[feat]: plot_discard

R/plot_discard.R

@@ -0,0 +1,147 @@
+#' Plot discards
+#' 
+#' Plot discards as a line graph.
+#'
+#' @inheritParams plot_spawning_biomass
+#'
+#' @returns A ggplot showing discards over time, usually by fleet.
+#' 
+#' @details The input is from an assessment model output file
+#' translated to a standardized output (\link[stockplotr]{convert_output}).
+#' There are options to return a `ggplot2` object or export an .rda object
+#' containing associated caption and alternative text for the figure.
+#' 
+#' @note
+#' All plotting functions automatically recognize indexing variables and will
+#' use them in groupings and/or facetting. @seealso [process_data()].
+#'
+#' @seealso [convert_output()], [plot_timeseries()], [calculate_reference_point()], [reference_line()], [filter_data()], [process_data()], [export_kqs()], [insert_kqs()], [create_rda()]
+#' 
+#' @export
+#'
+#' @examples
+#' plot_discard(
+#'   dat = example_data
+#'   
+#' )
+plot_discard <- function(
+    dat,
+    group = NULL,
+    facet = NULL,
+    unit_label = "mt",
+    era = NULL,
+    lbs = FALSE,
+    scale_amount = 1,
+    interactive = TRUE,
+    module = NULL,
+    make_rda = FALSE,
+    figures_dir = getwd()
+) {
+  # this assumes that the previous units were metric tons
+  if (lbs && unit_label %notin% c("lbs", "pounds", "lb")) {
+    cli::cli_alert_info("Unit label was not changed. Setting unit_label to 'lbs'.")
+    unit_label <- "lbs"
+  }
+
+  discard_label <- label_magnitude(
+        label = "Discard",
+        unit_label = unit_label,
+        scale_amount = dplyr::if_else(
+          lbs,
+          ifelse(unit_label %in% c("mt", "mts", "metric tons", "metric ton"), 1000, 1) * scale_amount,
+          scale_amount
+        ),
+        legend = TRUE
+      )
+
+  # Filter data for discards
+  prepared_data <- filter_data(
+    dat = dat,
+    label_name = "^discard$|discard_weight",
+    geom = "line",
+    era = era,
+    group = group,
+    facet = facet,
+    module = module,
+    scale_amount = scale_amount,
+    interactive = interactive
+  )
+
+  # Process the data to remove unneccessary columns and information
+  p_dat <- process_data(
+    prepared_data,
+    group = group,
+    facet = facet,
+    lbs = lbs
+  )
+  discards <- p_dat[[1]]
+  group <- p_dat[[2]]
+  facet <- p_dat[[3]]
+
+  # make the plot
+  plt <- plot_timeseries(
+    discards,
+    ylab = discard_label,
+    group = group,
+    facet = if (length(facet) > 0) facet else NULL#,
+    # ...
+  )
+
+  ### Make RDA ----
+  if (make_rda) {
+    if (relative) {
+      rel.ssb.min <- calc_kqs(returned_kq = "rel.ssb.min",
+                              final = final)
+
+
+      rel.ssb.max <- calc_kqs(returned_kq = "rel.ssb.max",
+                              final = final)
+
+      # calculate & export key quantities
+      export_kqs(rel.ssb.min, rel.ssb.max)
+
+      # Add key quantities to captions/alt text
+      insert_kqs(rel.ssb.min, rel.ssb.max)
+    } else {
+      ssb.min <- min(plot_data$estimate) |> round(digits = 3)
+      ssb.max <- max(plot_data$estimate) |> round(digits = 3)
+
+      export_kqs(ssb.min, ssb.max)
+      insert_kqs(ssb.min, ssb.max)
+    }
+
+    # Obtain relevant key quantities for captions/alt text
+    ssb.ref.pt <- as.character(ref_line)
+    ssb.units <- as.character(unit_label)
+    ssb.start.year <- min(plot_data$year)
+    ssb.end.year <- max(plot_data$year)
+
+    # calculate & export key quantities
+    export_kqs(
+      ssb.ref.pt,
+      ssb.units,
+      ssb.start.year,
+      ssb.end.year
+    )
+
+    # Add key quantities to captions/alt text
+    insert_kqs(
+      ssb.ref.pt,
+      ssb.units,
+      ssb.start.year,
+      ssb.end.year
+    )
+
+    create_rda(
+      object = final,
+      topic_label = "discards",
+      fig_or_table = "figure",
+      dat = rp_dat,
+      dir = figures_dir,
+      scale_amount = scale_amount,
+      unit_label = unit_label
+    )
+  }
+  # Output final plot
+  plt + theme_noaa()
+}

R/plot_spawning_biomass.R

@@ -228,6 +228,7 @@ plot_spawning_biomass <- function(
         ggplot2::geom_point(ggplot2::aes(x = min_year - 1, y = ref_point)) + # should I keep -1 or set as first year?
         theme_noaa()
     } else {
+      # add apply/purrr/or for loop for reference lines -- not just the first anymore
       final <- reference_line(
         plot = plt,
         dat = rp_dat,

inst/resources/bam_var_names.csv

@@ -244,10 +244,6 @@ LD.pr.tseries,L.klb,landings_weight
 LD.pr.tseries,L.knum,landings_numbers
 LD.pr.tseries,D.klb,discard_weight
 LD.pr.tseries,D.knum,discard_numbers
-LD.pr.tseries,l.klb,landings_weight
-LD.pr.tseries,l.knum,landings_numbers
-LD.pr.tseries,d.klb,discard_weight
-LD.pr.tseries,d.knum,discard_numbers
 a.series,length,length
 a.series,length.cv,length_cv
 a.series,length.sd,length_sd