adds plot_SAV

R/plot_SAV.R

@@ -0,0 +1,112 @@
+#' plot <dataset name>
+#'
+#' <Insert description of plot function.>
+#'
+#' @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_SAV <- 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
+  sav <- ecodata::SAV |>
+    dplyr::filter(!Var == "Baywide",
+                  !Var == "Oligohaline",
+                  !Var == "Mesohaline") |>
+      dplyr::mutate(Var = dplyr::recode(Var,
+                                 "Tidal" = "Tidal Fresh",
+                                 "Polyhaline" = "High Salinity"),
+                    Var = factor(Var, levels = c("Tidal Fresh", "High Salinity"))) |>
+      dplyr::mutate(Value = (Value/1000))
+
+  # 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$x.shade.max
+  #
+  p <- sav |>
+    ggplot2::ggplot(ggplot2::aes(x = Time, y = Value))+
+    ggplot2::annotate("rect", fill = setup$shade.fill, alpha = setup$shade.alpha,
+                      xmin = setup$x.shade.min , xmax = setup$x.shade.max,
+                      ymin = -Inf, ymax = Inf) +
+    ggplot2::geom_point()+
+    ggplot2::geom_line()+
+    #ecodata::geom_lm(aes(x = Time, y = Value))+
+    ggplot2::facet_wrap(~Var)+
+    ecodata::geom_gls(ggplot2::aes(x = Time, y = Value)) +
+    ecodata::theme_ts()+
+    ggplot2::theme(strip.text = ggplot2::element_text(hjust=0,
+                                           face = "italic"),
+                   axis.title.y = ggplot2::element_text(angle = 90),
+                   legend.title = ggplot2::element_blank()) +
+    # ggplot2::scale_color_discrete(name = "",
+    # labels = c("Lower bay",  "Upper Bay"))+
+    ecodata::theme_title()+
+    ggplot2::ylab(expression("Acres (10"^3*")"))+
+    ggplot2::xlab(ggplot2::element_blank())+
+    ggplot2::ggtitle("Submerged Aquatic Vegetation (SAV) Abundance")+
+    ecodata::theme_facet()
+
+   # 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
+  # ecodata::SAV %>%
+  # dplyr::filter(!Var == "Baywide",
+  #               !Var == "Oligohaline",
+  #               !Var == "Mesohaline") %>%
+  #   dplyr::mutate(Var = recode(Var,
+  #                              "Tidal" = "Tidal Fresh",
+  #                              "Polyhaline" = "High Salinity"),
+  #                 Var = factor(Var, levels = c("Tidal Fresh", "High Salinity"))) %>%
+  #   dplyr::mutate(Value = (Value/1000)) %>%
+  #   ggplot2::ggplot(aes(x = Time, y = Value))+
+  #   ggplot2::annotate("rect", fill = shade.fill, alpha = shade.alpha,
+  #                     xmin = x.shade.min , xmax = x.shade.max,
+  #                     ymin = -Inf, ymax = Inf) +
+  #   ggplot2::geom_point()+
+  #   ggplot2::geom_line()+
+  #   #ecodata::geom_lm(aes(x = Time, y = Value))+
+  #   ggplot2::facet_wrap(~Var)+
+  #   ecodata::geom_gls(aes(x = Time, y = Value)) +
+  #   ecodata::theme_ts()+
+  #   ggplot2::theme(strip.text=element_text(hjust=0,
+  #                                          face = "italic"),
+  #                  axis.title.y = element_text(angle = 90),
+  #                  legend.title = element_blank()) +
+  #   # ggplot2::scale_color_discrete(name = "",
+  #   # labels = c("Lower bay",  "Upper Bay"))+
+  #   ecodata::theme_title()+
+  #   ggplot2::ylab(expression("Acres (10"^3*")"))+
+  #   ggplot2::xlab(element_blank())+
+  #   ggplot2::ggtitle("Submerged Aquatic Vegetation (SAV) Abundance")+
+  #   ecodata::theme_facet()
+  #
+  #
+
+}