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

\linenumbers \pagenumbering{gobble} \setlength{\parindent}{1.0cm} \raggedright

source("figs_boxconstrain.R")
caption.fig1 <- "A - Fitted q01 by Simulated q01; B - Standardized (Fitted q01 - Simulated q01) by Number of Taxa (values above 0 indicate overestimation, and below 0 indicate underestimation); C - Fitted q10 by Simulated q10; D - Standardized (Fitted q01 - Simulated q01) by Number of Taxa (values above 0 indicate overestimation, and below 0 indicate underestimation); E - Fitted pSpec by Simulated pSpec; F - Standardized (Fitted pSpec - Simulated pSpec) by Number of Taxa (values above 0 indicate overestimation, and below 0 indicate underestimation)"
caption.fig2 <- "A - Fitted q01 by Simulated q01; B - Standardized (Fitted q01 - Simulated q01) by Number of Taxa (values above 0 indicate overestimation, and below 0 indicate underestimation); C - Fitted q10 by Simulated q10; D - Standardized (Fitted q01 - Simulated q01) by Number of Taxa (values above 0 indicate overestimation, and below 0 indicate underestimation); E - Fitted pSpec by Simulated pSpec; F - Standardized (Fitted pSpec - Simulated pSpec) by Number of Taxa (values above 0 indicate overestimation, and below 0 indicate underestimation)"

Symmetrical transition rates

Simulation parameters:

pSpec <- runif(n = 1000, min = 0, max = 2)
q01 <- runif(n = 1000, min = 0, max = 1)
q10 <- q01
ntaxa <- runif(n = 1000, min = 10, max = 100)
lambda <- runif(n = 1000, min = 0, max = 2)

p1 <-
    plot_grid(q01.sym + theme_cowplot(font_size = 10) + theme(legend.position = "none"),
          q01.sym.bytreesize + theme_cowplot(font_size = 10) + theme(legend.position = "none"),
          q10.sym + theme_cowplot(font_size = 10) + theme(legend.position = "none"),
          q10.sym.bytreesize + theme_cowplot(font_size = 10) + theme(legend.position = "none"),
          pSpec.sym + theme_cowplot(font_size = 10) + theme(legend.position = "none"),
          pSpec.sym.bytreesize + theme_cowplot(font_size = 10) + theme(legend.position = "none"),
          ncol = 2,
          align = 'hv',
          labels = LETTERS[1:6])

p2 <- plot_grid(
    p1,
    legend.sym,
    nrow = 2,
    rel_heights = c(0.9, 0.1)
)

p2

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Asymmetrical transition rates

Simulation parameters:

pSpec <- runif(n = 1000, min = 0, max = 2)
q01 <- runif(n = 1000, min = 0, max = 1)
q10 <- q01
ntaxa <- runif(n = 1000, min = 10, max = 100)
lambda <- runif(n = 1000, min = 0, max = 2)

p3 <-
    plot_grid(q01.asym + theme_cowplot(font_size = 10) + theme(legend.position = "none"),
          q01.asym.bytreesize + theme_cowplot(font_size = 10) + theme(legend.position = "none"),
          q10.asym + theme_cowplot(font_size = 10) + theme(legend.position = "none"),
          q10.asym.bytreesize + theme_cowplot(font_size = 10) + theme(legend.position = "none"),
          pSpec.asym + theme_cowplot(font_size = 10) + theme(legend.position = "none"),
          pSpec.asym.bytreesize + theme_cowplot(font_size = 10) + theme(legend.position = "none"),
          ncol = 2,
          align = 'hv',
          labels = LETTERS[1:6])

p4 <- plot_grid(
    p3,
    legend.asym,
    nrow = 2,
    rel_heights = c(0.9, 0.1)
)

p4