birthdeathSim: birthdeathSim

Description Usage Arguments Details Value Author(s)

Description

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

Usage

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

Arguments

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

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.

Value

an n x m matrix of branching times, where n is size CladeSize - NumberMissing and m is size NumberOfReps .

Author(s)

Dan Rabosky drabosky@umich.edu


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