Added Simpson diversity index

Author: mtomasini

exploration.ipynb

@@ -80,7 +80,7 @@ def neutral_interaction(self, interacting_individual: "Individual") -> None:
         mutation_random_number = np.random.rand()
         index_to_copy = np.random.choice(range(0, self.number_of_features))
         if mutation_random_number <= self.mutation_rate:
-            self.features[index_to_copy] = np.random.randint(low = 1, high = self.number_of_trait+1, size=1)
+            self.features[index_to_copy] = np.random.randint(low = 1, high = self.number_of_traits+1, size=1)
             self.number_of_mutations += 1
             self.number_of_changes += 1
         else:

metapypulation/individual.py

@@ -214,7 +214,32 @@ def metapopulation_test_sets(self) -> int:
 
         uniques = np.unique(traits, axis = 0)
 
-        return len(uniques)  
+        return len(uniques) 
+
+    def metapopulation_simpson(self) -> float:
+        """
+        Calculates Simpson diversity index over the whole metapopulation.
+
+        Returns:
+            float: Simpson diversity index of the metapopulation.
+        """
+        number_of_features = self.number_of_features
+        traits = np.zeros((self.get_metapopulation_size(), number_of_features))
+        i = 0
+        for subpopulation in self.subpopulations:
+            for individual in subpopulation.population:
+                traits[i] = (individual.features)
+                i += 1
+            
+        uniques, counts = np.unique(traits, axis = 0, return_counts = True)
+
+        simpson_denominators = []
+        for i in range(0, len(counts)):
+            simpson_denominators.append(counts[i]*(counts[i]-1))
+
+        simpson_diversity_index = self.get_metapopulation_size()*(self.get_metapopulation_size() - 1) / sum(simpson_denominators)
+        
+        return simpson_diversity_index
 
 
 class SubpopulationIterator(object):

metapypulation/metapopulation.py

@@ -208,6 +208,23 @@ def shannon_diversity(self) -> float:
 
         return shannon_index
 
+    def simpson_diversity(self) -> float:
+        """
+        Calculate the Simpson diversity index of the subpopulation.
+
+        Returns:
+            float: The Simpson diversity index of the subpopulation.
+        """
+        traits = self.return_traits_sets()    
+        uniques, counts = np.unique(traits, axis = 0, return_counts=True)
+        
+        simpson_denominators = []
+        for i in range(0, len(counts)):
+            simpson_denominators.append(counts[i]*(counts[i]-1))
+
+        simpson_diversity_index = self.get_population_size()*(self.get_population_size() - 1) / sum(simpson_denominators)
+
+        return simpson_diversity_index
 
 class IndividualsIterator(object):
     """