mbd_sim: Creates simulated trees under the multiple birth death...

In Giappo/mbd: Multiple Birth Death Diversification

Description

mbd_sim produces simulated trees allowing for three kind of events: sympatric speciation, multiple allopatric speciations and extinction.

Usage

mbd_sim(
  pars,
  n_0 = 2,
  age = 10,
  cond = 1,
  seed = NA,
  tips_interval = c(n_0 * (cond > 0), Inf),
  brts_precision = 8
)

Arguments

pars	vector of parameters: pars[1] is lambda, the sympatric speciation rate; pars[2] is mu, the extinction rate; pars[3] is nu, the multiple allopatric speciation trigger rate; pars[4] is q, the single-lineage speciation probability;
n_0	the number of lineages at time equals zero.
age	the age of the tree.
cond	sets the conditioning cond = 0: no conditioning; cond = 1: conditioning on stem or crown age and non-extinction of the phylogeny;
seed	the seed
tips_interval	sets tips boundaries constrain on simulated dataset. It works only if cond == 1, otherwise it must be set to c(0, Inf).
brts_precision	set the level of approximation on the branching times.

Author(s)

Giovanni Laudanno

Examples

out <- mbd_sim(
  pars = c(0.6, 0.1, 0.4, 0.1),
  n_0 = 2,
  age = 10,
  cond = 1
)
graphics::plot(out$full_tree)
graphics::plot(out$reconstructed_tree)
out$l_matrix

Giappo/mbd documentation built on March 3, 2020, 3:36 a.m.