setwd("~/Desktop/inPrep/pew/github/erp/Rmd")

Consumption of forage fish in Ecopath

This is an R Markdown document for the visualization of outputs from the Ecopath component of Ecopath with Ecosim (EwE) models of Northeast Atlantic regional seas. Models used in this work include those covering the extent of:

1. The Irish Sea (ICES VIIa),
2. The Celtic Sea (ICES VIIe, VIIf, VIIh, VIIj.2),
3. The West Coast of Scotland (VIa),
4. The Greater North Sea (IVa, IVb, IVc),
5. The Northern North Sea (IVa),
6. The Norwegian Sea and Barents Sea (Ia, Ib, IIa, IIb)

Ecopath components for all of the above models were available for this study. From these models, covering a single year snapshot, we have extracted the estimated consumption (tonnes per km-2) for key forage fish species. This analysis provides an overview of the ecosystem role of species in the available ecosystem models and enables regional comparison of 1) the quantity of forage fish species consumed and 2) the quantity of forage fish consumed by predator species.

# Code to create an ordered stacked bar char for the consumption of forage fish in each modelled region

# Create a new data frame with the sum of Consumption by Region
Forage_sum <- aggregate(Consumption ~ Region, data = Forage, FUN = sum)

# Order the Region variable based on the sum of Consumption
Forage_sum_ordered <- Forage_sum[order(Forage_sum$Consumption, decreasing = TRUE), ]

# Create the ordered stacked bar plot for forage fish consumed in each region
# Define the color palette from viridis for all prey categories
prey_colors <- viridis_pal(option = "D")(10)

# Set the "Unspecified" category to light grey
prey_colors[10] <- "lightgrey"

FF_consumption <- ggplot(Forage, aes(x = reorder(Region, -Consumption, FUN = sum), y = Consumption, fill = Prey)) +
  geom_bar(stat = "identity") +
  labs(x = "Model region", y = expression("Forage fish consumed t." ~ km^{-2}), fill = "Forage fish") +
  scale_fill_manual(name = "Forage fish", values = prey_colors) +
  theme_minimal() +
  theme(panel.background = element_rect(fill = "white", color = "black"),
        axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1))
FF_consumption

ggsave("../outputs/figs/FF_consumption.png", FF_consumption, dpi = 500)

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# Code to create an ordered stacked bar char for the consumption of forage fish by predator

# Create a new data frame with the sum of Consumption by Region
Forage_sum <- aggregate(Consumption ~ Region, data = Forage, FUN = sum)

# Order the Region variable based on the sum of Consumption
Forage_sum_ordered <- Forage_sum[order(Forage_sum$Consumption, decreasing = TRUE), ]

# Create the ordered stacked bar plot for forage fish consumption by predator
FF_preds<-ggplot(Forage, aes(x = reorder(Region, -Consumption, FUN = sum), y = Consumption, fill = Predator)) +
  geom_bar(stat = "identity") +
  labs(x = "Model region", y = expression("Forage fish consumed t." ~ km^{-2}), fill = "Forage fish") +
  scale_fill_viridis_d(name = "Predator") +
  theme_minimal() +
  theme(panel.background = element_rect(fill = "white", color = "black"),
        axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1))

ggsave("../outputs/figs/FF_preds.png", FF_preds, dpi = 500)

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FF_preds

library(cowplot)

# Your plot objects (FF_consumption and FF_preds)
# ...

# Add titles to the plots
plot_with_title1 <- plot_grid(FF_consumption + 
                                 ggtitle("a)"),
                              align = "v",
                              ncol = 1)

plot_with_title2 <- plot_grid(FF_preds + 
                               ggtitle("b)"),
                             align = "v",
                             ncol = 1)

# Arrange the plots with titles
grid_arranged <- plot_grid(plot_with_title1, plot_with_title2,
                           ncol = 2)

# Print or display the arranged plots
print(grid_arranged)

ggsave("../outputs/figs/FF_grid_plot.png", grid_arranged, dpi = 500, width=10)

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