R/plotDens.R

In qureshlatif/WoodpeckerHSI: Woodpecker habitat suitability models

plotDens <- function (dat.plot, dat.class, sampleHSIs, thresholds, binPntSize = 2, 
                      classPntSize = 5, axisLabSize = 20, tickLabSize = 15, BS = F, 
                      ylabel = "Observed density (nests per 100 ha)", xlabel = "Habitat Suitability Index (HSI)") 
{
  theme_set(theme_bw())
  if (nrow(dat.class) != (length(thresholds) + 1)) 
    stop("Incorrect number of thresholds provided for the number of suitability classes.")
  plt <- ggplot(dat.plot, aes(HSI.md, Density)) + geom_point(size = binPntSize, 
                                                             shape = 16)
  if (BS == T) 
    plt <- plt + geom_errorbar(data = dat.class,
                               aes(x = HSI.md, ymin = Dens95lo, ymax = Dens95hi),
                               size = 1, width = 0.05)
  plt <- plt + geom_point(data = dat.class, aes(x = HSI.md, y = Density),
                          size = classPntSize, shape = 16, colour = "white") +
    geom_point(data = dat.class, aes(x = HSI.md, y = Density),
               size = classPntSize, shape = 1, stroke = 1.5) +
    geom_rug(data = data.frame(HSI = sampleHSIs),
             aes(x = HSI, y = NULL), colour = "black", alpha = 0.3,
             size = 1) + ylab(ylabel) + xlab(xlabel) +
    theme(axis.text.x = element_text(size = tickLabSize)) + 
    theme(axis.text.y = element_text(size = tickLabSize)) + 
    theme(axis.title.x = element_text(size = axisLabSize)) + 
    theme(axis.title.y = element_text(size = axisLabSize))
  for (t in 1:length(thresholds)) plt <- plt + geom_vline(xintercept = thresholds[t], 
                                                          linetype = "dashed")
  return(plt)
}