Improved docs

Fixed several bugs
Added convenience methods in soil.analysis

examples/newsspread/NewsSpread.yml

@@ -0,0 +1,138 @@
+---
+default_state: {}
+load_module: newsspread
+environment_agents: []
+environment_params:
+  prob_neighbor_spread: 0.0
+  prob_tv_spread: 0.01
+interval: 1
+max_time: 30
+name: Sim_all_dumb
+network_agents:
+- agent_type: DumbViewer
+  state:
+    has_tv: false
+  weight: 1
+- agent_type: DumbViewer
+  state:
+    has_tv: true
+  weight: 1
+network_params:
+  generator: barabasi_albert_graph
+  n: 500
+  m: 5
+num_trials: 50
+---
+default_state: {}
+load_module: newsspread
+environment_agents: []
+environment_params:
+  prob_neighbor_spread: 0.0
+  prob_tv_spread: 0.01
+interval: 1
+max_time: 30
+name: Sim_half_herd
+network_agents:
+- agent_type: DumbViewer
+  state:
+    has_tv: false
+  weight: 1
+- agent_type: DumbViewer
+  state:
+    has_tv: true
+  weight: 1
+- agent_type: HerdViewer
+  state:
+    has_tv: false
+  weight: 1
+- agent_type: HerdViewer
+  state:
+    has_tv: true
+  weight: 1
+network_params:
+  generator: barabasi_albert_graph
+  n: 500
+  m: 5
+num_trials: 50
+---
+default_state: {}
+load_module: newsspread
+environment_agents: []
+environment_params:
+  prob_neighbor_spread: 0.0
+  prob_tv_spread: 0.01
+interval: 1
+max_time: 30
+name: Sim_all_herd
+network_agents:
+- agent_type: HerdViewer
+  state:
+    has_tv: true
+    id: infected
+  weight: 1
+- agent_type: HerdViewer
+  state:
+    has_tv: true
+    id: neutral
+  weight: 1
+network_params:
+  generator: barabasi_albert_graph
+  n: 500
+  m: 5
+num_trials: 50
+---
+default_state: {}
+load_module: newsspread
+environment_agents: []
+environment_params:
+  prob_neighbor_spread: 0.0
+  prob_tv_spread: 0.01
+  prob_neighbor_cure: 0.1
+interval: 1
+max_time: 30
+name: Sim_wise_herd
+network_agents:
+- agent_type: HerdViewer
+  state:
+    has_tv: true
+    id: infected
+  weight: 1
+- agent_type: WiseViewer
+  state:
+    has_tv: true
+  weight: 1
+network_params:
+  generator: barabasi_albert_graph
+  n: 500
+  m: 5
+num_trials: 50
+---
+default_state: {}
+load_module: newsspread
+environment_agents: []
+environment_params:
+  prob_neighbor_spread: 0.0
+  prob_tv_spread: 0.01
+  prob_neighbor_cure: 0.1
+interval: 1
+max_time: 30
+name: Sim_all_wise
+network_agents:
+- agent_type: WiseViewer
+  state:
+    has_tv: true
+    id: infected
+  weight: 1
+- agent_type: WiseViewer
+  state:
+    has_tv: true
+  weight: 1
+network_params:
+  generator: barabasi_albert_graph
+  n: 500
+  m: 5
+network_params:
+  generator: barabasi_albert_graph
+  n: 500
+  m: 5
+num_trials: 50

examples/newsspread/newsspread.py

@@ -0,0 +1,79 @@
+from soil.agents import BaseAgent,FSM, state, default_state
+import random
+import logging
+
+
+class DumbViewer(FSM):
+    '''
+    A viewer that gets infected via TV (if it has one) and tries to infect
+    its neighbors once it's infected.
+    '''
+    defaults = {
+        'prob_neighbor_spread': 0.5,
+        'prob_neighbor_cure': 0.25,
+    }
+
+    @default_state
+    @state
+    def neutral(self):
+        r = random.random()
+        if self['has_tv'] and r < self.env['prob_tv_spread']:
+            self.infect()
+        return
+
+    @state
+    def infected(self):
+        for neighbor in self.get_neighboring_agents(state_id=self.neutral.id):
+            prob_infect = self.env['prob_neighbor_spread']
+            r = random.random()
+            if r < prob_infect:
+                self.set_state(self.infected.id)
+                neighbor.infect()
+        return
+
+    def infect(self):
+        self.set_state(self.infected)
+
+class HerdViewer(DumbViewer):
+    '''
+    A viewer whose probability of infection depends on the state of its neighbors.
+    '''
+
+    level = logging.DEBUG
+ 
+    def infect(self):
+        infected = self.count_neighboring_agents(state_id=self.infected.id)
+        total = self.count_neighboring_agents()
+        prob_infect = self.env['prob_neighbor_spread'] * infected/total
+        self.debug('prob_infect', prob_infect)
+        r = random.random()
+        if r < prob_infect:
+            self.set_state(self.infected.id)
+
+class WiseViewer(HerdViewer):
+    '''
+    A viewer that can change its mind.
+    '''
+    @state
+    def cured(self):
+        prob_cure = self.env['prob_neighbor_cure']
+        for neighbor in self.get_neighboring_agents(state_id=self.infected.id):
+            r = random.random()
+            if r < prob_cure:
+                try:
+                    neighbor.cure()
+                except AttributeError:
+                    self.debug('Viewer {} cannot be cured'.format(neighbor.id))
+        return
+
+    def cure(self):
+        self.set_state(self.cured.id)
+
+    @state
+    def infected(self):
+        prob_cure = self.env['prob_neighbor_cure']
+        r = random.random()
+        if r < prob_cure:
+            self.cure()
+            return
+        return super().infected()