Merge pull request #228 from pph-collective/develop

v3.2.0

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "titan-model"
-version = "3.1.0"
+version = "3.2.0"
 description = "TITAN Agent Based Model"
 license = "GPL-3.0-only"
 authors = ["Sam Bessey <[email protected]>", "Mary McGrath <[email protected]>"]

tests/exposures/monkeypox_test.py

@@ -0,0 +1,135 @@
+import pytest
+
+from conftest import FakeRandom
+
+from titan.exposures import MonkeyPox
+from titan.agent import Relationship
+
+
+@pytest.mark.unit
+def test_monkeypox_expose(make_model, make_agent):
+    model = make_model()
+    model.run_random = FakeRandom(0.0)  # always less than param
+    a = make_agent()
+    p = make_agent()
+    a.partners["Sex"] = set()
+    p.partners["Sex"] = set()
+    rel = Relationship(a, p, 10, bond_type="Sex")
+
+    MonkeyPox.expose(model, "sex", rel, 1)
+
+    assert a.monkeypox.active is False
+    assert p.monkeypox.active is False
+
+    a.monkeypox.active = True
+    a.monkeypox.time = model.time
+    p.monkeypox.active = True
+    a.monkeypox.time = model.time
+
+    # test nothing happens
+    MonkeyPox.expose(model, "sex", rel, 10)
+
+    assert a.monkeypox.active
+    assert p.monkeypox.active
+
+    p.monkeypox.active = False
+
+    # test conversion happens
+    MonkeyPox.expose(model, "sex", rel, 10)
+
+    assert a.monkeypox.active
+    assert p.monkeypox.active
+
+
+@pytest.mark.unit
+def test_monkeypox_init(make_population, make_agent):
+    pop = make_population()
+    pop.pop_random = FakeRandom(0.0)
+    a = make_agent()
+
+    time = pop.params.monkeypox.start_time - 1
+
+    a.monkeypox.init_agent(pop, time)
+    assert a.monkeypox.active is False
+
+    time = pop.params.monkeypox.start_time
+
+    a.monkeypox.init_agent(pop, time)
+
+    assert a.monkeypox.active
+    assert a.monkeypox.time == time - pop.params.monkeypox.max_init_time
+    assert a.monkeypox.dx
+    assert a.monkeypox.dx_time == a.monkeypox.time
+    assert a in MonkeyPox.agents
+    assert MonkeyPox.dx_counts[a.race][a.sex_type] == 1
+
+
+@pytest.mark.unit
+def test_monkeypox_convert(make_model, make_agent):
+    model = make_model()
+    a = make_agent()
+
+    model.run_random = FakeRandom(-0.1)
+
+    a.monkeypox.convert(model)
+
+    assert a.monkeypox.active
+    assert a.monkeypox.time == model.time
+    assert a in MonkeyPox.agents
+
+
+# TODO talk with Ellen about why this is failing?
+@pytest.mark.unit
+def test_diagnose_monkeypox(make_model, make_agent):
+    model = make_model()
+    model.params.partner_tracing.prob = 1.0
+    model.time = 1
+    a = make_agent()
+    p = make_agent()
+    p.monkeypox.active = True
+    a.partners["Sex"].add(p)
+
+    model.run_random = FakeRandom(-0.1)  # always less than param
+    a.monkeypox.diagnose(model)
+
+    assert a.monkeypox.dx
+    assert a.monkeypox.dx_time == model.time
+
+
+@pytest.mark.unit
+def test_get_transmission_probability(make_model, make_agent):
+    model = make_model()
+    a = make_agent(race="white", SO="MSM")
+    a.sex_role = "versatile"
+
+    p = make_agent(race="white", SO="MSM")
+    p.sex_role = "versatile"
+
+    # test versatile-versatile relationship
+    p_sex = model.params.partnership.sex.acquisition.MSM.versatile
+    scale = model.params.calibration.acquisition
+
+    # must be in acute phase
+    a.monkeypox.active = True
+    a.monkeypox.time = model.time
+
+    assert a.monkeypox.get_transmission_probability(model, "sex", p, 1) == p_sex * scale
+    # Not transmissable with injection
+    assert a.monkeypox.get_transmission_probability(model, "inj", p, 1) == 0.0
+
+    # test one vers, one receptive
+    a.sex_role = "receptive"
+    p_sex_ins = model.params.partnership.sex.acquisition.MSM.insertive
+    p_sex_rec = model.params.partnership.sex.acquisition.MSM.receptive
+
+    assert a.hiv.get_transmission_probability(model, "sex", p, 1) == p_sex_ins * scale
+    assert p.hiv.get_transmission_probability(model, "sex", a, 1) == p_sex_rec * scale
+
+
+@pytest.mark.unit
+def test_get_acute_status(make_agent, make_model):
+    model = make_model()
+    a = make_agent()
+    assert a.monkeypox.get_acute_status(model.time + 2) is False
+    a.monkeypox.convert(model)
+    assert a.monkeypox.get_acute_status(model.time + 2) is True

