified code from ape in 'write.net.R' and 'read.net.R'. Crediting original copyright holder"))
	)
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. 
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.2.3
Suggests: testthat, knitr, rmarkdown, markdown
Imports: stats, ape, Rcpp, rstackdeque, lifecycle
VignetteBuilder: knitr
LinkingTo: Rcpp,
NeedsCompilation: yes
Packaged: 2023-04-14 19:59:56 UTC; justison
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@gmail.com>
Repository: CRAN
Date/Publication: 2023-04-14 20:10:02 UTC
Built: R 4.6.0; aarch64-apple-darwin23; 2026-04-26 01:59:25 UTC; unix
Archs: SiPhyNetwork.so.dSYM
