In lukejharmon/netphy: What the package does (short line)

Summarizing results from simulations with fixed Ntip and depth

library("cowplot")
results.small <- read.csv("results_symtrans_boxconstrain_fixed_n_depth_small.txt", sep = "\t")
results.large <- read.csv("results_symtrans_boxconstrain_fixed_n_depth_large.txt", sep = "\t")

results.full <- rbind(results.small[, 1:8], results.large[, 1:8])
results.full$size <- c(rep("Small Trees - 20 tips", 100), rep("Large Trees - 100 tips", 100))

g.small <- ggplot(data = results.small) +
    geom_violin(aes(x = 1, y = q01.fit)) +
    geom_jitter(aes(x = 1, y = q01.fit), colour = "darkgrey", alpha = 0.75, size = 1) +
    geom_point(aes(x = 1, y = q01.sim), colour = "darkred", size = 4) +
    ylim(0, 0.2) +
    labs(y = "Estimated q01", title = "Small trees - 20 tips") +
    theme(legend.position = "bottom")

g.large <- ggplot(data = results.large) +
    geom_violin(aes(x = 1, y = q01.fit)) +
    geom_jitter(aes(x = 1, y = q01.fit), colour = "darkgrey", alpha = 0.75, size = 1) +
    geom_point(aes(x = 1, y = q01.sim), colour = "darkblue", size = 4) +
    ylim(0, 0.01) +
    labs(y = "Estimated q01", title = "Large trees - 100 tips") +
    theme(legend.position = "bottom")

plot_grid(g.small,
          g.large,
          ncol = 2,
          align = 'h')

## logLik for small trees' fitting
summary(results.small$llik.fit)



## logLik for large trees' fitting
summary(results.large$llik.fit)

lukejharmon/netphy documentation built on May 21, 2019, 8:58 a.m.