treeducken

treeducken is a phylogenetic simulation package with the primary purpose of simulating host and symbiont phylogenies simultaneously using the machinery of birth-death models. This extends work on simulating cophylogenetic systems by allowing for scenarios where speciation in the host does not always imply speciation in the symbiont (Keller-Schmidt et al. 2011). This simulation also accounts for extinction in its simulation of host-symbiont systems. treeducken also can simulate under the three-tree model in a manner similar to that used in the SimPhy program (Mallo et al. 2016).

Brief usage example

Below is a quick example of how to use treeducken to simulate a set of ten host and symbiont tree sets. To do this we set a host birth rate, a host death rate, a symbiont birth rate, a symbiont death rate, a cospeciation rate, and a host expansion rate. These parameters are further described in the manuscript (in prep.) and the vignette (cophylogenetic_sim.Rmd). Finally, we have to set the number of sets we would like and the time to simulate until. Note that since this is a time-based birth-death simulation some of the host and symbiont trees will have 3 or less tips and be fairly uninteresting (in my opinion).

In R:

library(treeducken)
h_lambda <- 0.5
h_mu <- 0.3
c_lambda <- 0.5

s_lambda <- 1.0
s_mu <- 0.3
s_her <- 0.0

host_symb_sets <- sim_cophyBD(hbr = h_lambda,
                            hdr = h_mu,
                            sbr = s_lambda,
                            cosp_rate = c_lambda,
                            sdr = s_mu,
                            host_exp_rate = s_her,
                            time_to_sim = 2.0,
                            numbsim = 10)

Installation

You may install the development version using the devtools package.

In R:

library(devtools)
install_github("wadedismukes/treeducken")

You may install the package itself from CRAN:

In R:

install.packages("treeducken")