add plot_hms_cpue

NAMESPACE

@@ -37,6 +37,7 @@ export(plot_harborporpoise)
 export(plot_heatwave)
 export(plot_heatwave_peak_date)
 export(plot_heatwave_year)
+export(plot_hms_cpue)
 export(plot_ichthyo_diversity)
 export(plot_long_term_sst)
 export(plot_mab_inshore_survey)

R/plot_hms_cpue.R

@@ -0,0 +1,108 @@
+#' plot hms_cpue
+#'
+#' Plot time series of NEUS Highly Migratory Species (HMS) groups: sharks or tunas.
+#'
+#' @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 plot for both)
+#' @param varName Character string. Which Variable to plot ("shark", "tuna"). Sharks
+#' are categorized as large coastal, pelagic, prohibited, and small coastal, while
+#' tuna are by species.
+#'
+#' @return ggplot object
+#'
+#'
+#' @export
+#'
+
+plot_hms_cpue <- function(shadedRegion = shadedRegion,
+                          report="MidAtlantic",
+                          varName = "shark") {
+
+  # 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
+  varabbr <- stringr::str_to_upper(varName)
+
+  sp_cat<- ecodata::hms_category
+
+  hms <- ecodata::hms_cpue |>
+    dplyr::filter(stringr::str_detect(Var, varabbr)) #|>
+
+  if(varName=="shark"){
+    hms <-  hms |>
+    dplyr::rename(COMMON_POP = Var) |>
+    dplyr::left_join(sp_cat) |>
+    dplyr::group_by(Time, SP_CATEGORY) |>
+    dplyr::summarise(Value = sum(Value)) |>
+    dplyr::rename("Var" = "SP_CATEGORY") |>
+    dplyr::filter(!Var == "NA")
+  }
+
+  #if(varName=="all") hms <- ecodata::hms_cpue
+
+  # 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$x.shade.max
+  #
+  p <- hms |>
+    ggplot2::ggplot()+
+    ggplot2::annotate("rect", fill = setup$shade.fill, alpha = setup$shade.alpha,
+                      xmin = setup$x.shade.min , xmax = setup$x.shade.max,
+                      ymin = -Inf, ymax = Inf) +
+    ggplot2::geom_point(ggplot2::aes(x=Time, y = Value, color = Var))+
+    ggplot2::geom_line(ggplot2::aes(x=Time, y = Value, color = Var))+
+    ggplot2::scale_color_discrete(name = "Category")+
+    #{if(varName=="all") ggplot2::facet_wrap(~Var, scales = "free")}+
+    ggplot2::ggtitle(paste("HMS POP", varabbr, "CPUE"))+
+    ggplot2::ylab("Number per Haul")+
+    ecodata::theme_ts()+
+    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
+  # one code chunk: macrofauna_MAB.Rmd-hms-cpue-sharks.R
+  # sp_cat<- ecodata::hms_category
+  # ecodata::hms_cpue %>%
+  #   filter(stringr::str_detect(Var, "SHARK")) %>%
+  #   rename(COMMON_POP = Var) %>%
+  #   left_join(sp_cat) %>%
+  #   group_by(Time, SP_CATEGORY) %>%
+  #   summarise(Value = sum(Value)) %>%
+  #   rename("Var" = "SP_CATEGORY") %>%
+  #   filter(!Var == "NA") %>%
+  #   ggplot()+
+  #   ggplot2::annotate("rect", fill = shade.fill, alpha = shade.alpha,
+  #                     xmin = x.shade.min , xmax = x.shade.max,
+  #                     ymin = -Inf, ymax = Inf) +
+  #   ggplot2::geom_point(aes(x=Time, y = Value, color = Var))+
+  #   ggplot2::geom_line(aes(x=Time, y = Value, color = Var))+
+  #   ggplot2::scale_color_discrete(name = "Category")+
+  #   #ggplot2::facet_wrap(~Var, scales = "free")+
+  #   ggplot2::ggtitle("HMS POP SHARK CPUE")+
+  #   ggplot2::ylab("Number per Haul")+
+  #   ecodata::theme_ts()+
+  #   ecodata::theme_title()
+  #
+  #
+
+}