sim.punc {paleoTS}R Documentation

Simulate evolutionary time-series with changing dynamics

Description

These functions simulate evolutionary time-series in which the dynamics are not constant over time. These correspond to unsampled punctuations (sim.punc), sampled punctuations (sim.sgs), and random walks with parameter values change over time.

Usage

sim.punc(ns = c(10, 10), theta = c(0, 1), omega=rep(0,length(theta)), nn = rep(30, sum(ns)), tt = 1:sum(ns), vp = 1)
sim.sgs(ns = c(20, 20, 20), theta = 0, omega = 1, ms = 1, vs = 0.1, nn=rep(30, times=sum(ns)), tt = 1:sum(ns), vp = 1)
sim.GRW.shift(ns = c(10, 10), ms = c(0, 1), vs = c(0.5, 0.5), nn = rep(30, sum(ns)), tt = 1:sum(ns), vp = 1)

Arguments

ns vector with the number of samples in each segment
theta evolutionary optimum, Stasis model
omega evolutionary variance, Stasis model
nn a vector of sample sizes per sample
tt vector of sample ages, increasing from oldest to youngest
vp within-sample phenotypic variance
ms mean step in GRW model for puncuated interval
vs step variance in GRW model for puncuated interval

Details

These three models are elaborations of the standard random walk, directional evolution and stasis models to allow for heterogeneous evolutionary dynamics within a sequence. These heterogeneous dynamics include sampled punctuations (sim.sgs), unsampled punctuations sim.punc and shifting random walk dynamics (sim.GRW.shift).

Value

A paleoTS object.

Author(s)

Gene Hunt

References

Hunt, G. 2006. Fitting and comparing models of phyletic evolution: random walks and beyond. Paleobiology32:578–601.
Hunt, G. 2008. Gradual or pulsed evolution: when should punctuational explanations be preferred? Paleobiology34:In press.

See Also

opt.punc, opt.sgs, opt.GRW.shift

Examples

# illustrate differences between sampled and unsampled punctuations
x1<- sim.sgs(ms=0.4, omega=0.5)
x2<- sim.punc(ns=c(30,30), theta=c(0, mean(x1$mm[41:60])), omega=c(0.5,0.5))
layout(1:2)
plot(x1, nse=2, col="red", main="Sampled Punctuation")
rect(20,min(x1$mm), 40, max(x1$mm))
text(30, max(x1$mm), "sampled\ntransition", font=3, pos=1, cex=0.8)
plot(x2, nse=2, col="black", main="Unsampled Punctuation")
rect(30,min(x2$mm),31,max(x2$mm))
text(31, mean(x2$mm), "unsampled\ntransition", font=3, pos=4, cex=0.8)

[Package paleoTS version 0.3-1 Index]