Merge pull request #198 from LABSS/setup_siblings

Added setup siblings

mesa/Person.py

@@ -108,7 +108,6 @@ def random_links(self, exclude_partner_net=False):
                 self.neighbors.get(net).add(self.m.rng.choice(Person.persons))
             self.neighbors.get(net).discard(self)
 
-
     @staticmethod
     def NumberOfLinks():
         return sum([ 
@@ -232,7 +231,7 @@ def enroll_to_school(self, level):
         self.my_school = self.m.rng.choice(self.potential_school)
         self.my_school.my_students.add(self)
 
-    def get_link_list(self, net_name):
+    def get_neighbor_list(self, net_name):
         """
         Given the name of a network, this method returns a list of agents within the network.
         If the network is empty, it returns an empty list.

mesa/mesaPROTON_OC.py

@@ -401,34 +401,54 @@ def setup_persons_and_friendship(self):
         # nx.draw(watts_strogatz, with_labels=True)
         # plt.show()
 
-    def incestuos(self, ego, candidates):
-        all_potential_siblings = [ego] + candidates + list(ego.neighbors.get('sibling')) + [s for c in candidates for s
-                                                                                            in
-                                                                                            c.neighbors.get('sibling')]
-        return ego.neighbors.get("partner").pop() in all_potential_siblings
+    def list_contains_problems(self, ego, candidates):
+        """
+        This procedure checks if there are any links between partners within the candidate pool.
+        Returns True if there are, None if there are not.
+        It is used during the setup_siblings procedure to avoid incestuous marriages.
+        :param ego: Person
+        :param candidates: list of Person objects
+        :return: bool, True if there are links between partners, None otherwise.
+        """
+        all_potential_siblings = [ego] + ego.get_neighbor_list("sibling") + candidates + [sibling for candidate in candidates for sibling in candidate.neighbors.get('sibling')]
+        for sibling in all_potential_siblings:
+            if sibling.get_neighbor_list("partner") and sibling.get_neighbor_list("partner")[0] in all_potential_siblings:
+                return True
 
     def setup_siblings(self):
-        for p in [p for p in self.schedule.agents if
-                  p.neighbors.get('parent')]:  # simulates people who left the original household.
-            num_siblings = self.rng.poisson(0.5)  # 0.5 -> the number of links is N^3 agents, so let's keep this low
+        """
+        Right now, during setup, links between agents are only those within households, between friends
+        and related to the school. At this stage of the standard setup, agents are linked through "siblings" links
+        outside the household. To simulate agents who have left the original household, agents who have
+        children are taken and "sibling" links are created taking care not to create incestuous relationships.
+        :return: None
+        """
+        agent_left_household = [p for p in self.schedule.agents if p.neighbors.get('offspring')] # simulates people who left the original household.
+        for agent in agent_left_household:
+            num_siblings = self.rng.poisson(0.5)
+            # 0.5 -> the number of links is N^3 agents, so let's keep this low
             # at this stage links with other persons are only relatives inside households and friends.
-            candidates = [c for c in self.schedule.agents if
-                          c.neighbors.get('parent') and not p.isneighbor(c) and abs(p.age() - c.age()) < 5]
-            candidates = [c for c in self.schedule.agents if not p.isneighbor(c) and abs(p.age() - c.age()) < 5]
-            candidates = self.rng.choice(candidates, min(len(candidates), 5), False).tolist()
-            print("len cand:" + str(len(candidates)))
-            # remove couples from candidates and their neighborhoods
-            while len(candidates) > 0 and not self.incestuos(p, candidates):
-                # trouble should exist, or incestous would be false.
-                trouble = self.rng.choice(
-                    [x for x in candidates if x.neighbors.get("partner").pop()], 1).tolist()
-                candidates = cadidates.remove(trouble)
-            targets = p + self.rng.choice(candidates,
-                                           min(len(candidates, num_siblings))
-                                           )
-            targets = targets + set([x.neighbors.get("siblings") for x in targets])
-            for x in targets:
-                x.addSiblingLinks(p)
+            candidates = [c for c in agent_left_household if c not in agent.neighbors.get("household") and abs(agent.age() - c.age()) < 5 and c != agent]
+            # remove couples from candidates and their neighborhoods (siblings)
+            if len(candidates) >= 50:
+                candidates = self.rng.choice(candidates, 50, replace=False).tolist()
+            while len(candidates) > 0 and self.list_contains_problems(agent, candidates):
+                # trouble should exist, or check-all-siblings would fail
+                potential_trouble = [x for x in candidates if agent.get_neighbor_list("partner")]
+                trouble = self.rng.choice(potential_trouble)
+                candidates.remove(trouble)
+            targets = [agent] + self.rng.choice(candidates, min(len(candidates),num_siblings)).tolist()
+            for sib in targets:
+                if sib in agent_left_household:
+                    agent_left_household.remove(sib)
+            for target in targets:
+                target.addSiblingLinks(targets)
+                # this is a good place to remind that the number of links in the sibling link neighbors is not the "number of brothers and sisters"
+                # because, for example, 4 brothers = 6 links.
+            other_targets = targets + [s for c in targets for s in c.neighbors.get('sibling')]
+            for target in other_targets:
+                target.addSiblingLinks(other_targets)
+
 
     def generate_households(self):
         # this mostly follows the third algorithm from Gargiulo et al. 2010
@@ -672,6 +692,7 @@ def setup(self, n_agent):
         if self.unemployment_multiplier != "base":
             self.fix_unemployment(self.unemployment_multiplier)
         self.generate_households()
+        self.setup_siblings()
 
     def assign_jobs_and_wealth(self):
         """
@@ -735,7 +756,4 @@ def conclude_wedding(ego, partner):
     print(m.total_num_links())
     # m.setup_siblings()
     print("num links:")
-    print(m.total_num_links())
-
-
-
+    print(m.total_num_links())

mesa/testProton.py

@@ -84,9 +84,9 @@ def test_weddings():
         m.wedding()
     # print(Person.NumberOfLinks()-l)
     for agent in m.schedule.agents:
-        if agent.get_link_list("partner"):
-            assert agent.get_link_list("partner")[0].get_link_list("partner")[0] == agent
-    assert m.number_weddings == len([x for x in m.schedule.agents if x.get_link_list("partner")]) / 2
+        if agent.get_neighbor_list("partner"):
+            assert agent.get_neighbor_list("partner")[0].get_neighbor_list("partner")[0] == agent
+    assert m.number_weddings == len([x for x in m.schedule.agents if x.get_neighbor_list("partner")]) / 2
     assert m.number_weddings > 0
     # coherent state of weddings