Merge pull request #182 from NOAA-EDAB/andy_newplots

New index plots + chl_pp

NAMESPACE

@@ -10,6 +10,7 @@ export(plot_aggregate_biomass)
 export(plot_annual_chl_pp)
 export(plot_aquaculture)
 export(plot_bennet)
+export(plot_benthos_index)
 export(plot_blue_runner)
 export(plot_bottom_temp_glorys)
 export(plot_bottom_temp_insitu)
@@ -54,7 +55,6 @@ export(plot_nao)
 export(plot_narw)
 export(plot_ne_inshore_survey)
 export(plot_observed_sharks)
-export(plot_phyto_size)
 export(plot_ppr)
 export(plot_productivity_anomaly)
 export(plot_rec_hms)
@@ -88,6 +88,7 @@ export(plot_zoo_abundance_anom)
 export(plot_zoo_diversity)
 export(plot_zoo_regime)
 export(plot_zoo_strat_abun)
+export(plot_zooplankton_index)
 export(theme_facet)
 export(theme_map)
 export(theme_title)

R/benthos_index.R

@@ -0,0 +1,17 @@
+#' Benthos Index
+#'
+#' Data include Megabenthos and Macrobenthos biomass and center of gravity indices from predator diet data from NEFSC bottom trawl survey.
+#'
+#'
+#' @format n rows and 5 columns.
+#'
+#' \itemize{
+#'     \item Value: Value of variable \code{Var}.
+#'     \item Var: Variable calculated.
+#'     \item Time: Year.
+#'     \item EPU: Ecological Production Unit (EPU) where sampling occurred.
+#'     \item Units: grams per stomach.
+#' }
+#'
+#' @details Methods used to calculate data are available at \url{https://noaa-edab.github.io/tech-doc/benthos_index.html}.
+"benthos_index"

R/chl_pp.R

@@ -1,4 +1,4 @@
-#' Chlorophyll \emph{a} and primary production
+#' Chlorophyll \emph{a} and primary production and phytoplankton size class
 #'
 #' These data are time series of remotely sensed chlorophyll \emph{a} (CHL) and primary production (PP) data from the Northeast Continental Shelf.
 #' Included are median and anomaly CHL and PP estimates for Ecological Production Units, along with subsets for CHL and PP by
@@ -17,7 +17,7 @@
 #'     \item EPU: Ecological Production Unit (EPU) where sampling occurred.
 #' }
 #'
-#' @details Methods used to calculate median and anomaly data are available at \url{https://noaa-edab.github.io/tech-doc/chl-pp.html}. Methods
+#' @details Methods used to calculate median and anomaly data are available at \url{https://noaa-edab.github.io/tech-doc/chl_pp.html}. Methods
 #' used to find phytoplankton size-class information are forthcoming.
 #'
 "chl_pp"

R/forage_index.R

@@ -13,5 +13,5 @@
 #'     \item Units: grams per stomach.
 #' }
 #'
-#' @details Methods used to calculate data are available at \url{https://noaa-edab.github.io/tech-doc/forage-fish-biomass-indices.html}.
+#' @details Methods used to calculate data are available at \url{https://noaa-edab.github.io/tech-doc/forage_index.html}.
 "forage_index"

R/plot_aggregate_biomass.R

@@ -225,8 +225,7 @@ plot_aggregate_biomass <- function(shadedRegion = NULL,
 
   ### Planktivore
   p3<-agg_bio |>
-    dplyr::filter(stringr::str_detect(Var,"Planktivore"),
-                  Time <= 2023) |>
+    dplyr::filter(stringr::str_detect(Var,"Planktivore")) |>
     dplyr::mutate(Mean = dplyr::case_when(Mean >80 ~ 90,
                                            TRUE ~ Mean)) |>
 

