R/create_figure_ess_distribution_likelihood.R

In richelbilderbeek/wiritttea: WIRITTTE analysis

#' Create 'figure_ess_distribution_likelihood'
#' @param parameters parameters, as returned from read_collected_parameters
#' @param esses the ESSes, as returned from read_collected_esses
#' @param filename name of the file the figure will be saved to
#' @author Richel Bilderbeek
#' @export
create_figure_ess_distribution_likelihood <- function(
  parameters,
  esses,
  filename
) {

  sti <- NULL; rm(sti) # nolint, should fix warning: no visible binding for global variable
  ai <- NULL; rm(ai) # nolint, should fix warning: no visible binding for global variable
  nltt_stat <- NULL; rm(nltt_stat) # nolint, should fix warning: no visible binding for global variable
  scr <- NULL; rm(scr) # nolint, should fix warning: no visible binding for global variable
  mean_durspec <- NULL; rm(mean_durspec) # nolint, should fix warning: no visible binding for global variable
  sequence_length <- NULL; rm(sequence_length) # nolint, should fix warning: no visible binding for global variable
  ..eq.label.. <- NULL; rm(..eq.label..) # nolint, should fix warning: no visible binding for global variable
  ..adj.rr.label.. <- NULL; rm(..adj.rr.label..) # nolint, should fix warning: no visible binding for global variable

  # Melt data, convert to long form
  esses_long <- reshape2::melt(esses,
    id = c("filename", "sti", "ai", "pi")
  )
  testit::assert(is.factor(esses_long$variable))

  esses_long <- dplyr::rename(esses_long, parameter = variable)
  esses_long <- dplyr::rename(esses_long, ess = value)

  # print("Connect the ESSes and parameters")
  testit::assert("filename" %in% names(parameters))
  testit::assert("filename" %in% names(esses))
  df <- merge(x = parameters, y = esses_long, by = "filename", all = TRUE)

  ggplot2::ggplot(
    data = df[ df$parameter == "likelihood", ],
    ggplot2::aes(x = ess)) +
    ggplot2::geom_histogram(alpha = 0.5, position = "identity", binwidth = 50, na.rm = TRUE, color = "black") +
    ggplot2::facet_grid(erg ~ scr) +
    ggplot2::coord_cartesian(ylim = c(0, 100)) +
    ggplot2::labs(
      title = "Tree likelihood ESS distribution",
      x = "Tree likelihood ESS",
      y = "Count",
      caption = filename
    ) +
    ggplot2::theme(plot.title = ggplot2::element_text(hjust = 0.5)) +
    ggplot2::geom_vline(xintercept = 200, linetype = "dotted")

  ggplot2::ggsave(file = filename, width = 7, height = 7)
}