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.
The goal of SiPhyNetwork is to generate Phylogenetic networks in a process-based manner. SiPhyNetwork considers a birth-death-hybridization proccess for simulating Networks. We allow for hybridization to be lineage generative, lineage degenerative, and lineage neutral.
You can install the development version from GitHub with:
# install.packages("devtools")
devtools::install_github("jjustison/SiPhyNetwork")
See the Rmarkdown labelled Introduction.rmd in the vignette folder to see how to use the package