add plot_harborporpoise

NAMESPACE

@@ -33,6 +33,7 @@ export(plot_grayseal)
 export(plot_gsi)
 export(plot_habitat_diversity)
 export(plot_habs)
+export(plot_harborporpoise)
 export(plot_ichthyo_diversity)
 export(plot_long_term_sst)
 export(plot_mab_inshore_survey)

R/plot_harborporpoise.R

@@ -0,0 +1,89 @@
+#' plot harborporpoise
+#'
+#'Time series of annual and 5 year rolling mean harbor porpoise bycatch with potential
+#' biological removal (PRB) threshold. Same plot for both regions.
+#'
+#' @param shadedRegion Numeric vector. Years denoting the shaded region of the plot (most recent 10)
+#' @param report Character string. Which SOE report ("MidAtlantic", "NewEngland")
+#'
+#' @return ggplot object
+#'
+#'
+#' @export
+#'
+
+plot_harborporpoise <- 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
+  ribbon<- ecodata::harborporpoise |>
+    tidyr::pivot_wider(names_from = Var, values_from = Value)
+
+  # 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 <- ecodata::harborporpoise |>
+    dplyr::filter(Var %in% c("pbr", "totalest5y", "totalest1y")) |>
+    ggplot2::ggplot()+
+    ggplot2::geom_line(ggplot2::aes(x = Time, y = Value, linetype = Var, color = Var))+
+    ggplot2::geom_ribbon(data = ribbon, ggplot2::aes(ymin = total5yLCI, ymax =total5yUCI, x = Time), fill = "blue", alpha = 0.2)+
+    ggplot2::ggtitle("Harbor Porpoise Bycatch")+
+    ggplot2::ylab("Estimated Bycatch (n)")+
+    ggplot2::scale_linetype_manual(name="",
+                                   values=c(1,2,1),
+                                   labels = c("PBR", "Annual Estimates", "5yr rolling mean and CI"))+
+    ggplot2::scale_color_manual(name="",values = c('red', 'black','blue'),
+                                labels = c("PBR", "Annual Estimates", "5yr rolling mean and CI"))+
+    ggplot2::theme(#legend.position = "none",
+      legend.title = ggplot2::element_blank(),
+      legend.position = c(0.75, 0.8),
+      legend.text = ggplot2::element_text(size = 8),
+      legend.background = ggplot2::element_rect(
+        colour = "transparent", fill = "transparent"))+
+    #ggplot2::guides(color = "none")+
+    ecodata::theme_ts()+
+    ecodata::theme_title()
+
+    return(p)
+
+  # Paste commented original plot code chunk for reference
+  # ribbon<- ecodata::harborporpoise %>%
+  #   tidyr::pivot_wider(names_from = Var, values_from = Value)
+  #
+  # ecodata::harborporpoise %>%
+  #   dplyr::filter(Var %in% c("pbr", "totalest5y", "totalest1y")) %>%
+  #   ggplot2::ggplot()+
+  #   ggplot2::geom_line(aes(x = Time, y = Value, linetype = Var, color = Var))+
+  #   ggplot2::geom_ribbon(data = ribbon, aes(ymin = total5yLCI, ymax =total5yUCI, x = Time), fill = "blue", alpha = 0.2)+
+  #   ggplot2::ggtitle("Harbor Porpoise Bycatch")+
+  #   ggplot2::ylab("Estimated Bycatch (n)")+
+  #   ggplot2::scale_color_manual(name = element_blank(), values = c('red', 'black','blue'))+
+  #   ggplot2::scale_linetype_manual(values=c(1,2,1),
+  #                                  labels = c("PBR", "Annual Estimates", "5yr rolling mean and CI"))+
+  #   ggplot2::theme(#legend.position = "none",
+  #     legend.title = element_blank(),
+  #     legend.position = c(0.75, 0.8),
+  #     legend.text = element_text(size = 8),
+  #     legend.background = element_rect(
+  #       colour = "transparent", fill = "transparent"))+
+  #   guides(color = FALSE)+
+  #   ecodata::theme_ts()+
+  #   ecodata::theme_title()
+  #
+  #
+
+}