################################################################################ # # Plot correlation factors of episodic birth-death process # with environmental variables # # # authors: Sebastian Hoehna # ################################################################################ library(RevGadgets) library(ggplot2) MODEL = "fixed" # specify the input file file <- paste0("output/primates_EBD_",MODEL,"_env.log") trace_env <- readTrace(path = file, burnin = 0.25) # plot the prior vs the posterior plot <- plotTrace(trace_env, vars=c("beta_speciation", "beta_extinction"))[[1]] + # modify legend location using ggplot2 theme(legend.position = c(0.80,0.80)) ggsave(paste0("EBD_",MODEL,"_env_factors.png"), plot, height=5, width=5) BF <- c(3.2, 10, 100) p = BF/(1+BF) # produce the plot object, showing the posterior distributions of the rates. p <- plotTrace(trace = trace_env, vars = c("speciation_corr_neg_prob", "extinction_corr_neg_prob", "speciation_corr_pos_prob", "extinction_corr_pos_prob"))[[1]] + ylim(0,1) + geom_hline(yintercept=0.5, linetype="solid", color = "black") + geom_hline(yintercept=p, linetype=c("longdash","dashed","dotted"), color = "red") + geom_hline(yintercept=1-p, linetype=c("longdash","dashed","dotted"), color = "red") + # modify legend location using ggplot2 theme(legend.position = c(0.825,0.525), legend.key.size = unit(0.4, 'cm'), #change legend key size legend.title = element_text(size=8), #change legend title font size legend.text = element_text(size=6)) ggsave(paste0("EBD_",MODEL,"_env_prob.png"), p, height=5, width=5)