WIP soil

* Pandas integration
* Improved environment
* Logging and data dumps
* Tests
* Added Finite State Machine models
* Rewritten ipython notebook and documentation

soil/agents/SISaModel.py

@@ -0,0 +1,93 @@
+import random
+import numpy as np
+from . import FSM, state
+
+
+class SISaModel(FSM):
+    """
+    Settings:
+        neutral_discontent_spon_prob
+        
+        neutral_discontent_infected_prob
+        
+        neutral_content_spong_prob
+        
+        neutral_content_infected_prob
+        
+        discontent_neutral
+        
+        discontent_content
+        
+        variance_d_c
+        
+        content_discontent
+        
+        variance_c_d
+        
+        content_neutral
+        
+        standard_variance
+    """
+
+    def __init__(self, environment=None, agent_id=0, state=()):
+        super().__init__(environment=environment, agent_id=agent_id, state=state)
+
+        self.neutral_discontent_spon_prob = np.random.normal(environment.environment_params['neutral_discontent_spon_prob'],
+                                                             environment.environment_params['standard_variance'])
+        self.neutral_discontent_infected_prob = np.random.normal(environment.environment_params['neutral_discontent_infected_prob'],
+                                                                 environment.environment_params['standard_variance'])
+        self.neutral_content_spon_prob = np.random.normal(environment.environment_params['neutral_content_spon_prob'],
+                                                          environment.environment_params['standard_variance'])
+        self.neutral_content_infected_prob = np.random.normal(environment.environment_params['neutral_content_infected_prob'],
+                                                              environment.environment_params['standard_variance'])
+
+        self.discontent_neutral = np.random.normal(environment.environment_params['discontent_neutral'],
+                                                   environment.environment_params['standard_variance'])
+        self.discontent_content = np.random.normal(environment.environment_params['discontent_content'],
+                                                   environment.environment_params['variance_d_c'])
+
+        self.content_discontent = np.random.normal(environment.environment_params['content_discontent'],
+                                                   environment.environment_params['variance_c_d'])
+        self.content_neutral = np.random.normal(environment.environment_params['content_neutral'],
+                                                environment.environment_params['standard_variance'])
+
+    @state
+    def neutral(self):
+        # Spontaneous effects
+        if random.random() < self.neutral_discontent_spon_prob:
+            return self.discontent
+        if random.random() < self.neutral_content_spon_prob:
+            return self.content
+
+        # Infected
+        discontent_neighbors = self.count_neighboring_agents(state_id=self.discontent)
+        if random.random() < discontent_neighbors * self.neutral_discontent_infected_prob:
+            return self.discontent
+        content_neighbors = self.count_neighboring_agents(state_id=self.content.id)
+        if random.random() < content_neighbors * self.neutral_content_infected_prob:
+            return self.content
+        return self.neutral
+
+    @state
+    def discontent(self):
+        # Healing
+        if random.random() < self.discontent_neutral:
+            return self.neutral
+
+        # Superinfected
+        content_neighbors = self.count_neighboring_agents(state_id=self.content.id)
+        if random.random() < content_neighbors * self.discontent_content:
+            return self.content
+        return self.discontent
+
+    @state
+    def content(self):
+        # Healing
+        if random.random() < self.content_neutral:
+            return self.neutral
+
+        # Superinfected
+        discontent_neighbors = self.count_neighboring_agents(state_id=self.discontent.id)
+        if random.random() < discontent_neighbors * self.content_discontent:
+            self.discontent
+        return self.content