## ----include=FALSE------------------------------------------------------------ options(rmarkdown.html_vignette.check_title = FALSE) ## ----------------------------------------------------------------------------- ## ----------------------------------------------------------------------------- library(evolved) library(ape) ## ----------------------------------------------------------------------------- data("whale_phylo") ## ----fig.height=12, fig.width=6, fig.align='center', eval=FALSE--------------- # plot(whale_phylo, cex = 0.6) # axisPhylo() ## ----fig.height=12, fig.width=6, fig.align='center'--------------------------- plotPaintedWhales(knitr = TRUE) ## ----fig.height=5, fig.width=6, fig.align='center'---------------------------- lttPlot(whale_phylo, knitr = T) ## ----------------------------------------------------------------------------- whalerate = estimateSpeciation(whale_phylo) ## ----fig.height=5, fig.width=6, fig.align='center'---------------------------- sims=vector() for(i in 1:10000){ sims = c(sims, simulateBirthDeathRich(S = whalerate, E=0, t = 36)) } hist(sims, breaks = 100) ## ----fig.height=5, fig.width=6, fig.align='center'---------------------------- t = simulateTree(c(whalerate, 0), max.taxa = 40, max.t = Inf) ape::ltt.plot(t, col="white", ylim=c(0,87)) for(i in 1:100){ t = simulateTree(c(whalerate, 0), max.taxa = 40, max.t = Inf) ape::ltt.lines(t, col="#FF000032") } #Now, we add the actual whale phylogeny: ape::ltt.lines(whale_phylo, col="black")