added plot_habs

- PSP
- Alexandrium

NAMESPACE

@@ -3,6 +3,8 @@
 export(geom_gls)
 export(geom_lm)
 export(geom_regime)
+export(plot_HMS_species_distribution)
+export(plot_SAV)
 export(plot_bottom_temp_anomaly_glorys)
 export(plot_bottom_temp_anomaly_space)
 export(plot_bottom_temp_anomaly_survey)
@@ -11,6 +13,7 @@ export(plot_forage_anomaly)
 export(plot_forage_index)
 export(plot_function_template)
 export(plot_habitat_diversity)
+export(plot_habs)
 export(plot_setup)
 export(plot_sst)
 export(plot_sst_anomaly)

R/plot_habitat_diversity.R

@@ -13,7 +13,7 @@
 #'
 
 plot_habitat_diversity <- function(shadedRegion = shadedRegion,
-                              report="MidAtlantic",Var = "Diversity") {
+                              report="MidAtlantic",varName = "Diversity") {
 
   # generate plot setup list (same for all plot functions)
   setup <- ecodata::plot_setup(shadedRegion = shadedRegion,
@@ -30,10 +30,10 @@ plot_habitat_diversity <- function(shadedRegion = shadedRegion,
 
   # optional code to wrangle ecodata object prior to plotting
   # e.g., calculate mean, max or other needed values to join below
-  if (Var == "Diversity") {
-    varName <- "Shannon"
+  if (varName == "Diversity") {
+    varNames <- "Shannon"
     fix<- ecodata::habitat_diversity |>
-      dplyr::filter(Var == varName,
+      dplyr::filter(Var == varNames,
                     EPU %in% filterEPUs) |>
       dplyr::group_by(EPU) |>
       dplyr::mutate(mean = as.numeric(Value),
@@ -46,7 +46,7 @@ plot_habitat_diversity <- function(shadedRegion = shadedRegion,
   # xmin = setup$x.shade.min , xmax = setup$x.shade.max
   #
   p <- ecodata::habitat_diversity |>
-    dplyr::filter(grepl(varName,Var)) |>
+    dplyr::filter(grepl(varNames,Var)) |>
     dplyr::group_by(EPU) |>
     dplyr::mutate(mean = as.numeric(Value),
                   Time = as.numeric(Time),
@@ -69,9 +69,9 @@ plot_habitat_diversity <- function(shadedRegion = shadedRegion,
     ecodata::theme_title()
 
   } else { # Richness
-    varName <- "Richness"
+    varNames <- "Richness"
     fix<- ecodata::habitat_diversity |>
-      dplyr::filter(grepl(varName,Var),
+      dplyr::filter(grepl(varNames,Var),
                     EPU %in% filterEPUs) |>
       tidyr::separate(Var, into = c("Var", "Richness"),sep = "-") |>
       tidyr::pivot_wider(values_from = "Value", names_from = "Var") |>
@@ -88,7 +88,7 @@ plot_habitat_diversity <- function(shadedRegion = shadedRegion,
     # xmin = setup$x.shade.min , xmax = setup$x.shade.max
     #
     p <- ecodata::habitat_diversity |>
-      dplyr::filter(grepl(varName,Var)) |>
+      dplyr::filter(grepl(varNames,Var)) |>
       tidyr::separate(Var, into = c("Var", "Richness"),sep = "-") |>
       tidyr::pivot_wider(values_from = "Value", names_from = "Var") |>
       dplyr::group_by(EPU) |>

R/plot_habs.R

@@ -0,0 +1,67 @@
+#' plot harmful algal bloom
+#'
+#' Plots alexandrium counts, PSP
+#'
+#' @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. Which Variable to plot ("Alexandrium", "PSP")
+#'
+#' @return ggplot object
+#'
+#'
+#' @export
+#'
+
+plot_habs <- function(shadedRegion = shadedRegion,
+                              report="MidAtlantic",
+                              varName = "Alexandrium") {
+
+  # 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","NE")
+  }
+
+  if (varName == "PSP"){
+    plotTitle <- "Percent PSP Samples in Blue Mussels"
+    plotylab <- "Percentage of samples that exceed the threshold"
+    plotLegend <- "State"
+  } else if(varName == "Alexandrium") {
+    plotTitle <- "Gulf of Maine Alexandrium Cyst Abundance"
+    plotylab <- expression("Cyst Abundance (10"^6*"Cells)")
+    plotLegend <- "Region"
+
+  }
+
+  # 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$x.shade.max
+
+  p <-  ecodata::habs |>
+     dplyr::filter(Source == varName,
+                   EPU %in% filterEPUs) |>
+     ggplot2::ggplot(ggplot2::aes(x = Time, y = Value, color = Var))+
+     ggplot2::annotate("rect", fill = setup$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::theme_ts()+
+     ggplot2::scale_color_discrete(name = plotLegend)+
+     ecodata::theme_title()+
+     ggplot2::ylab(plotylab)+
+     ggplot2::xlab(ggplot2::element_blank())+
+     ggplot2::ggtitle(plotTitle)+
+     ecodata::theme_facet()
+
+
+    return(p)
+
+
+}