add plot_hms_stock_status

NAMESPACE

@@ -39,6 +39,7 @@ export(plot_heatwave_peak_date)
 export(plot_heatwave_year)
 export(plot_hms_cpue)
 export(plot_hms_landings)
+export(plot_hms_stock_status)
 export(plot_ichthyo_diversity)
 export(plot_long_term_sst)
 export(plot_mab_inshore_survey)

R/plot_hms_stock_status.R

@@ -0,0 +1,152 @@
+#' plot hms_stock_status
+#'
+#' Kobe plot of F/Fmsy vs B/Bmsy for Highly Migratory Species (HMS) stocks.
+#'
+#' @param shadedRegion Numeric vector. Years denoting the shaded region of the plot (most recent 10)
+#' @param report Character string. Which SOE report ("MidAtlantic" default, same for both)
+#'
+#' @return list of 2 items
+#'
+#' \item{p}{ggplot object}
+#' \item{unknown}{data frame listing stocks with unklnown status}
+#'
+#' @export
+#'
+
+plot_hms_stock_status <- function(shadedRegion = shadedRegion,
+                              report="MidAtlantic") {
+
+  # generate plot setup list (same for all plot functions)
+  setup <- ecodata::plot_setup(shadedRegion = shadedRegion,
+                               report=report)
+
+  # which report? this may be bypassed for some figures
+  if (report == "MidAtlantic") {
+    filterEPUs <- c("MAB")
+  } else {
+    filterEPUs <- c("GB", "GOM")
+  }
+
+  # optional code to wrangle ecodata object prior to plotting
+  # e.g., calculate mean, max or other needed values to join below
+  y.max <- 5
+  x.max <- 2
+  #Get data, spread for plotting, and filter
+  # for now include legend because it has 2 species not in table??
+  unknownp <- data.frame(text = c("Unknown Status", "ATL SBH", "SPF", "WA BFT"),
+                        x = rep(0.9*x.max,4), y = seq(0.88*y.max,3.5,-0.3))
+
+
+
+
+  stock_status<-ecodata::hms_stock_status |>
+    #tidyr::spread(.,Var,Value) |>
+    tidyr::separate(Var, c("species_abr", "spp", "Var"), ":") |>
+    tidyr::pivot_wider(names_from = Var, values_from = Value) |>
+    dplyr::group_by(spp) |>
+    dplyr::filter(!species_abr == "------",
+                  !species_abr == "-----") |>
+    dplyr::mutate(score = case_when(
+      #(B.Bmsy <0.5) ~"a",
+      #(B.Bmsy == 0.5) ~"a",
+      #(B.Bmsy <1) ~"a",
+      #(B.Bmsy == 1) ~"a",
+      (F.Fmsy == 1) ~ "a",
+      (F.Fmsy >1) ~ "a",
+      #(F.Fmsy < 1 & B.Bmsy > 0.5 & B.Bmsy < 1) ~ "b",
+      (F.Fmsy < 1 & B.Bmsy < 1) ~ "b",
+      (F.Fmsy < 1 & B.Bmsy > 1) ~ "c"))
+
+  unknown <- stock_status |>
+    dplyr::filter(is.na(F.Fmsy) | is.na(B.Bmsy)) |>
+    dplyr::select(spp,F.Fmsy,B.Bmsy)
+
+
+  # code for generating plot object p
+  # ensure that setup list objects are called as setup$...
+  # e.g. fill = setup$shade.fill, alpha = setup$shade.alpha,
+  # xmin = setup$x.shade.min , xmax = setup$x.shade.max
+  #
+  p <- stock_status |>
+    ggplot2::ggplot() +
+    ggplot2::geom_vline(xintercept = 1, linetype = "dotted", color = "grey60")+
+    #ggplot2::geom_vline(xintercept = 0.5, linetype = "dashed", color = "grey60")+
+    ggplot2::geom_hline(yintercept = 1, linetype = "dashed", color = "grey60") +
+    ggplot2::geom_point(ggplot2::aes(x = B.Bmsy,
+                            y = F.Fmsy,
+                            color = stock_status$score)) +
+    ggrepel::geom_text_repel(ggplot2::aes(x = B.Bmsy, #geom_text_repel auto-jitters text around points
+                                 y = F.Fmsy,
