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).
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).
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)
You may install the development version using the
You may install the package itself from CRAN:
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