Description Usage Arguments Value Examples

sim.fbd.rateshift.taxa: Simulating fossilized birth death trees incorporating rate shifts.

1 | ```
sim.fbd.rateshift.taxa(n, numbsim, lambda, mu, psi, times, complete = FALSE)
``` |

`n` |
Number of extant sampled tips. |

`numbsim` |
Number of trees to simulate. |

`lambda` |
Vector of speciation rates, the rate in entry i is the speciation rate prior (ancestral) to time times[i]. |

`mu` |
Vector of extinction rates, the rate in entry i is the extinction rate prior (ancestral) to time times[i]. |

`psi` |
Vector of fossil sampling rates, the rate in entry i is the fossil sampling rate prior (ancestral) to time times[i]. |

`times` |
Vector of mass extinction and rate shift times. Time is 0 today and increasing going backwards in time. Specify the vector as times[i]<times[i+1]. times[1]=0 (today). |

`complete` |
If TRUE, the tree including the extinct lineages and non-sampled lineages is returned. If FALSE, the extinct lineages and non-sampled lineages are suppressed. |

List of numbsim simulated SAtrees with n extant sampled tips.

1 2 3 | ```
n = 10
numbsim = 1
sim.fbd.rateshift.taxa(n, numbsim, lambda = c(2,1), mu = c(0,0.3), psi = c(1,0.1), times = c(0,0.3))
``` |

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