R/plot_sim_metrics.R

In tece-lab/DAISIEutils: Utility Functions for the DAISIE Package

#' Plots metrics from simulations
#'
#' @param sim_metrics A list of metrics output from [calc_sim_metrics()]
#'
#' @return none Four plots are shown: histogram of the number of species,
#' histogram of the number of colonizations, histogram of the largest clade size
#' and histogram of the rank of the largest clade
#' @author Joshua W. Lambert
plot_sim_metrics <- function(sim_metrics) {
  # workaround nonstandard evaluation of global variables
  number_spec <- NULL
  number_colonists <- NULL
  sumstats <- NULL
  overall_results <- NULL
  ylim4 <- NULL

  plotting_data <- data.frame(
    number_spec = sim_metrics$number_spec,
    number_colonists = sim_metrics$number_colonists,
    size_largest_clade = sim_metrics$size_largest_clade
  )

  num_spec <- ggplot2::ggplot(data = plotting_data) +
    ggplot2::geom_histogram(ggplot2::aes(x = number_spec),
      fill = "cornsilk3"
    ) +
    ggplot2::geom_vline(ggplot2::aes(xintercept = stats::median(number_spec))) +
    ggplot2::theme_classic() +
    ggplot2::xlab("Number of Species") +
    ggplot2::ylab("Frequency")

  num_col <- ggplot2::ggplot(data = plotting_data) +
    ggplot2::geom_histogram(ggplot2::aes(x = number_colonists),
      fill = "cornsilk3"
    ) +
    ggplot2::geom_vline(ggplot2::aes(
      xintercept = stats::median(number_colonists)
    )) +
    ggplot2::theme_classic() +
    ggplot2::xlab("Number of Colonisation events") +
    ggplot2::ylab("Frequency")

  size_largest_clade <- ggplot2::ggplot(data = plotting_data) +
    ggplot2::geom_histogram(ggplot2::aes(x = size_largest_clade),
      fill = "cornsilk3"
    ) +
    ggplot2::geom_vline(
      ggplot2::aes(xintercept = stats::median(size_largest_clade))
    ) +
    ggplot2::theme_classic() +
    ggplot2::xlab("Size of largest clade") +
    ggplot2::ylab("Frequency")

  cowplot::plot_grid(num_spec, num_col, size_largest_clade, nrow = 1)

  bar_colors <- rep("cornsilk3", 5)
  bar_colors[sumstats[4]] <- "blue"
  graphics::barplot(
    height = overall_results$tt[, 2],
    names.arg = c("1st", "2nd", "3rd", "4th", "5th"),
    col = bar_colors,
    border = bar_colors,
    xlab = "Rank largest clade",
    ylab = "Density",
    ylim = c(0, ylim4)
  )
}