Rev Language Reference


simBirthDeath

Simulates a tree under a very general birth-death process. Parameters are fed in as a n_cats by n_intervals matrix, such that the ith row is the rate vector for the ith category.

Usage

simBirthDeath(RealPos[] timeline, RealPos[][] lambda, RealPos[][] mu, RealPos[][] phi, Probability[][] r, Probability[][] Lambda, Probability[][] Mu, Probability[][] Phi, Probability[][] R, Simplex rootCategory, RealPos time)

Arguments

timeline : RealPos[] (pass by const reference)
The endpoints of the time intervals (episodes). You should include 0 at the end. We use ages before the present.
Default : [ 0.000 ]
lambda : RealPos[][] (pass by const reference)
The speciation rates for each interval.
mu : RealPos[][] (pass by const reference)
The extinction rates for each interval.
Default : 0
phi : RealPos[][] (pass by const reference)
The sampling rates for each interval.
Default : 0
r : Probability[][] (pass by const reference)
The extinction probability when rate-sampling happens for each interval.
Default : 0
Lambda : Probability[][] (pass by const reference)
The burst probability at the end of each interval.
Default : 0
Mu : Probability[][] (pass by const reference)
The (mass) extinction probability at the end of each interval.
Default : 0
Phi : Probability[][] (pass by const reference)
The sampling probability at the end of each interval.
Default : 0
R : Probability[][] (pass by const reference)
The extinction probability when event-sampling happens for each interval.
Default : 0
rootCategory : Simplex (pass by const reference)
The probabilities of the categories for the root.
Default : [ 1.000 ]
time : RealPos (pass by const reference)
The time/age before the present.

Return Type