A few uncommitted commits

Author: mtomasini

exploration.ipynb

@@ -25,4 +25,36 @@ def plot_comparison(dataset_1, dataset_2, title, legend_1, legend_2, output_file
     plt.grid(linestyle=':', linewidth=0.5)
     plt.title(title)
 
+    plt.savefig(output_file)
+
+
+
+def metapopulation_plot_comparison(dataset_1, dataset_2, title, legend_1, legend_2, output_file, dataset_3 = None, legend_3 = None):
+    dataset_1_global = pd.read_csv(f"{dataset_1}_metapop_set_counts.csv", index_col=0)
+    dataset_2_global = pd.read_csv(f"{dataset_2}_metapop_set_counts.csv", index_col=0)
+    
+    plt.plot(dataset_1_global.mean(axis=1), color = 'xkcd:blue')
+    plt.plot(dataset_2_global.mean(axis=1), color = 'xkcd:puce')
+    
+    plt.fill_between(dataset_1_global.index, dataset_1_global.mean(axis=1) - dataset_1_global.std(axis=1), dataset_1_global.mean(axis=1) + dataset_1_global.std(axis=1), color='xkcd:blue', alpha=0.3)
+    plt.fill_between(dataset_2_global.index, dataset_2_global.mean(axis=1) - dataset_2_global.std(axis=1), dataset_2_global.mean(axis=1) + dataset_2_global.std(axis=1), color='xkcd:puce', alpha=0.3)
+    
+    plt.axvline(500, color="black", linestyle='--', ymax=1)
+
+    if dataset_3 is not None:
+        dataset_3_global = pd.read_csv(f"{dataset_3}_metapop_set_counts.csv", index_col=0)
+        plt.plot(dataset_3_global.mean(axis=1), color = 'xkcd:light purple')
+        plt.fill_between(dataset_3_global.index, dataset_3_global.mean(axis=1) - dataset_3_global.std(axis=1), dataset_3_global.mean(axis=1) + dataset_3_global.std(axis=1), color='xkcd:light purple', alpha=0.3)
+
+
+    if dataset_3 is not None:
+        plt.legend([f"{legend_1}", f"{legend_2}", f"{legend_3}"])
+    else:
+        plt.legend([f"{legend_1}", f"{legend_2}"])
+
+    plt.ylabel("Number of feature sets")
+    plt.xlabel("Generations (x100)")
+    plt.grid(linestyle=':', linewidth=0.5)
+    plt.title(title)
+
     plt.savefig(output_file)

plotting.py

@@ -4,39 +4,43 @@
 
 from metapypulation.simulation import Simulation
 
-total_population = 800
-replicates = 1
-migrations = ['island', 'stepping_stone']
-interactions = ['neutral_interaction', 'axelrod_interaction']
+total_population = 200
+replicates = 25
+migrations = ['island'] # 'stepping_stone'
+interactions = ['neutral_interaction'] # 'axelrod_interaction'
+#number_of_subpopulations = [4]
+subpopulations = 4
+population_sizes = [[50, 50, 50, 50]]
 
 start_time = time.time()
 
+count = 0
+
 for migration in migrations:
     for interaction in interactions:
-        
-        subpopulations = 8
-        rate_of_migration = 0.001
-
-        carrying_capacity = int(np.ceil(total_population / subpopulations)) # [283, 39, 39, 39]# 
-        generations = 200000
-        burn_in = 50000
-
-        simulation = Simulation(generations, 
-                                subpopulations, 
-                                migration, 
-                                interaction,
-                                carrying_capacity,
-                                replicates,
-                                f"./Outputs/TAG2024/01-neutral-axelrod/{subpopulations}subpop_{migration}_{interaction}",
-                                burn_in = burn_in,
-                                migration_rate = rate_of_migration)
-
-        simulation.run_simulation()
-
+        for rate_of_migration in [0.001, 0.1]:
+            # rate_of_migration = 0.001
+
+            carrying_capacity = int(np.ceil(total_population / subpopulations)) # [283, 39, 39, 39]# 
+            generations = 200000 #350000
+            burn_in = 0
+
+            simulation = Simulation(generations = generations, 
+                                    number_of_subpopulations=subpopulations, 
+                                    migration_matrix = migration, 
+                                    interaction = interaction,
+                                    carrying_capacities = carrying_capacity,
+                                    replicates = replicates,
+                                    output_path = f"./Outputs/{subpopulations}subpop_popsize{population_sizes[0]}_{migration}_{interaction}_{rate_of_migration}_noburnin",  #TAG2024/04-migration-rates/{subpopulations}subpop_{migration}_{interaction}_m{rate_of_migration}",
+                                    burn_in = burn_in,
+                                    migration_rate = rate_of_migration)
+
+            simulation.run_simulation()
+            count = count + 1
     #f"./Outputs/SourceSink/pop{total_population}/{migrations}/{subpopulations}subpop_m1e-3_burnin_{carrying_capacity[0]}",
 
 end_time = time.time() - start_time
 hours = round(end_time//3600)
-minutes = round(end_time//60)
+minutes = round(end_time//60) - hours*60
 seconds = round(end_time) - hours*3600 - minutes*60
-print(f"Simulation of {replicates} replicates finished in {hours}h, {minutes}m and {seconds}s")
+print(f"Simulation of {count} sets of parameters, {replicates} replicates each, finished in {hours}h, {minutes}m and {seconds}s")