R/plot_benthos_index.R

@@ -0,0 +1,134 @@
+#' plot benthos index
+#'
+#' Description should be here. This needs to be reworked to uncouple GB and GOM
+#'
+#' @param shadedRegion Numeric vector. Years denoting the shaded region of the plot (most recent 10)
+#' @param report Character string. Which SOE report ("MidAtlantic", "NewEngland")
+#' @param varName Character string. Benthos group name ("Macrobenthos", "Megabenthos")
+#' @param plottype Character string. Benthos biomass index by region, or coastwide center of gravity ("index", "cog")
+#' @param n Numeric scalar. Number of years used (from most recent year) to estimate short term trend . Default = 0 (No trend calculated)
+#'
+#' @return ggplot object
+#'
+#'
+#' @export
+#'
+
+plot_benthos_index <- function(shadedRegion = NULL,
+                              report="MidAtlantic",
+                              varName = "Macrobenthos",
+                              plottype = "index",
+                              n = 0) {
+
+  setup <- ecodata::plot_setup(shadedRegion = shadedRegion,
+                               report=report)
+
+  # convert to leading capital
+  varName <- stringr::str_to_sentence(varName)
+  if (!(varName %in% c("Megabenthos","Macrobenthos"))){
+    stop("varName should be either Megabenthos or Macrobenthos")
+  }
+
+
+  if (plottype == "index") {
+
+    if (report == "MidAtlantic") {
+      filterEPUs <- c("MAB")
+    } else {
+      filterEPUs <- c("GB", "GOM")
+    }
+
+    fix<- ecodata::benthos_index |>
+      dplyr::filter(Var %in% c(paste("Fall",varName,"Biomass Index Estimate"),
+                               paste("Spring",varName,"Megabenthos Biomass Index Estimate")),
+                    EPU %in% filterEPUs) |>
+      dplyr::group_by(EPU) |>
+      dplyr::summarise(max = max(Value))
+
+    p <- ecodata::benthos_index |>
+      dplyr::filter(Var %in% c(paste("Fall",varName,"Biomass Index Estimate"),
+                               paste("Fall",varName,"Biomass Index Estimate SE"),
+                               paste("Spring",varName,"Biomass Index Estimate"),
+                               paste("Spring",varName,"Biomass Index Estimate SE")),
+                    EPU %in% filterEPUs) |>
+      dplyr::group_by(EPU) |>
+      tidyr::separate(Var, into = c("Season", "A", "B", "C", "D", "Var")) |>
+      dplyr::mutate(Var = tidyr::replace_na(Var, "Mean")) |> #,
+      #max = as.numeric(Value)) |>
+      tidyr::pivot_wider(names_from = Var, values_from = Value) |>
+      dplyr::left_join(fix) |>
+      dplyr::mutate(#Value = Value/resca,
+        Mean = as.numeric(Mean),
+        #max = as.numeric(Value),
+        Mean = Mean/max,
+        SE = SE/max,
+        Upper = Mean + SE,
+        Lower = Mean - SE) |>
+      ggplot2::ggplot(ggplot2::aes(x = Time, y = Mean, group = Season))+
+      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_ribbon(ggplot2::aes(ymin = Lower, ymax = Upper, fill = Season), alpha = 0.5)+
+      ggplot2::geom_point()+
+      ggplot2::geom_line()+
+      ggplot2::ggtitle("")+
+      ggplot2::ylab(paste("Relative",varName,"Biomass"))+
+      ggplot2::xlab(ggplot2::element_blank())+
+      ggplot2::facet_wrap(.~EPU)+
+      ecodata::geom_gls()+
+      ecodata::geom_lm(n=n)+
+      ecodata::theme_ts()+
+      ecodata::theme_facet()+
+      ecodata::theme_title()
+
+    if (report == "NewEngland") {
+      p <- p +
+        ggplot2::theme(legend.position = "bottom",
+                       legend.title = ggplot2::element_blank())
+
+    }
+  }
+
+  if (plottype == "cog"){
+
+    p <- ecodata::benthos_index |>
+      dplyr::filter(Var %in% c(paste("Fall",varName,"Eastward Center of Gravity"),
+                               paste("Fall",varName,"Eastward Center of Gravity SE"),
+                               paste("Fall",varName,"Northward Center of Gravity"),
+                               paste("Fall",varName,"Northward Center of Gravity SE"),
+                               paste("Spring",varName,"Eastward Center of Gravity"),
+                               paste("Spring",varName,"Eastward Center of Gravity SE"),
+                               paste("Spring",varName,"Northward Center of Gravity"),
+                               paste("Spring",varName,"Northward Center of Gravity SE"))) |>
+      tidyr::separate(Var, into = c("Season", "A", "Direction", "B", "C", "D", "Var")) |>
+      dplyr::mutate(Var = tidyr::replace_na(Var, "Mean")) |>
+      tidyr::pivot_wider(names_from = Var, values_from = Value) |>
+      dplyr::mutate(Mean = as.numeric(Mean),
+                    Upper = Mean + SE,
+                    Lower = Mean - SE) |>
+      ggplot2::ggplot(ggplot2::aes(x = Time, y = Mean, group = Season))+
+      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_ribbon(ggplot2::aes(ymin = Lower, ymax = Upper, fill = Season), alpha = 0.3)+ #
+      ggplot2::geom_point()+
+      ggplot2::geom_line()+
+      ggplot2::ggtitle("")+
+      ggplot2::ylab(paste(varName," Center of Gravity, km"))+
+      ggplot2::xlab(ggplot2::element_blank())+
+      ggplot2::facet_wrap(~Direction, scales = "free_y")+ #Season
+      ecodata::geom_gls()+
+      ecodata::geom_lm(n=n)+
+      ecodata::theme_ts()+
+      ecodata::theme_facet()+
+      ecodata::theme_title()
+
+  }
+
+  return(p)
+
+}
+
+attr(plot_benthos_index,"report") <- c("MidAtlantic","NewEngland")
+attr(plot_benthos_index, "varName") <- c("Microbenthos", "Macrobenthos")
+attr(plot_benthos_index, "plottype") <- c("index", "cog")