Merge remote-tracking branch 'origin/main' into partner-services

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "titan-model"
-version = "3.3.0"
+version = "3.3.2"
 description = "TITAN Agent Based Model"
 license = "GPL-3.0-only"
 authors = ["Sam Bessey <[email protected]>", "Mary McGrath <[email protected]>"]
@@ -12,18 +12,22 @@ classifiers = ["Operating System :: OS Independent"]
 packages = [{ include = "titan" }]
 
 [tool.poetry.dependencies]
+<<<<<<< HEAD
 python = "^3.8"
+=======
+python = "^3.9"
+>>>>>>> origin/main
 paraml= "^0.1"
 networkx = "^2.4"
 nanoid = "^2.0"
-numpy = "^1.18"
+numpy = "^1.26"
 black = {version = "^23.1.0", optional = true}
 flake8 = {version = "^3.8", optional = true}
 mypy = {version = "^1.0.0", optional = true}
-mkdocs = {version = "^1.1", optional = true}
-mkdocs-material = {version = "^7.0", optional = true}
-mkdocstrings = {version = "^0.15.0", optional = true}
+mkdocs = {version = "^1.2.4", optional = true}
 oyaml = "^1.0"
+mkdocstrings = {version = "^0.25.1", extras = ["python"], optional = true}
+mkdocs-material = {version = "^9.5.26", optional = true}
 
 [tool.poetry.dev-dependencies]
 pytest = "^6.2"

tests/params/basic.yml

@@ -355,7 +355,7 @@ features:
   timeline_scaling: true
 
 model:
-  num_pop: 100
+  num_pop: 1000
   network:
     enable: true
   num_reps: 1

titan/exposures/hiv.py

@@ -9,7 +9,7 @@
 
 class HIV(base_exposure.BaseExposure):
     name: str = "hiv"
-    stats: List[str] = ["hiv", "hiv_dx", "hiv_aids", "hiv_new", "hiv_dx_new"]
+    stats: List[str] = ["hiv", "hiv_dx", "hiv_aids", "hiv_new", "hiv_dx_new", "hiv_tested_negative_new"]
     """
         HIV collects the following stats:
 
@@ -34,7 +34,9 @@ def __init__(self, agent: "agent.Agent"):
         self.dx = False
         self.dx_time: Optional[int] = None
         self.aids = False
-
+        self.tested_negative = False #has this agent tested negative for hiv?
+        self.tested_negative_time = None #time agent tested negative
+
     @classmethod
     def init_class(cls, params):
         """
@@ -67,7 +69,7 @@ def init_agent(self, pop: "population.Population", time: int):
 
         # HIV
         if (
-            pop.pop_random.random() < agent_params.hiv.init
+            pop.pop_random.random() < agent_params.hiv.init #0.13 for white, 0.175 for latino and 0.434 for blacks
             and time >= pop.params.hiv.start_time
         ):
             self.active = True
@@ -82,7 +84,7 @@ def init_agent(self, pop: "population.Population", time: int):
             if pop.pop_random.random() < agent_params.hiv.aids.init:
                 self.aids = True
 
-            if pop.pop_random.random() < agent_params.hiv.dx.init:
+            if pop.pop_random.random() < agent_params.hiv.dx.init: #0.6 - 0.8 depending on race
                 self.dx = True
                 # agent was diagnosed at a random time between conversion and now
                 self.dx_time = utils.safe_random_int(self.time, time, pop.pop_random)
@@ -99,23 +101,34 @@ def update_agent(self, model: "model.TITAN"):
         args:
             model: the instance of TITAN currently being run
         """
+
         if self.active and model.time >= model.params.hiv.start_time:
-            if not self.dx:
-                test_prob = (
-                    self.agent.location.params.demographics[self.agent.race]
-                    .sex_type[self.agent.sex_type]
-                    .drug_type[self.agent.drug_type]
-                    .hiv.dx.prob
-                )
-
-                # Rescale based on calibration param
-                test_prob *= model.calibration.test_frequency
-
-                if model.run_random.random() < test_prob:
-                    self.diagnose(model)
-
             self.progress_to_aids(model)
+
+        test_prob = (
+            self.agent.location.params.demographics[self.agent.race]
+            .sex_type[self.agent.sex_type]
+            .drug_type[self.agent.drug_type]
+            .hiv.dx.prob
+        )
+
+        # Rescale based on calibration param
+        test_prob *= model.calibration.test_frequency #freq is 1 so test_prob remains at 0.025
 
