Correct temperature use case

use_cases/tritrophic-biomass-vs-temperature.jl

@@ -3,28 +3,27 @@ import ColorSchemes: tol_light
 using CairoMakie
 using DataFrames
 using EcologicalNetworksDynamics
+import EcologicalNetworksDynamics: ExtinctionCallback
 
 # Temperature gradient from 0 to 40°C, converted to Kelvin, with increments of 1°.
 T0 = 273.15 # 0°C in Kelvin.
 T40 = T0 + 40 # 40°C in Kelvin.
 T_values = values(T0:1:T40)
 
-# DataFrame to store the simulations outputs.
 df = DataFrame(; T = Float64[], trophic_level = Int64[], Beq = Float64[])
-# `set_temperature!()` expresses rates in seconds,
-# then simulation time is expressed in seconds as well.
-# Simulation length and time steps are taken from Binzer et al., 2012.
 tmax = 315_360_000_000 # From Binzer et al., 2012.
 verbose = false # Do not show '@info' messages during simulation run.
-# callback = ExtinctionCallback(1e-6, params, verbose) # Remove TerminateSteadyState callback.
 trophic_lvl = [1, 2, 3]
+callback_function(m) = ExtinctionCallback(1e-12, m._value, verbose)
 
 # Run simulations for each temperature across gradient.
 @info "Start simulations..."
 for T in T_values
-    m = default_model(Foodweb([3 => 2, 2 => 1]), ClassicResponse(; h = 1), Temperature(T))
+    m = default_model(Foodweb([3 => 2, 2 => 1]), Temperature(T))
+    m.h = 1 # Set hill exponent to 1.
     B0 = m.K[1] / 8 # Inital biomass.
-    solution = simulate(m, [B0]; tmax)
+    callback = callback_function(m)
+    solution = simulate(m, B0; tmax, callback)
     Beq_vec = solution[end]
     for (Beq, tlvl) in zip(Beq_vec, trophic_lvl)
         push!(df, [T, tlvl, Beq])
@@ -54,6 +53,5 @@ Legend(
     tellheight = true, # Adjust top subfigure height to legend height.
     tellwidth = false, # Do not adjust bottom subfigure width to legend width.
 )
-
 # To save the figure, uncomment and execute the line below.
-save("/tmp/plot.png", fig; resolution = (450, 300), px_per_unit = 3)
+save("/tmp/plot.png", fig; size = (450, 300), px_per_unit = 3)