R/create_figure_posterior_bd.R

In richelbilderbeek/wiritttea: WIRITTTE analysis

#' Create 'figure_posterior_distributions_bd'
#' @param parameters parameters, as returned from read_collected_parameters
#' @param filename name of the file the figure will be saved to
create_figure_posterior_bd <- function(
  parameters,
  filename
) {


  # Multiple plot function
  #
  # ggplot objects can be passed in ..., or to plotlist (as a list of ggplot objects)
  # - cols:   Number of columns in layout
  # - layout: A matrix specifying the layout. If present, 'cols' is ignored.
  #
  # If the layout is something like matrix(c(1,2,3,3), nrow=2, byrow=TRUE),
  # then plot 1 will go in the upper left, 2 will go in the upper right, and
  # 3 will go all the way across the bottom.
  #
  # From http://www.cookbook-r.com/Graphs/Multiple_graphs_on_one_page_(ggplot2)/
  multiplot <- function(..., plotlist=NULL, file, cols=1, layout=NULL) {
    library(grid)

    # Make a list from the ... arguments and plotlist
    plots <- c(list(...), plotlist)

    numPlots = length(plots)

    # If layout is NULL, then use 'cols' to determine layout
    if (is.null(layout)) {
      # Make the panel
      # ncol: Number of columns of plots
      # nrow: Number of rows needed, calculated from # of cols
      layout <- matrix(seq(1, cols * ceiling(numPlots/cols)),
                      ncol = cols, nrow = ceiling(numPlots/cols))
    }

   if (numPlots==1) {
      print(plots[[1]])

    } else {
      # Set up the page
      grid.newpage()
      pushViewport(viewport(layout = grid.layout(nrow(layout), ncol(layout))))

      # Make each plot, in the correct location
      for (i in 1:numPlots) {
        # Get the i,j matrix positions of the regions that contain this subplot
        matchidx <- as.data.frame(which(layout == i, arr.ind = TRUE))

        print(plots[[i]], vp = viewport(layout.pos.row = matchidx$row,
                                        layout.pos.col = matchidx$col))
      }
    }
  }


  print("Select all Birth-Death parameters")
  bd_parameters <- parameters[ parameters$scr == max(parameters$scr) & parameters$erg > 0.0, ]
  head(bd_parameters)

  set.seed(10)
  posterior <- NA
  filename <- NA
  while (length(posterior) < 2) {

    print("Pick random filename")
    filename_short <- rownames(dplyr::sample_n(bd_parameters, size = 1))
    print(paste0("Picked '", filename_short, "'"))
    filename <- paste0(raw_data_path, filename_short)
    testit::assert(file.exists(filename))

    print("Get posterior of that filename (if fails, try again)")
    tryCatch({
      posterior <- wiritttes::get_posterior(
        wiritttes::read_file(filename), sti = 1, ai = 1, pi = 1)
      },
        error = function(cond) {}
    )
  }

  print(paste0("File '", filename, "' has a good posterior"))
  p <- parameters[ rownames(parameters) == basename(filename), ]
  p
  # If a range goes from [0, crownTreeHeight], multiply it by
  # 'tree_scale' to let it go from [0, crown_age]
  tree_scale <- p$age / median(posterior$estimates$TreeHeight)


  # BirthDeath
  # * Unknown meaning
  # * Called 'rho' in BEAST2

  #  birthRate2:
  # * called 'r' in BEAST2
  # * birth rate - death rate
  real_birthRate2 <- (p$sirg - p$erg) * tree_scale

  # Crown age, called 'TreeHeight' in BEAST2
  real_TreeHeight <- p$age


  # relativeDeathRate2:
  # * mu / lambda
  # * birth rate/death rate ratio
  # * as mu < lambda, has range [0,1]
  # * called 'a' in BEAST2
  real_relativeDeathRate2 <- p$erg / p$sirg


  # realtiveDeathRate = GL: mu / lambda

  print("Extract values to be plotted: 'BirthDeath', 'birthRate2', 'relativeDeathRate2'")
  df <- dplyr::select(posterior$estimates, c("BirthDeath", "birthRate2", "relativeDeathRate2", "TreeHeight"))

  some_values <- dplyr::sample_n(df, size = 5)


  print("Convert to long form")
  df <- reshape2::melt(df, measure.vars = names(df))
  head(df)

  print("Plot the variables individually")



  p1 <- ggplot2::ggplot(
    df[ df$variable == "BirthDeath", ],
    ggplot2::aes(x = value)
  ) +
    ggplot2::geom_histogram(bins = 1000) +
    ggplot2::labs(
      title = "BirthDeath distribution",
      caption = paste0(filename, ", figure_posterior_distribution_bd_bd")
    ) +
    ggplot2::theme(plot.title = ggplot2::element_text(hjust = 0.5))

  p2 <- ggplot2::ggplot(
    df[ df$variable == "birthRate2", ],
    ggplot2::aes(x = value)
  ) +
    ggplot2::geom_histogram(bins = 100) +
    ggplot2::geom_vline(xintercept = real_birthRate2, linetype = "dotted") +
    ggplot2::labs(
      title = "birthRate2 distribution",
      caption = paste0(filename, ", figure_posterior_distribution_bd_br2")
    ) +
    ggplot2::theme(plot.title = ggplot2::element_text(hjust = 0.5))

  p2

  p3 <- ggplot2::ggplot(
    df[ df$variable == "relativeDeathRate2", ],
    ggplot2::aes(x = value)
  ) +
    ggplot2::geom_histogram(bins = 100) +
    ggplot2::geom_vline(xintercept = real_relativeDeathRate2, linetype = "dotted") +
    ggplot2::labs(
      title = "relativeDeathRate2 distribution",
      caption = paste0(filename, ", figure_posterior_distribution_bd_rdr2")
    ) +
    ggplot2::theme(plot.title = ggplot2::element_text(hjust = 0.5))

  p3

  p4 <- ggplot2::ggplot(
    df[ df$variable == "TreeHeight", ],
    ggplot2::aes(x = value)
  ) +
    ggplot2::geom_histogram(bins = 1000) +
    ggplot2::labs(
      title = "TreeHeight distribution",
      caption = paste0(filename, ", figure_posterior_distribution_bd_th")
    ) +
    ggplot2::theme(plot.title = ggplot2::element_text(hjust = 0.5))

  p4

  p5 <- ggplot2::ggplot(
    df,
    ggplot2::aes(x = value)
  ) +
    ggplot2::geom_histogram(bins = 100) +
    ggplot2::facet_wrap(~variable, ncol = 4, nrow = 1, shrink = TRUE, scales = "free") +
    ggplot2::labs(
      title = "Distributions of estimated BD parameters",
      caption = paste0(filename, ", figure_posterior_distribution_bd_all")
    ) +
    ggplot2::theme(plot.title = ggplot2::element_text(hjust = 0.5))
  p5



  svg("~/figure_posterior_distribution_bd_bd.svg")
  p1
  dev.off()
  svg("~/figure_posterior_distribution_bd_br2.svg")
  p2
  dev.off()
  svg("~/figure_posterior_distribution_bd_rdr2.svg")
  p3
  dev.off()
  svg("~/figure_posterior_distribution_bd_all.svg")
  p4

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