added plot_stock_status

DESCRIPTION

@@ -23,7 +23,8 @@ Imports:
   scales,
   sf,
   stringr,
-  kableExtra
+  kableExtra,
+  ggrepel
 Suggests:
     knitr,
     rmarkdown,

NAMESPACE

@@ -20,6 +20,7 @@ export(plot_seasonal_bt_anomaly_gridded)
 export(plot_seasonal_oisst_anom)
 export(plot_seasonal_sst_anomaly_gridded)
 export(plot_setup)
+export(plot_stock_status)
 export(plot_stom_fullness)
 export(plot_storminess)
 export(plot_survey_shannon)

R/plot_stock_status.R

@@ -0,0 +1,99 @@
+#' plot stock_Status
+#'
+#' Kobe plots of regional stock status
+#'
+#' @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 list of 2 items
+#'
+#' \item{p}{ggplot object}
+#' \item{unknown}{data frame listing stocks with unklnown status}
+#'
+#'
+#' @export
+#'
+
+plot_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") {
+    councils <- c("MAFMC","Both")
+  } else {
+    councils <- c("NEFMC","Both")
+  }
+
+  # optional code to wrangle ecodata object prior to plotting
+  # e.g., calculate mean, max or other needed values to join below
+   fix<- ecodata::stock_status |>
+     dplyr::mutate(Code = dplyr::recode(Code, "Dogfish" = "Sp. Dogfish" ),
+                   Code = dplyr::recode(Code, "Mackerel" = "At. Mackerel"))
+   fix <- tidyr::pivot_wider(fix,names_from=Var,values_from=Value) |>
+     dplyr::filter(Council %in% councils) |>
+     (\(.) { . ->> unfiltered})() |>
+     dplyr::group_by(Stock) |>
+     dplyr::mutate(score = dplyr::case_when(
+       #(B.Bmsy < 0.5) ~"a",
+       (F.Fmsy > 1 & B.Bmsy > 0.5 & B.Bmsy < 1) ~ "a",
+       (F.Fmsy < 1 & B.Bmsy > 0.5 & B.Bmsy < 1) ~ "b",
+       (F.Fmsy < 1 & B.Bmsy > 1) ~ "c",
+       (F.Fmsy > 1 & B.Bmsy < 0.5) ~ "d",
+       (F.Fmsy < 1 & B.Bmsy < 0.5) ~ "b",
+       (F.Fmsy > 1 & B.Bmsy > 1) ~ "c")) |>
+     dplyr::mutate(Council = dplyr::recode(Council, "Both" = "NEFMC/MAFMC")) |>
+     dplyr::filter(!(is.na(F.Fmsy) | is.na(B.Bmsy)))
+
+   unknown <- unfiltered |>
+     dplyr::filter(is.na(F.Fmsy) | is.na(B.Bmsy)) |>
+     dplyr::select(Stock,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$x.shade.max
+  #
+  p <- fix |>
+    ggplot2::ggplot()+
+    ggplot2::geom_vline(xintercept = 1, linetype = "dotted")+
+    ggplot2::geom_vline(xintercept = 0.5, linetype = "dashed")+
+    ggplot2::geom_hline(yintercept = 1, linetype = "dashed") +
+    ggplot2::geom_point(ggplot2::aes(x = B.Bmsy,
+                            y = F.Fmsy,
+                            shape = Council,
+                            color = score)) +
+    ggrepel::geom_text_repel(ggplot2::aes(x = B.Bmsy, #geom_text_repel auto-jitters text around points
+                                 y = F.Fmsy,
+                                 label = Code,
+                                 color = score),
+                             show.legend = FALSE, nudge_y = -0.01, nudge_x = 0.05) +
+    ggplot2::scale_color_brewer(palette = "Dark2",
+                                breaks = fix$score) +
+    # ggplot2::ylim(0,y.max) +
+    # ggplot2::xlim(0,x.max) +
+    # ggplot2::geom_text(data = unknown, ggplot2::aes(x = x-0.5, y = y+0.2, label = text), #Custom legend for unknown stock status
+    #                    size = c(4.75,rep(4,6))) +
+    ggplot2::xlab(expression(~B/B[msy])) +
+    ggplot2::ylab(expression(~F/F[msy])) +
+    ggplot2::guides(color = "none") +
+    ggplot2::ggtitle(paste0(report,": stock status"))+
+    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(list(p=p,unknown=unknown))
+
+
+
+}