In cboettig/wrightscape: wrightscape

``` {r include=FALSE, echo=FALSE} require(wrightscape) require(ggplot2) require(reshape2) require(grid) theme_publish <- theme_set(theme_bw(8)) theme_publish <- theme_update( panel_background = theme_blank(), panel.grid.major = theme_blank(), panel.grid.minor = theme_blank()) plot.path_sim <- function(x, ...) ggplot(x) + geom_line(aes(time, value, group = rep), alpha = 0.05) reps <- 500 X <- bm_path_sim(reps = reps) Y <- ou_path_sim(reps = reps, alpha = 6) Z <- release_path_sim(reps = reps, alpha = 6, release_frac = 0.7) W <- brownie_path_sim(reps = reps, sigma = sqrt(1/0.7)/sqrt(2 * 6), sigma2 = 1, release_frac = 0.7) # has 1/release_frac time = 2 px <- plot.path_sim(X) + opts(title = "Brownian Motion") + coord_cartesian(ylim = c(-2, 2)) + ylab("trait value") py <- plot.path_sim(Y) + opts(title = "Ornstein-Uhlenbeck") + coord_cartesian(ylim = c(-2, 2)) + ylab("trait value") pz <- plot.path_sim(Z) + opts(title = "Release of Constraint") + coord_cartesian(ylim = c(-2, 2)) + ylab("trait value") pw <- plot.path_sim(W) + opts(title = "Accelerated Evolution") + coord_cartesian(ylim = c(-2, 2)) + ylab("trait value")

``` {r alpha_v_sigma, fig.width=7, fig.height=7, dev='Cairo_pdf'}
px
py
pw
pz

``` {r } load("wrightscape.rda")

``` {r figure4}  
ggplot(subset(lr_dat, value > -10000 & value < 10000), aes(x=value)) +
  geom_density(aes(fill=model), alpha=.8, adjust=2) + 
  facet_wrap(~trait, scale="free") + 
  geom_vline(data=LR, aes(xintercept=value)) + xlab("likelihood ratio")

cboettig/wrightscape documentation built on May 13, 2019, 2:12 p.m.