| sim.punc {paleoTS} | R Documentation |
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.
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)
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 |
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).
A paleoTS object.
Gene Hunt
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.
opt.punc, opt.sgs, opt.GRW.shift
# 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)