birthdeathSim: birthdeathSim
Description
Simulate Branching Times Under the birth-death model and/or with incomplete sampling
Usage
birthdeathSim(b, d, CladeSize, NumberMissing, NumberOfReps)
Arguments
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
Value
an n x m matrix of branching times, where n is size CladeSize - NumberMissing
and m is size NumberOfReps .
Details
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.