Description Usage Arguments Details Value Author(s)

Simulate Branching Times Under the birth-death model and/or with incomplete sampling

1 | ```
birthdeathSim(b, d, CladeSize, NumberMissing, NumberOfReps)
``` |

`b` |
the speciation rate |

`d` |
the extinction rate |

`CladeSize` |
the true clade size you wish to simulate |

`NumberMissing` |
the number of taxa missing from the 'real' tree |

`NumberOfReps` |
the number of phylogenies to simulated |

This generates a matrix of branching times that can be used with
`fitdAICrc.batch`

under any parameterization of a general birth-death
model with or without incomplete sampling.

To simulate a clade with incomplete sampling, note that `CladeSize`

is
the true size of a phylogeny, and `NumberMissing`

is the number of missing taxa,
so if you specified `CladeSize = 100`

and `NumberMissing = 20`

, your resulting
trees would have 80 tips (Trees with 100 tips would be simulated, but then 20 taxa
would be dropped randomly to simulate incomplete sampling).

THis function is basically a wrapper for the `birthdeath.tree`

function
from Geiger, but makes it more amenable to calculation of the delta AIC test
statistic for detecting temporal changes in diversification rates.

an n x m matrix of branching times, where n is size `CladeSize`

- `NumberMissing`

and m is size ` NumberOfReps `

.

Dan Rabosky drabosky@umich.edu

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