paleoTS (version 0.5-1)

sim.punc: 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 = 0:(sum(ns)-1), vp = 1)
sim.sgs(ns = c(20, 20, 20), theta = 0, omega = 1, ms = 1, vs = 0.1, 
        nn=rep(30, sum(ns)), tt = 0:(sum(ns)-1), 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 = 0:(sum(ns)-1), 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

Value

A paleoTS object.

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).

References

Hunt, G. 2006. Fitting and comparing models of phyletic evolution: random walks and beyond. Paleobiology 32:578--601. Hunt, G. 2008. Gradual or pulsed evolution: when should punctuational explanations be preferred? Paleobiology 34:360-377.

See Also

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

Examples

# NOT RUN {
# 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$mm[41:60])), omega=c(0.5,0.5))
layout(1:2)
plot(x1, nse=2, col="red", main="Sampled Punctuation")
rect(x1$tt[20],min(x1$mm), x1$tt[40], max(x1$mm))
text(x1$tt[30], max(x1$mm), "sampled\ntransition", font=3, pos=1, cex=0.8)
plot(x2, nse=2, col="black", main="Unsampled Punctuation")
rect(x2$tt[30],min(x2$mm),x2$tt[31],max(x2$mm))
text(x2$tt[31], mean(x2$mm), "unsampled\ntransition", font=3, pos=4, cex=0.8)
# }