Adds real metrics for diseases to the log

README

@@ -159,6 +159,11 @@ agentDepressionPercentage: float
     Note: The starting agent population will have this same percentage of depressed agents.
     Default: 0.0
 
+agentDiseaseProtectionChance: [float, float]
+    Sets the chance an agent can get infected by another agent.
+    Note: a value of 0.0 mean no protection, while a value of 1.0 means complete protection
+    Default: [0.0, 1.0]
+
 agentFemaleInfertilityAge: [int, int]
     Set the timestep age at which female agents become infertile.
     Default: [0, 0]
@@ -301,6 +306,10 @@ diseaseFertilityPenalty: [float, float]
     Note: Negative values constitute a fertility decrease.
     Default: [0, 0]
 
+diseaseIncubationPeriod: [int, int]
+    Set the number of timesteps a disease can remain hidden while still infecting other agents.
+    Default: [0, 0]
+
 diseaseMovementPenalty: [int, int]
     Set the impact a disease will have on an agent's movement distance.
     Note: Negative values constitute a decrease in movement range.
@@ -311,6 +320,10 @@ diseaseSpiceMetabolismPenalty: [float, float]
     Note: Negative values constitute a decrease in agent spice metabolism.
     Default: [0, 0]
 
+diseaseStartTimeframe: [int, int]
+    Set the timestep a disease can be initialized.
+    Default: [0, 0]
+
 diseaseSugarMetabolismPenalty: [float, float]
     Set the impact a disease will have on an agent's sugar metabolism rate.
     Note: Negative values constitute a decrease in agent sugar metabolism.
@@ -321,6 +334,10 @@ diseaseTagStringLength: [int, int]
     The longer the length, the longer an agent will have the disease.
     Default: [0, 0]
 
+diseaseTransmissionChance: [float, float]
+    Set the chance a disease can transmit between agents.
+    Default: [0.0, 1.0]
+
 diseaseVisionPenalty: [int, int]
     Set the impact a disease will have on an agent's vision.
     Note: Negative values constitute a decrease in agent vision.

cell.py

@@ -1,7 +1,7 @@
 import math
 
 class Cell:
-    def __init__(self, x, y, environment, maxSugar=0, maxSpice=0, growbackRate=0):
+    def __init__(self, x, y, environment, maxSugar=0, maxSpice=0):
         self.x = x
         self.y = y
         self.environment = environment

config.json

@@ -19,6 +19,7 @@
         "agentDecisionModelLookaheadFactor": 0,
         "agentDecisionModelTribalFactor": [-1, -1],
         "agentDepressionPercentage": 0,
+        "agentDiseaseProtectionChance": [0.0, 1.0],
         "agentFemaleInfertilityAge": [40, 50],
         "agentFemaleFertilityAge": [12, 15],
         "agentFertilityFactor": [1, 1],
@@ -51,10 +52,13 @@
         "debugMode": ["none"],
         "diseaseAggressionPenalty": [-1, 1],
         "diseaseFertilityPenalty": [-1, 1],
+        "diseaseIncubationPeriod": [0,10],
         "diseaseMovementPenalty": [0, 0],
         "diseaseSpiceMetabolismPenalty": [1, 3],
         "diseaseSugarMetabolismPenalty": [1, 3],
+        "diseaseStartTimeframe": [0, 0],
         "diseaseTagStringLength": [11, 21],
+        "diseaseTransmissionChance": [0.0, 1.0],
         "diseaseVisionPenalty": [-1, 1],
         "environmentEquator": -1,
         "environmentHeight": 50,
@@ -87,8 +91,8 @@
         "interfaceHeight": 1000,
         "interfaceWidth": 900,
         "keepAlivePostExtinction": false,
-        "logfile": "log.json",
-        "logfileFormat": "json",
+        "logfile": "log.csv",
+        "logfileFormat": "csv",
         "neighborhoodMode": "vonNeumann",
         "profileMode": false,
         "screenshots": false,

disease.py

@@ -7,11 +7,21 @@ def __init__(self, diseaseID, configuration):
         self.configuration = configuration
         self.aggressionPenalty = configuration["aggressionPenalty"]
         self.fertilityPenalty = configuration["fertilityPenalty"]
+        self.incubationPeriod = configuration["incubationPeriod"]
         self.movementPenalty = configuration["movementPenalty"]
         self.spiceMetabolismPenalty = configuration["spiceMetabolismPenalty"]
         self.sugarMetabolismPenalty = configuration["sugarMetabolismPenalty"]
         self.tags = configuration["tags"]
+        self.transmissionChance = configuration["transmissionChance"]
         self.visionPenalty = configuration["visionPenalty"]
 
+        self.newInfections = 0
+        self.infectors = set()
+        self.startingInfectedAgents = 0
+
+    def resetRStats(self):
+        self.newInfections = 0
+        self.infectors = set()
+
     def __str__(self):
         return f"{self.ID}"

gui.py

@@ -124,6 +124,7 @@ def configureButtons(self, window):
 
         statsLabel = tkinter.Label(window, text=self.defaultSimulationString, font="Roboto 10", justify=tkinter.CENTER)
         statsLabel.grid(row=1, column=0, columnspan=self.menuTrayColumns, sticky="nsew")
+        # need to add diseases to default agent string
         cellLabel = tkinter.Label(window, text=f"{self.defaultCellString}\n{self.defaultAgentString}", font="Roboto 10", justify=tkinter.CENTER)
         cellLabel.grid(row=2, column=0, columnspan=self.menuTrayColumns, sticky="nsew")
 
@@ -476,7 +477,7 @@ def drawLines(self):
         elif self.activeNetwork.get() == "Disease":
             for agent in self.sugarscape.agents:
                 if agent.isSick() == True:
-                    for diseaseRecord in agent.diseases:
+                    for diseaseRecord in agent.symptomaticDiseases:
                         # Starting diseases without an infector are not considered
                         if "infector" not in diseaseRecord:
                             continue
@@ -596,7 +597,7 @@ def lookupFillColor(self, cell):
         elif self.activeColorOptions["agent"] == "Depression":
             return self.colors["sick"] if agent.depressed == True else self.colors["healthy"]
         elif self.activeColorOptions["agent"] == "Disease":
-            return self.colors["sick"] if len(agent.diseases) > 0 else self.colors["healthy"]
+            return self.colors["sick"] if agent.isSick() else self.colors["healthy"]
         elif self.activeColorOptions["agent"] == "Metabolism":
             return self.colors["metabolism"][agent.sugarMetabolism + agent.spiceMetabolism]
         elif self.activeColorOptions["agent"] == "Movement":
@@ -679,6 +680,7 @@ def updateHighlightedCellStats(self):
                 agentStats = f"Agent: {str(agent)} | Age: {agent.age} | Vision: {round(agent.findVision(), 2)} | Movement: {round(agent.findMovement(), 2)} | "
                 agentStats += f"Sugar: {round(agent.sugar, 2)} | Spice: {round(agent.spice, 2)} | "
                 agentStats += f"Metabolism: {round(((agent.findSugarMetabolism() + agent.findSpiceMetabolism()) / 2), 2)} | Decision Model: {agent.decisionModel} | Tribe: {agent.tribe}"
+                # add disease to end
             else:
                 agentStats = self.defaultAgentString
             cellStats += f"\n{agentStats}"