✨ explore weighted endemism metric

src/07_endemism.jl

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+import Pkg; Pkg.activate(".")
+using Distributed
+@time @everywhere include("src/required.jl")
+
+## Conditional arguments
+# outcome = "raw" # desired outcome (required)
+# outcome = "sdm" # desired outcome (required)
+# save_figures = true # should figures be overwritten (optional)
+
+# Make sure "outcome" is defined
+if !(@isdefined outcome)
+  @warn "'outcome' not defined, must be either 'raw' or 'sdm'"
+elseif (outcome != "raw" && outcome != "sdm")
+  @warn "'outcome' invalid, must be either 'raw' or 'sdm'"
+else
+  @info "'outcome' currently set to '$(outcome)'"
+end
+
+## Load distributions for all species
+@load "data/jld2/$(outcome)-distributions.jld2" distributions
+## Load matrix Y
+@load "data/jld2/$(outcome)-Y-matrices.jld2" Y Yobs Ytransf inds_obs inds_notobs
+
+## Weighted endemism
+# AOO (Area of occurrence): Species add 1/(number of sites occupied) to site scores
+
+# Number of occupied sites per species
+n_occ = map(x -> sum(filter(!isnan, x)), eachcol(Y))
+# Weight site score by number of occupied sites per species
+Yweight = hcat([replace(Y[:,i], 1 => 1/n_occ[i]) for i in 1:size(Y,2)]...)
+# Sum scores per site for all species
+endemism_scores = sum.(eachrow(Yweight))
+# Check stats
+describe(filter(!isnan, endemism_scores))
+sort(filter(!isnan, endemism_scores), rev=true) # possibly some outliers, scaling problems for visualization
+# Reshape to grid format
+endemism_grid = reshape(endemism_scores, size(distributions[1]))
+
+# Create SimpleSDMLayer with endemism values
+endemism = SimpleSDMResponse(endemism_grid, distributions[1].left, distributions[1].right, distributions[1].bottom, distributions[1].top)
+
+## Plot results
+# Raw endemism scores
+endemism_plot = plotSDM(endemism, c=:viridis)
+heatmap!(endemism_plot,
+          title = "Endemism ($outcome distributions)",
+          colorbar_title = "Weigthed endemism (area of occurrence)",
+          dpi=300)
+# Quantile endemism scores
+endemism_qplot = plotSDM(quantiles(endemism), c=:viridis)
+heatmap!(endemism_qplot,
+          title = "Endemism quantiles ($outcome distributions)",
+          colorbar_title = "Weighted endemism quantile (area of occurrence)",
+          dpi=300)
+
+## Save result
+# save_figures = true # should figures be overwritten (optional)
+if (@isdefined save_figures) && save_figures == true
+    @info "Figures saved ($(outcome) lcbd)"
+    savefig(endemism_plot, "fig/$(outcome)/07_$(outcome)_endemism.pdf")
+else
+    @info "Figures not saved ($(outcome) lcbd)"
+end
+if (@isdefined save_figures) && save_figures == true
+    @info "Figures saved ($(outcome) lcbd)"
+    savefig(endemism_qplot, "fig/quantiles/07_$(outcome)_endemism_quantiles.pdf")
+else
+    @info "Figures not saved ($(outcome) lcbd)"
+end