tests/features/vaccine_test.py

@@ -64,3 +64,29 @@ def test_vaccine_cquisition_risk_multiplier(make_agent):
     a.vaccine.vaccinate(0)
 
     assert a.vaccine.get_acquisition_risk_multiplier(1, "sex") < 1.0
+
+
+@pytest.mark.unit
+def test_vaccine_HVTN(make_agent):
+    a = make_agent()
+    print(a.location.params.vaccine.type)
+    a.location.params.vaccine.type = "HVTN702"
+    assert a.vaccine.get_acquisition_risk_multiplier(0, "sex") == 1.0
+
+    a.vaccine.vaccinate(0)
+    assert a.vaccine.get_acquisition_risk_multiplier(1, "sex") < 1.0
+
+
+@pytest.mark.unit
+def test_vaccine_other(make_agent):
+    a = make_agent()
+    print(a.location.params.vaccine.type)
+    a.location.params.vaccine.type = "other"
+    assert a.vaccine.get_acquisition_risk_multiplier(0, "sex") == 1.0
+
+    a.vaccine.vaccinate(0)
+    # no risk multiplier
+    assert a.vaccine.get_acquisition_risk_multiplier(1, "sex") == 1.0
+
+    a.location.params.vaccine.efficacy = 0.5
+    assert a.vaccine.get_acquisition_risk_multiplier(1, "sex") == 0.5

tests/integration_test.py

@@ -103,6 +103,7 @@ def test_model_reproducible(tmpdir):
         assert res_a[i]["pseed"] == res_b[i]["pseed"]
         assert res_a[i]["agents"] == res_b[i]["agents"]
         assert res_a[i]["hiv"] == res_b[i]["hiv"]
+        assert res_a[i]["monkeypox"] == res_b[i]["monkeypox"]
         assert res_a[i]["prep"] == res_b[i]["prep"]
         assert res_a[i]["death"] == res_b[i]["death"]
         assert res_a[i]["hiv_aids"] == res_b[i]["hiv_aids"]

tests/params/basic.yml

@@ -44,6 +44,11 @@ demographics:
                 prob: 0.1
               aids:
                 init: 0.1
+            monkeypox:
+              init: 0.1
+              dx:
+                init: 0.1
+                prob: 0.1
             haart:
               init: 0.1
               enroll: &haart_prob
@@ -75,6 +80,11 @@ demographics:
                 prob: 0.1
               aids:
                 init: 0.1
+            monkeypox:
+              init: 0.1
+              dx:
+                init: 0.1
+                prob: 0.1
             num_partners:
               Sex:
                 dist_type: poisson
@@ -324,6 +334,7 @@ outputs:
 exposures:
   hiv: true
   knowledge: true
+  monkeypox: true
 
 haart:
   use_reinit: true

tests/params/basic_seeded.yml

@@ -39,6 +39,11 @@ demographics:
                 prob: 0.1
               aids:
                 init: 0.1
+            monkeypox:
+              init: 0.1
+              dx:
+                init: 0.1
+                prob: 0.1
             haart:
               init: 0.1
               enroll:
@@ -59,6 +64,11 @@ demographics:
                 prob: 0.1
               aids:
                 init: 0.1
+            monkeypox:
+              init: 0.1
+              dx:
+                init: 0.1
+                prob: 0.1
             num_partners:
               Sex:
                 dist_type: poisson
@@ -296,6 +306,7 @@ outputs:
 
 exposures:
   hiv: true
+  monkeypox: true
   knowledge: true
 
 features:

tests/population_test.py

@@ -94,6 +94,9 @@ def test_add_remove_agent_to_pop(make_population):
     agent.hiv.aids = True
     agent.hiv.dx = True
     agent.hiv.add_agent(agent)
+    agent.monkeypox.active = True
+    agent.monkeypox.dx = True
+    agent.monkeypox.add_agent(agent)
 
     pop.add_agent(agent)
 

titan/agent.py

@@ -88,7 +88,7 @@ def __str__(self) -> str:
         """
         return (
             f"\t{self.id}\t{self.age}\t{self.sex_type}\t{self.drug_type}\t"  # type: ignore[attr-defined]
-            f"{self.race}\t{self.hiv.active}"  # type: ignore[attr-defined]
+            f"{self.race}\t{self.hiv.active}\t{self.prep.active}"  # type: ignore[attr-defined]
         )
 
     def __repr__(self) -> str:

titan/exposures/__init__.py

@@ -2,3 +2,4 @@
 from .base_exposure import *
 from .hiv import *
 from .knowledge import *
+from .monkeypox import MonkeyPox