+        if (
+            model.run_random.random() < test_prob 
+            and not self.dx # has not yet been diagnosed
+        ):
+            if self.active and model.time >= model.params.hiv.start_time:
+                self.diagnose(model)
+            else:
+                self.tested_negative = True
+                self.tested_negative_time = model.time
+
+        if self.tested_negative and self.tested_negative_time < model.time:
+            self.tested_negative = False
+            self.tested_negative_time = None
+
     @classmethod
     def add_agent(cls, agent: "agent.Agent"):
         """
@@ -157,7 +170,9 @@ def set_stats(self, stats: Dict[str, int], time: int):
                 stats["hiv_dx"] += 1
                 if self.dx_time == time:
                     stats["hiv_dx_new"] += 1
-
+        if self.tested_negative and self.tested_negative_time == time:
+            stats["hiv_tested_negative_new"] += 1
+
     @staticmethod
     def expose(
         model: "model.TITAN",

titan/features/haart.py

@@ -13,7 +13,7 @@ class HAART(base_feature.BaseFeature):
     """
 
     name = "haart"
-    stats = ["haart"]
+    stats = ["haart", "ps_haart_count"]
     """
         HAART collects the following stats:
 
@@ -28,7 +28,7 @@ def __init__(self, agent: "agent.Agent"):
         self.active = False
         self.ever = False
         self.adherent = False
-
+        
     @classmethod
     def init_class(cls, params: "ObjMap"):
         """
@@ -41,6 +41,8 @@ def init_class(cls, params: "ObjMap"):
             race: {sex_type: 0 for sex_type in params.classes.sex_types}
             for race in params.classes.races
         }
+
+        cls.ps_haart_count = 0
 
     def init_agent(self, pop: "population.Population", time: int):
         """
@@ -132,10 +134,25 @@ def remove_agent(cls, agent: "agent.Agent"):
         """
         cls.counts[agent.race][agent.sex_type] -= 1
 
+    @classmethod
+    def ps_add_stat(cls):
+        cls.ps_haart_count += 1
+
+    @classmethod
+    def ps_remove_stat(cls): # do we subtract agents who stop using haart?
+        pass
+        #cls.ps_haart_count -= 1
+
+    @classmethod
+    def ps_get_stat(cls):
+        return cls.ps_haart_count
+
     def set_stats(self, stats: Dict[str, int], time: int):
         if self.active:
             stats["haart"] += 1
-
+
+        stats["ps_haart_count"] = self.ps_get_stat()
+
     def get_transmission_risk_multiplier(self, time: int, interaction_type: str):
         """
         Get a multiplier for how haart reduces hiv transmission risk based on interaction type and params.
@@ -182,6 +199,7 @@ def enroll(self, model: "model.TITAN", haart_params: ObjMap):
             model: the instance of TITAN currently being run
             haart_params: the HAART demographic params for this agent
         """
+
         if self.agent.location.params.haart.use_cap:
             self.enroll_cap(model, haart_params)
         else:
@@ -201,11 +219,22 @@ def enroll_cap(self, model: "model.TITAN", haart_params: ObjMap):
         # HAART agents based on % of diagnosed agents
         num_dx_agents = self.agent.hiv.dx_counts[race][sex_type]  # type: ignore[attr-defined]
         num_haart_agents = self.counts[race][sex_type]
-
-        # take value from dictionary for cap
-        if num_haart_agents < (haart_params.cap * num_dx_agents):
-            self.initiate(model.run_random, haart_params, "prob")
-
+
+        # if agent is diagnosed through PS, use PS parameter
+        if self.agent.partner_tracing.ps_dx:
+            cap = self.agent.partner_tracing.get_positive_count() * self.agent.location.params.partner_tracing.treatment_prob
+            # initiate agent only if required capacity is not yet met
+            if self.ps_get_stat() < cap:
+                self.initiate(model.run_random, haart_params, "prob")
+                self.ps_add_stat()
+
+        # else, use base parameter
+        else:
+            cap = haart_params.cap
+            # initiate agent only if required capacity is not yet met
+            if num_haart_agents < (cap * num_dx_agents):
+                self.initiate(model.run_random, haart_params, "prob")
+
     def enroll_prob(self, model: "model.TITAN", haart_params: ObjMap):
         """
         Determine whether to enroll an agent in HAART using probability method.
@@ -214,9 +243,19 @@ def enroll_prob(self, model: "model.TITAN", haart_params: ObjMap):
             model: the instance of TITAN currently being run
             haart_params: the HAART demographic params for this agent
         """
+        # if agent has ever been on haart and use_reinit is true, use reinit probability
         if self.ever and self.agent.location.params.haart.use_reinit:
             if model.run_random.random() < haart_params.reinit.prob:
                 self.initiate(model.run_random, haart_params, "prob")
+
+        # if agent has been diagnosed through PS, use PS treatment (haart) probability
+        elif self.agent.partner_tracing.ps_dx:
+            enroll_prob = self.agent.location.params.partner_tracing.treatment_prob
+            if model.run_random.random() < enroll_prob:
+                self.initiate(model.run_random, haart_params, "prob")
+                self.ps_add_stat()
+
+        # else, use normal base probability scaled by time since diagnoses
         else:
             # Find enroll probability based on time since diagnosis
             enroll_prob = 0.0