rlineage: Tree Simulation Under the Time-Dependent Birth--Death Models

Description

These two functions simulate phylogenies under any time-dependent birth--death model. lineage generates a complete tree including the species that go extinct; rbdtree generates a tree with only the species until present; drop.fossil is a utility function to remove the extinct species.

Usage

rlineage(birth, death, Tmax = 50, BIRTH = NULL,
         DEATH = NULL, eps = 1e-6)
rbdtree(birth, death, Tmax = 50, BIRTH = NULL,
        DEATH = NULL, eps = 1e-6)
drop.fossil(phy, tol = 1e-8)

Arguments

Value

An object of class "phylo".

Details

Both functions use continuous-time algorithms described in the references. The models are time-dependent birth--death models as described in Kendall (1948). Speciation (birth) and extinction (death) rates may be constant or vary through time according to an Rfunction specified by the user. In the latter case, BIRTH and/or DEATH may be used of the primitives of birth and death are known. In these functions time is the formal argument and must be named t.

References

Kendall, D. G. (1948) On the generalized ``birth-and-death'' process. Annals of Mathematical Statistics, 19, 1--15.

Paradis, E. (2011) Time-dependent speciation and extinction from phylogenies: a least squares approach. Evolution, 65, 661--672.

Examples

Run this code

plot(rlineage(0.1, 0)) # Yule process with lambda = 0.1
plot(rlineage(0.1, 0.05)) # simple birth-death process
b <- function(t) 1/(1 + exp(0.2*t - 1)) # logistic
layout(matrix(0:3, 2, byrow = TRUE))
curve(b, 0, 50, xlab = "Time", ylab = "")
mu <- 0.07
segments(0, mu, 50, mu, lty = 2)
legend("topright", c(expression(lambda), expression(mu)),
       lty = 1:2, bty = "n")
plot(rlineage(b, mu), show.tip.label = FALSE)
title("Simulated with 'rlineage'")
plot(rbdtree(b, mu), show.tip.label = FALSE)
title("Simulated with 'rbdtree'")

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