R/utils_fish_plot_diversity.R

In Rare-Technology/ECO_Dashboard: An Amazing Shiny App

plot_fish_diversity <- function(data_filtered, sel_geom, facet_maa) {
  data_aggreg <- aggregate_data(data_filtered, 'species')
  data_summary <- summarySE(data_aggreg, 'species', facet_maa)
  years <- sort(unique(data_summary$year))
  out <- list(data = data_summary)
  
  p <- plot_bar(
    data = data_summary,
    x = "year",
    y = "species",
    fill = "location_status",
    title = "Fish diversity",
    y_label = "Number of unique species",
    years = years
  )
    
  if (sel_geom == "Distribution plots") {
    if (facet_maa) {
      data_local <- data_aggreg # diversity is a special case for this
    } else {
      # this feels a bit sneaky but it should work: pretend we're faceting maa so
      # calculate data_summary in that case BUT call it data_local
      data_local <- summarySE(data_aggreg, 'species', !facet_maa) # note the !
    }
    
    out$data <- data_local
    
    p <- p + plot_samples(
      data_local = data_local,
      x = "year",
      y = "species",
      fill = "location_status"
    )
  }
  
  out$plot <- p
  out
}