birthdeathSim: birthdeathSim
In laser: Likelihood Analysis of Speciation/Extinction Rates from Phylogenies

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

laser documentation built on Jan. 15, 2017, 4:49 p.m.