geiger-package {geiger} | R Documentation |
A package for macroevolutionary simulation and estimating parameters related to diversification from comparative phylogenetic data.
Package: | geiger |
Type: | Package |
Version: | 1.0 |
Date: | 2007-01-19 |
License: | GPL version 2 or greater? |
Luke J. Harmon, Jason Weir, Chad Brock, and Wendell Challenger
Maintainer: Luke Harmon <harmon@zoology.ubc.ca>
# Disparity-through-time, as in Harmon et al. 2003 data(geospiza) attach(geospiza) dtt.full(geospiza.tree, geospiza.data) # Simulation tester - verifies that simulations produce expected vcv structure sims<-sim.char(geospiza.tree, as.matrix(1.0), n=100000) m<-var(t(sims[,1,])) m2<-vcv.phylo(geospiza.tree) round(m-m2) # Equal to zero because the vcv matrices are as expected. #Test models of evolution fitContinuous(geospiza.tree, geospiza.data) # Reconstruct evolutionary vcv matrix v<-cbind(c(4.0, -1.5),c(-1.5, 9.0)) n<-1000 sims<-sim.char(geospiza.tree, v, n) r<-array(dim=c(2, 2, n)) for(i in 1:n) r[,,i]<-ic.sigma(geospiza.tree, sims[,,i]) v.recon<-apply(r, c(1,2), mean) v-v.recon # Discrete character evolution q<-list(rbind(c(-.01, .01), c(.01, -.01))) sims<-sim.char(geospiza.tree, q, model="discrete", n=100)