analysis/Supp_Info_FIG_3.R

In LorenzoCattarino/priorityeffort: Prioritization of conservation management effort.

# load R packages
library(ggplot2)
library(grid)
library(gridExtra)

# load R functions
source(file.path('R','post_processing','plotting_expert_responses.R'))

# load data
Species_Responses_Data <- read.csv (file.path('data', 'Species_Responses_all_threats.csv'), header=TRUE, sep = ',')

# keep only data for threats 1, 2, 4 ans 7
species_responses <- species_response_data[which(species_response_data[,'Threat']==1 | species_response_data[,'Threat']==2 | species_response_data[,'Threat']==4 | species_response_data[,'Threat']==7),]

# change threat names
species_responses[which(species_responses[,'Threat']==1),'Threat'] <- 'Buffalos'
species_responses[which(species_responses[,'Threat']==2),'Threat'] <- 'Pigs'
species_responses[which(species_responses[,'Threat']==4),'Threat'] <- 'Grazing'
species_responses[which(species_responses[,'Threat']==7),'Threat'] <- 'Paragrass'

# change faunal group names
species_responses[which(species_responses[,'FaunalGroup']==1),'FaunalGroup'] <- 'Fishes'
species_responses[which(species_responses[,'FaunalGroup']==2),'FaunalGroup'] <- 'Turtles'
species_responses[which(species_responses[,'FaunalGroup']==3),'FaunalGroup'] <- 'Waterbirds'

## change ecological group names
# for fishes
species_responses[which(species_responses[,'FaunalGroup']=='Fishes' & species_responses[,'EcologicalGroup']==1),'EcologicalGroup'] <- 'Large-bodied migratory carnivores'
species_responses[which(species_responses[,'FaunalGroup']=='Fishes' & species_responses[,'EcologicalGroup']==2),'EcologicalGroup'] <- 'Large-bodied herbivore/omnivores'
species_responses[which(species_responses[,'FaunalGroup']=='Fishes' & species_responses[,'EcologicalGroup']==3),'EcologicalGroup'] <- 'Large-bodied carnivores'
species_responses[which(species_responses[,'FaunalGroup']=='Fishes' & species_responses[,'EcologicalGroup']==4),'EcologicalGroup'] <- 'Small-bodied migratory invertivore'
species_responses[which(species_responses[,'FaunalGroup']=='Fishes' & species_responses[,'EcologicalGroup']==5),'EcologicalGroup'] <- 'Grunters'
species_responses[which(species_responses[,'FaunalGroup']=='Fishes' & species_responses[,'EcologicalGroup']==6),'EcologicalGroup'] <- 'Small-bodied invertivore'
# for turltes
species_responses[which(species_responses[,'FaunalGroup']=='Turtles' & species_responses[,'EcologicalGroup']==1),'EcologicalGroup'] <- 'Pig-nosed turtle'
species_responses[which(species_responses[,'FaunalGroup']=='Turtles' & species_responses[,'EcologicalGroup']==2),'EcologicalGroup'] <- 'Sandstone snake-necked turtle'
species_responses[which(species_responses[,'FaunalGroup']=='Turtles' & species_responses[,'EcologicalGroup']==3),'EcologicalGroup'] <- 'Northern snake-necked turtle'
species_responses[which(species_responses[,'FaunalGroup']=='Turtles' & species_responses[,'EcologicalGroup']==4),'EcologicalGroup'] <- 'Northern snapping turtle'
species_responses[which(species_responses[,'FaunalGroup']=='Turtles' & species_responses[,'EcologicalGroup']==5),'EcologicalGroup'] <- 'Common sawshell turtle'
species_responses[which(species_responses[,'FaunalGroup']=='Turtles' & species_responses[,'EcologicalGroup']==6),'EcologicalGroup'] <- 'Short-necked turtles'
# for waterbirds
species_responses[which(species_responses[,'FaunalGroup']=='Waterbirds' & species_responses[,'EcologicalGroup']==1),'EcologicalGroup'] <- 'Ducks, small grebes and Jacana'
species_responses[which(species_responses[,'FaunalGroup']=='Waterbirds' & species_responses[,'EcologicalGroup']==2),'EcologicalGroup'] <- 'Herbivores'
species_responses[which(species_responses[,'FaunalGroup']=='Waterbirds' & species_responses[,'EcologicalGroup']==3),'EcologicalGroup'] <- 'Large wading birds'
species_responses[which(species_responses[,'FaunalGroup']=='Waterbirds' & species_responses[,'EcologicalGroup']==4),'EcologicalGroup'] <- 'Small wading birds and shorebirds'
species_responses[which(species_responses[,'FaunalGroup']=='Waterbirds' & species_responses[,'EcologicalGroup']==5),'EcologicalGroup'] <- 'Small piscivores'
species_responses[which(species_responses[,'FaunalGroup']=='Waterbirds' & species_responses[,'EcologicalGroup']==6),'EcologicalGroup'] <- 'Large piscivores'

# set factors for ggplot
species_responses$Intensity <- factor(species_responses$Intensity)
species_responses$EcologicalGroup <- factor(species_responses$EcologicalGroup)
species_responses$FaunalGroup <- factor(species_responses$FaunalGroup)
species_responses$Threat <- factor(species_responses$Threat)

