Generated biomass plot

NAMESPACE

@@ -4,4 +4,5 @@ export(add_theme)
 export(plot_landings)
 export(plot_recruitment)
 export(plot_spawning_biomass)
+export(plot_total_biomass)
 export(table_indices)

R/plot_biomass.R

@@ -0,0 +1,120 @@
+#' Plot Total Biomass
+#'
+#' @inheritParamsplot_recruitment
+#' @param show_warnings Option to suppress warnings
+#' @param units units for biomass
+#' @param scaled TRUE/FALSE; indicate whether the output values for biomass and recruitment are scaled
+#' @param scale_amount indicate the exact amount of scale (i.e. 1000)
+#' @param ref_line choose with reference point to plot a reference line and use
+#' in relative totb calculations
+#' @param end_year input the end year of the stock assessment data (not including
+#' projections). This parameter will be deprecated once the output converter is fully developed.
+#' @param relative Plot relative total biomass. Ref line indicates which reference point to use
+#'
+#' @return Plot total biomass from a stock assessment model as found in a NOAA
+#' stock assessment report. Units of total biomass can either be manually added
+#' or will be extracted from the provided file if possible. In later releases, model will not
+#' @export
+#'
+plot_total_biomass <- function(dat,
+                                  model = "standard",
+                                  show_warnings = FALSE,
+                                  units = NULL,
+                                  scaled = FALSE,
+                                  scale_amount = 1000,
+                                  ref_line = c("target", "MSY", "msy", "unfished"),
+                                  end_year = NULL,
+                                  relative = FALSE
+){
+
+  if(length(ref_line)>1){
+    ref_line = "target"
+  } else {
+    ref_line <- match.arg(ref_line, several.ok = FALSE)
+  }
+
+  # check units
+  if(!is.null(units)){
+    bu <- units
+  } else {
+    bu <- "metric tons"
+  }
+
+  if(model == "standard"){
+    output <- read.csv(dat)
+    totb <- output |>
+      dplyr::filter(label == "biomass",
+                    module_name == "DERIVED_QUANTITIES" | module_name == "t.series") |> # SS3 and BAM target module names
+      dplyr::mutate(estimate = as.numeric(estimate),
+                    year = as.numeric(year))
+    if (is.null(end_year)){
+      endyr <- max(totb$year)
+    }
+    # Select value for reference line and label
+    # update the target option later
+    if (any(grepl("target", output$label))) {
+      ref_line_val <- as.numeric(output[grep("(?=.*biomass)(?=.*target)", output$label, perl = TRUE),]$estimate)
+      ref_line_label <- "target"
+      if (scaled) {
+        ann_add <- ggplot2::annotate("text", x = endyr + 0.05, y=ref_line_val, label = bquote(B[target])) # this might need to change
+      } else {
+        ann_add <- ggplot2::annotate("text", x = endyr + 0.05, y=ref_line_val/1000, label = bquote(B[target]))
+      }
+    } else if (ref_line == "MSY" | ref_line == "msy") {
+      ref_line_val <- as.numeric(output[grep("(^biomass_msy)", output$label, perl = TRUE),]$estimate)
+      ref_line_label <- "MSY"
+      if (scaled) {
+        ann_add <- ggplot2::annotate("text", x = endyr + 0.05, y=ref_line_val, label = bquote(B[ref_line]))
+      } else {
+        ann_add <- ggplot2::annotate("text", x = endyr + 0.05, y=ref_line_val/1000, label = bquote(B[MSY]))
+      }
+    } else if (ref_line == "unfished") {
+      ref_line_val <- as.numeric(output[grep("(^biomass_unfished)", output$label, perl = TRUE),]$estimate)
+      ref_line_label <- "unfished"
+      if (scaled) {
+        ann_add <- ggplot2::annotate("text", x = endyr + 0.05, y=ref_line_val, label = bquote(B[unfished]))
+      } else {
+        ann_add <- ggplot2::annotate("text", x = endyr + 0.05, y=ref_line_val/1000, label = bquote(B[unfished]))
+      }
+    }
+    # Choose number of breaks for x-axis
+    x_n_breaks <- round(length(subset(totb, year<=endyr)$year)/10)
+    if (x_n_breaks <= 5) {
+      x_n_breaks <- round(length(subset(totb, year<=endyr)$year)/5)
+    }
+    if (relative) {
+      # plot relative TOTB
+      plt <- ggplot2::ggplot(data = subset(totb, year<=endyr)) +
+        ggplot2::geom_line(ggplot2::aes(x = year, y = estimate/ref_line_val), linewidth = 1) +
+        # ggplot2::geom_ribbon(ggplot2::aes(x = year, ymin = (value/ref_line_val - stddev/ref_line_val), ymax = (value/ref_line_val + stddev/ref_line_val)), colour = "grey", alpha = 0.3) +
+        ggplot2::geom_hline(yintercept = ref_line_val/ref_line_val, linetype = 2) +
+        ggplot2::labs(x = "Year",
+                      y = paste("Biomass (", bu, ")", sep = "")) +
+        ggplot2::scale_x_continuous(n.breaks = x_n_breaks,
+                                    guide = ggplot2::guide_axis(minor.ticks = TRUE))
+    } else {
+      if(scaled){
+        plt <- ggplot2::ggplot(data = totb) +
+          ggplot2::geom_line(ggplot2::aes(x = year, y = estimate), linewidth = 1) +
+          ggplot2::geom_hline(yintercept = ref_line_val, linetype = 2) +
+          ggplot2::labs(x = "Year",
+                        y = paste("Biomass (", bu, ")", sep = "")) +
+          ggplot2::scale_x_continuous(n.breaks = x_n_breaks,
+                                      guide = ggplot2::guide_axis(minor.ticks = TRUE))
+        plt <- plt + ann_add
+      } else {
+        plt <- ggplot2::ggplot(data = totb) +
+          ggplot2::geom_line(ggplot2::aes(x = year, y = estimate/1000), linewidth = 1) +
+          # ggplot2::geom_ribbon(ggplot2::aes(x = year, ymin = (value/1000 - stddev/1000), ymax = (value/1000 + stddev/1000)), colour = "grey", alpha = 0.3) +
+          ggplot2::geom_hline(yintercept = ref_line_val/1000, linetype = 2) +
+          ggplot2::labs(x = "Year",
+                        y = paste("Biomass (", bu, ")", sep = "")) +
+          ggplot2::scale_x_continuous(n.breaks = x_n_breaks,
+                                      guide = ggplot2::guide_axis(minor.ticks = TRUE))
+        plt <- plt + ann_add
+      }
+    }
+    plt_fin <- add_theme(plt)
+  }
+  return(plt_fin)
+}

R/plot_recruitment.R

@@ -1,10 +1,6 @@
 #' Plot Recruitment
 #'
-#' @param dat Stock assessment output file containing estimates parameters and
-#' other associated metrics.
-#' @param model Acryonym of the stock assessment model that produced the output file.
-#' Currently, only stock synthesis (SS3) and Beaufort Assessment Model (BAM)
-#' are options for plotting spawning biomass.
+#' @inheritParams plot_recruitment
 #' @param params Print/export the parameters of the stock recruitment function?
 #' @param params_only Only export the stock recruitment function or both the parameters and the plot(s)?
 #' @param units If units are not available in the output file, in metric tons,