add plot_hms_landings

NAMESPACE

@@ -38,6 +38,7 @@ export(plot_heatwave)
 export(plot_heatwave_peak_date)
 export(plot_heatwave_year)
 export(plot_hms_cpue)
+export(plot_hms_landings)
 export(plot_ichthyo_diversity)
 export(plot_long_term_sst)
 export(plot_mab_inshore_survey)

R/plot_hms_landings.R

@@ -0,0 +1,114 @@
+#' plot hms_landings
+#'
+#' Plot time series of Highly Migratory Species (HMS) commercial landings.
+#'
+#' @param shadedRegion Numeric vector. Years denoting the shaded region of the plot (most recent 10)
+#' @param report Character string. Which SOE report ("MidAtlantic", "NewEngland").
+#' HMS landings are by Mid Atlantic or New England, not EPU
+#'
+#' @return ggplot object
+#'
+#'
+#' @export
+#'
+
+plot_hms_landings <- 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("NE")
+  }
+
+  # optional code to wrangle ecodata object prior to plotting
+  # e.g., calculate mean, max or other needed values to join below
+  apex<-ecodata::hms_landings |>
+    dplyr::filter(stringr::str_detect(Var, "Landings")) |>
+    tidyr::separate(Var, c("Var", "trash"), sep = "_") |>
+    dplyr::filter(EPU %in% filterEPUs) |>
+    dplyr::group_by(Var) |>
+    dplyr::mutate(hline = mean(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$x.shade.max
+  #
+  p <- apex |>
+    ggplot2::ggplot(ggplot2::aes(x = Time, y = Value, color = Var)) +
+    ggplot2::geom_line(size = setup$lwd) +
+    ggplot2::geom_point(size = setup$pcex) +
+    ggplot2::geom_hline(ggplot2::aes(yintercept = hline,
+                            color = Var,
+                            size = Var),
+                        size = setup$hline.size,
+                        alpha = setup$hline.alpha,
+                        linetype = setup$hline.lty)+
+    ecodata::theme_facet() +
+    ggplot2::theme(strip.text=ggplot2::element_text(hjust=0),
+                   legend.position = "bottom",
+                   legend.direction = "horizontal",
+                   legend.title = ggplot2::element_blank())+
+    ggplot2::ylab(expression("Landings (metric tons)")) +
+    ggplot2::xlab("Time")+
+    ggplot2::ggtitle(paste("HMS", setup$region, "Commercial Landings"))+
+    ecodata::theme_title()
+
+   # # optional code for New England specific (2 panel) formatting
+   #  if (report == "NewEngland") {
+   #    p <- p +
+   #      ggplot2::theme(legend.position = "bottom",
+   #                     legend.title = ggplot2::element_blank())
+   #
+   #  }
+
+    return(p)
+
+  # Paste commented original plot code chunk for reference
+  #Get data for plotting
+  # ## Apex pred
+  # apex<-ecodata::hms_landings %>%
+  #   dplyr::filter(stringr::str_detect(Var, "Landings")) %>%
+  #   #dplyr::mutate(Value = as.numeric(Value)) %>%
+  #   separate(Var, c("Var", "trash"), sep = "_") #%>%
+  # #dplyr::filter(!Var == "Smoothhound Sharks")
+  #
+  # ##Plot
+  # p1<-apex %>%
+  #   dplyr::filter(EPU == "NE") %>%
+  #   dplyr::group_by(Var) %>%
+  #   dplyr::mutate(hline = mean(Value)) %>%
+  #
+  #   ggplot2::ggplot(aes(x = Time, y = Value, color = Var)) +
+  #   ggplot2::annotate("rect", fill = shade.fill, alpha = shade.alpha,
+  #                     xmin = x.shade.min , xmax = x.shade.max,
+  #                     ymin = -Inf, ymax = Inf) +
+  #   ggplot2::geom_line(size = lwd) +
+  #   ggplot2::geom_point(size = pcex) +
+  #   # ggplot2::geom_hline(aes(yintercept = hline,
+  #   #                color = Var,
+  #   #                size = Var),
+  #   #            size = hline.size,
+  #   #            alpha = hline.alpha,
+  #   #            linetype = hline.lty)+
+  #   ecodata::theme_facet() +
+  #   ggplot2::theme(strip.text=element_text(hjust=0),
+  #                  legend.position = "bottom",
+  #                  legend.direction = "horizontal",
+  #                  legend.title = element_blank())+
+  #   ggplot2::ylab("Landings (metric tons)")+
+  #   ggplot2::ggtitle("HMS Commercial Landings")
+  # ggplot2::xlab(element_blank())+
+  #   ecodata::theme_title()
+  #
+  # p1
+  #
+
+}