# subdivide data in three faunal groups
species_responses_fishes <- species_responses[which(species_responses[,'FaunalGroup']=='Fishes'),]
species_responses_turtles <- species_responses[which(species_responses[,'FaunalGroup']=='Turtles'),]
species_responses_waterbirds <- species_responses[which(species_responses[,'FaunalGroup']=='Waterbirds'),]

#dev.new(width=20, height=15)

plot_1 <- ggplot(species_responses_fishes, aes(x=Intensity, y=PP_BestGuess, fill=EcologicalGroup)) +
  facet_grid(Threat~FaunalGroup) +
  geom_bar(position=position_dodge(), stat="identity",
           colour="black", # Use black outlines,
           size=.3) +      # Thinner lines
  geom_errorbar(aes(ymin=norm_Lb, ymax=norm_Ub),
                size=.5,    # Thinner lines
                width=.5,
                position=position_dodge(.9)) +
  xlab("") +
  ylab("Probability of persistence") +
  ggtitle("") +
  scale_y_continuous(limits=c(0, 1)) +
  theme_bw() +
  theme(plot.margin=unit(c(0.5,0,0.5,0.5), "cm")) +
  scale_fill_brewer(name="Ecological groups of fishes", # Legend label, use darker colors
                    breaks=c("Grunters", "Large-bodied carnivores", "Large-bodied herbivore/omnivores", "Large-bodied migratory carnivores", "Small-bodied invertivore", "Small-bodied migratory invertivore"),
                    labels=c("Grunters", "Large-bodied carnivores", "Large-bodied herbivore/omnivores", "Large-bodied migratory carnivores", "Small-bodied invertivore", "Small-bodied migratory invertivore"),
                    palette='Blues')

plot_2 <- ggplot(species_responses_turtles, aes(x=Intensity, y=PP_BestGuess, fill=EcologicalGroup)) +
  facet_grid(Threat~FaunalGroup) +
  geom_bar(position=position_dodge(), stat="identity",
           colour="black", # Use black outlines,
           size=.3) +      # Thinner lines
  geom_errorbar(aes(ymin=norm_Lb, ymax=norm_Ub),
                size=.5,    # Thinner lines
                width=.5,
                position=position_dodge(.9)) +
  xlab("Threat intensity") +
  ggtitle("") +
  scale_y_continuous(limits=c(0, 1)) +
  theme_bw() +
  theme(axis.line=element_blank(),
        axis.text.y=element_blank(),
        axis.ticks=element_blank(),
        axis.title.y=element_blank()) +
  theme(plot.margin=unit(c(0.5,0,0.5,0), "cm")) +
  scale_fill_brewer(name="Ecological groups of turtles", # Legend label, use darker colors
                    breaks=c("Common sawshell turtle", "Northern snake-necked turtle", "Northern snapping turtle", "Pig-nosed turtle", "Sandstone snake-necked turtle", "Short-necked turtles"),
                    labels=c("Common sawshell turtle", "Northern snake-necked turtle", "Northern snapping turtle", "Pig-nosed turtle", "Sandstone snake-necked turtle", "Short-necked turtles"),
                    palette='YlOrBr')

plot_3 <- ggplot(species_responses_waterbirds, aes(x=Intensity, y=PP_BestGuess, fill=EcologicalGroup)) +
  facet_grid(Threat~FaunalGroup) +
  geom_bar(position=position_dodge(), stat="identity",
           colour="black", # Use black outlines,
           size=.3) +      # Thinner lines
  geom_errorbar(aes(ymin=norm_Lb, ymax=norm_Ub),
                size=.5,    # Thinner lines
                width=.5,
                position=position_dodge(.9)) +
  xlab("") +
  ylab("Probability of persistence") +
  ggtitle("") +
  scale_y_continuous(limits=c(0, 1)) +
  theme_bw() +
  theme(axis.line=element_blank(),
        axis.text.y=element_blank(),
        axis.ticks=element_blank(),
        axis.title.y=element_blank()) +
  theme(plot.margin=unit(c(0.5,0.5,0.5,0), "cm")) +
  scale_fill_brewer(name="Ecological groups of waterbirds", # Legend label, use darker colors
                    breaks=c("Ducks, small grebes and Jacana", "Herbivores", "Large piscivores", "Large wading birds", "Small piscivores", "Small wading birds and shorebirds"),
                    labels=c("Ducks, small grebes and Jacana", "Herbivores", "Large piscivores", "Large wading birds", "Small piscivores", "Small wading birds and shorebirds"),
                    palette='YlGn')

g_legend<-function(a.gplot){
  tmp <- ggplot_gtable(ggplot_build(a.gplot))
  leg <- which(sapply(tmp$grobs, function(x) x$name) == "guide-box")
  legend <- tmp$grobs[[leg]]
  legend
}

legend_1 <- g_legend(plot_1)
legend_2 <- g_legend(plot_2)
legend_3 <- g_legend(plot_3)

tiff(filename = file.path('figures', 'plot_of_expert_responses.tif'),
     width = 35, height = 20, units = "cm", pointsize = 12,
     compression = "lzw",
     bg = "white", res = 300)

grid.arrange(cbind(ggplotGrob(plot_1 + theme(legend.position = 'none')), ggplotGrob(plot_2 + theme(legend.position = 'none')), ggplotGrob(plot_3 + theme(legend.position = 'none')), size="last"), rbind(legend_1,legend_2,legend_3, size="last"), ncol = 2, widths=c(4/5,1/5))

dev.off()