treeducken-package: treeducken: simulates cophylogenetic systems & nested...
In treeducken: Nested Phylogenetic Tree Simulator

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treeducken simulates cophylogenetic systems such as host and symbiont pairs. This is done using the sim_cophylo_bdp function. This function simulates a host tree and a symbiont tree simultaneously using a matrix describing the associations between contemporaneous hosts and symbionts. These simulations allow for varying rates of host-shift speciation and cospeciation in addition to independent birth and death rates of the host and the symbiont trees. treeducken is also able to simulate nested phylogenies such as might be expected in the case of gene tree and species tree scenarios.