+                                 label = species_abr,
+                                 color = stock_status$score), show.legend = FALSE,
+                             nudge_y = -0.01, nudge_x = 0.05) +
+    ggplot2::ylim(0,y.max) +
+    ggplot2::xlim(0,x.max*1.1) +
+    ggplot2::geom_text(data = unknownp, ggplot2::aes(x = x, y = y, label = text), #Custom legend for unknown stock status
+                       size = c(4.75,rep(4,3))) +
+    ggplot2::annotate(geom="text", x=0.43, y=5, label="ATL SBN (F/Fmsy = 22.5)",
+                      color="#1B9E77")+
+    ggplot2::scale_color_brewer(palette = "Dark2", #Change legend labels for clarity
+                                breaks = stock_status$score) +
+    ggplot2::xlab(expression(~B/B[msy])) +
+    ggplot2::ylab(expression(~F/F[msy])) +
+    ggplot2::guides(color = FALSE) +
+    ecodata::theme_ts()
+
+
+  return(list(p=p,unknown=unknown))
+
+  # Paste commented original plot code chunk for reference
+  # y.max <- 5
+  # x.max <- 2
+  # #Get data, spread for plotting, and filter
+  # unknown <- data.frame(text = c("Unknown Status", "ATL SBH", "SPF", "WA BFT"),
+  #                       x = rep(0.9*x.max,4), y = seq(0.88*y.max,3.5,-0.3))
+  #
+  #
+  #
+  # stock_status<-ecodata::hms_stock_status %>%
+  #   #tidyr::spread(.,Var,Value) %>%
+  #   tidyr::separate(Var, c("species_abr", "spp", "Var"), ":") %>%
+  #   tidyr::pivot_wider(names_from = Var, values_from = Value) %>%
+  #   dplyr::group_by(spp) %>%
+  #   dplyr::filter(!species_abr == "------",
+  #                 !species_abr == "-----") %>%
+  #   dplyr::mutate(score = case_when(
+  #     (B.Bmsy <0.5) ~"a",
+  #     (B.Bmsy == 0.5) ~"a",
+  #     (F.Fmsy == 1) ~ "a",
+  #     (F.Fmsy >1) ~ "a",
+  #     (F.Fmsy < 1 & B.Bmsy > 0.5 & B.Bmsy < 1) ~ "b",
+  #     (F.Fmsy < 1 & B.Bmsy > 1) ~ "c"))
+  # #Plot constants
+  #
+  #
+  # #Plotting code
+  # ggplot2::ggplot(data = stock_status) +
+  #   ggplot2::geom_vline(xintercept = 1, linetype = "dotted", color = "grey60")+
+  #   ggplot2::geom_vline(xintercept = 0.5, linetype = "dashed", color = "grey60")+
+  #   ggplot2::geom_hline(yintercept = 1, linetype = "dashed", color = "grey60") +
+  #   ggplot2::geom_point(aes(x = B.Bmsy,
+  #                           y = F.Fmsy,
+  #                           color = stock_status$score)) +
+  #   ggrepel::geom_text_repel(aes(x = B.Bmsy, #geom_text_repel auto-jitters text around points
+  #                                y = F.Fmsy,
+  #                                label = species_abr,
+  #                                color = stock_status$score), show.legend = FALSE,
+  #                            nudge_y = -0.01, nudge_x = 0.05) +
+  #   ggplot2::ylim(0,y.max) +
+  #   ggplot2::xlim(0,x.max*1.1) +
+  #   ggplot2::geom_text(data = unknown, aes(x = x, y = y, label = text), #Custom legend for unknown stock status
+  #                      size = c(4.75,rep(4,3))) +
+  #   ggplot2::annotate(geom="text", x=0.43, y=5, label="ATL SBN (F/Fmsy = 22.5)",
+  #                     color="#1B9E77")+
+  #   ggplot2::scale_color_brewer(palette = "Dark2", #Change legend labels for clarity
+  #                               breaks = stock_status$score) +
+  #   ggplot2::xlab(expression(~B/B[msy])) +
+  #   ggplot2::ylab(expression(~F/F[msy])) +
+  #   ggplot2::guides(color = FALSE) +
+  #   ecodata::theme_ts()
+  #
+
+}