TreeSim: Simulating trees under the birth-death model

The package simulates phylogenetic trees under a constant-rate birth-death process, conditioned on having a fixed number of final tips (sim.bd.taxa), or a fixed age (sim.bd.age), or a fixed age and number of tips (sim.bd.taxa.age). When conditioning on the number of final tips, the method allows for shifts in rates and mass extinction events during the birth-death process (sim.rateshift.taxa). When fixing on the age, the method further allows the speciation rate to change in a density-dependent way (sim.bd.age), and one can plot the average LTT plot (LTT.average.root). TreeSim further samples appropriately trees with n final tips from a set of trees generated by the common sampling algorithm stopping when a fixed number m>>n of leaves is first reached (bd.gsa.taxa). This latter method is appropriate for m-tip trees generated under a big class of models (details in the bd.gsa.taxa man page). For incomplete phylogeny, the missing speciation events can be added through simulations (corsim).

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