sim_stBD: Simulates species trees using constant rate birth-death...
In treeducken: Nested Phylogenetic Tree Simulator

Description Usage Arguments Value References Examples

Forward simulates to a number of tips. This function does so using the general algorithm of Hartmann et al. 2010. Short for simulate species tree under birth-death process.

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sim_stBD(sbr, sdr, numbsim, n_tips, gsa_stop_mult = 10L)

sim_sptree_bdp(sbr, sdr, numbsim, n_tips, gsa_stop_mult = 10)

`sbr`	species birth rate (i.e. speciation rate)
`sdr`	species death rate (i.e. extinction rate)
`numbsim`	number of species trees to simulate
`n_tips`	number of tips to simulate to
`gsa_stop_mult`	number of tips to simulate the GSA tip to

List of objects of the tree class (as implemented in APE)

K. Hartmann, D. Wong, T. Stadler. Sampling trees from evolutionary models. Syst. Biol., 59(4): 465-476, 2010.

T. Stadler. Simulating trees on a fixed number of extant species. Syst. Biol., 60: 676-684, 2011.

mu <- 0.5 # death rate
lambda <- 2.0 # birth rate
numb_replicates <- 10
numb_extant_tips <- 4
# simulate trees under the GSA so first simulates a tree with
# numb_extant_tips * 100 tips counting each time we have a tree with 10 tips
# then randomly picks one of those trees

tree_list <- sim_stBD(sbr = lambda,
                sdr = mu,
                numbsim = numb_replicates,
                n_tips = numb_extant_tips)