Albrja/mic-6068/rate-to-probability-configuration (#521)

Albrja/mic-6068/rate-to-probability-configuration

Update RateTransition to have rate conversion type configurable
- *Category*: Feature
- *JIRA issue*: https://jira.ihme.washington.edu/browse/MIC-6068

Changes and notes
-Update RateTransition to have rate conversion type configurable

### Testing
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Author: albrja

CHANGELOG.rst

@@ -1,3 +1,7 @@
+**4.1.0 - 05/20/25**
+
+  - Feature: Update RateTransition to have configuration key for rate conversion type
+
 **4.0.2 - 05/01/25**
 
   - Bugfix: Fix configuration key for untracking age in FertilityCrudeBirthRate

setup.py

@@ -42,7 +42,7 @@
         long_description = f.read()
 
     install_requirements = [
-        "vivarium>=3.2.3",
+        "vivarium>=3.4.0",
         "layered_config_tree>=1.0.1",
         "loguru",
         "numpy<2.0.0",

src/vivarium_public_health/disease/model.py

@@ -14,14 +14,16 @@
 from typing import Any
 
 import pandas as pd
+from layered_config_tree import ConfigurationError
 from vivarium.framework.engine import Builder
+from vivarium.framework.event import Event
 from vivarium.framework.population import SimulantData
 from vivarium.framework.state_machine import Machine
 from vivarium.types import DataInput, LookupTableData
 
 from vivarium_public_health.disease.exceptions import DiseaseModelError
 from vivarium_public_health.disease.state import BaseDiseaseState, SusceptibleState
-from vivarium_public_health.disease.transition import TransitionString
+from vivarium_public_health.disease.transition import RateTransition, TransitionString
 
 
 class DiseaseModel(Machine):
@@ -118,6 +120,18 @@ def setup(self, builder: Builder) -> None:
             required_resources=["age", "sex"],
         )
 
+    def on_post_setup(self, event: Event) -> None:
+        conversion_types = set()
+        for state in self.states:
+            for transition in state.transition_set.transitions:
+                if isinstance(transition, RateTransition):
+                    conversion_types.add(transition.rate_conversion_type)
+        if len(conversion_types) > 1:
+            raise ConfigurationError(
+                "All transitions in a disease model must have the same rate conversion type."
+                f" Found: {conversion_types}."
+            )
+
     def on_initialize_simulants(self, pop_data: SimulantData) -> None:
         """Initialize the simulants in the population.
 

src/vivarium_public_health/disease/transition.py

@@ -48,6 +48,7 @@ def configuration_defaults(self) -> dict[str, Any]:
                 "data_sources": {
                     "transition_rate": self._rate_source,
                 },
+                "rate_conversion_type": "linear",
             },
         }
 
@@ -143,6 +144,7 @@ def setup(self, builder: Builder) -> None:
             component=self,
             required_resources=lookup_columns + ["alive", self.joint_paf],
         )
+        self.rate_conversion_type = self.configuration["rate_conversion_type"]
 
     #################
     # Setup methods #
@@ -184,7 +186,12 @@ def compute_transition_rate(self, index: pd.Index) -> pd.Series:
     ##################
 
     def _probability(self, index: pd.Index) -> pd.Series:
-        return pd.Series(rate_to_probability(self.transition_rate(index)))
+        return pd.Series(
+            rate_to_probability(
+                self.transition_rate(index),
+                rate_conversion_type=self.rate_conversion_type,
+            )
+        )
 
 
 class ProportionTransition(Transition):

tests/disease/test_disease.py

@@ -1,6 +1,9 @@
+from unittest.mock import patch
+
 import numpy as np
 import pandas as pd
 import pytest
+from layered_config_tree import ConfigurationError, LayeredConfigTree
 from vivarium import Component, InteractiveContext
 from vivarium.framework.state_machine import Transition
 from vivarium.framework.utilities import from_yearly
@@ -554,3 +557,101 @@ def test_artifact_transition_keys(mocker, disease):
     # check remission rate
     remissive_transition = with_condition.add_rate_transition(healthy)
     assert remissive_transition._rate_source == f"cause.{cause}.remission_rate"
+
+
+@pytest.mark.parametrize("rate_conversion_type", ["linear", "exponential"])
+def test_transition_rate_to_probability_configuration(
+    base_config: LayeredConfigTree,
+    base_plugins: LayeredConfigTree,
+    disease: str,
+    rate_conversion_type: str,
+):
+    """
+    Test that the transition rate to probability configuration is set correctly.
+    """
+    healthy = BaseDiseaseState("healthy")
+    sick = DiseaseState("sick")
+    key = "sequela.acute_myocardial_infarction_first_2_days.incidence_rate"
+    transition = RateTransition(
+        input_state=healthy,
+        output_state=sick,
+        get_data_functions={"incidence_rate": lambda builder, _: builder.data.load(key)},
+    )
+    healthy.transition_set.append(transition)
+    model = DiseaseModel(disease, initial_state=healthy, states=[healthy, sick])
+
+    base_config.update(
+        {
+            f"{transition.name}": {
+                "rate_conversion_type": rate_conversion_type,
+            }
+        }
+    )
+
+    # Sets the configuration
+    sim = InteractiveContext(
+        components=[TestPopulation(), model],
+        configuration=base_config,
+        plugin_configuration=base_plugins,
+        setup=True,
+    )
+
+    assert transition.rate_conversion_type == rate_conversion_type
+    with patch(
+        "vivarium_public_health.disease.transition.rate_to_probability", return_value=1.0
+    ) as mock_rate_to_probability:
+        idx = pd.Index(list(range(10)))
+        transition._probability(idx)
+
+        mock_rate_to_probability.assert_called_once()
+        args, kwargs = mock_rate_to_probability.call_args
+        assert len(args) == 1
+        assert len(kwargs) == 1
+        assert args[0].index.equals(idx)
+        assert kwargs["rate_conversion_type"] == rate_conversion_type
+
+
+def test_disease_model_rate_conversion_config_error(
+    base_config: LayeredConfigTree,
+    base_plugins: LayeredConfigTree,
+    disease: str,
+):
+    """
+    Test that the transition rate to probability configuration is set correctly.
+    """
+    healthy = BaseDiseaseState("healthy")
+    sick = DiseaseState("sick")
+    key = "sequela.acute_myocardial_infarction_first_2_days.incidence_rate"
+    transition = RateTransition(
+        input_state=healthy,
+        output_state=sick,
+        get_data_functions={"incidence_rate": lambda builder, _: builder.data.load(key)},
+    )
+    another_transition = RateTransition(
+        input_state=sick,
+        output_state=healthy,
+        get_data_functions={"incidence_rate": lambda builder, _: builder.data.load(key)},
+    )
+    healthy.transition_set.append(transition)
+    sick.transition_set.append(another_transition)
+    model = DiseaseModel(disease, initial_state=healthy, states=[healthy, sick])
+
+    base_config.update(
+        {
+            f"{transition.name}": {
+                "rate_conversion_type": "linear",
+            },
+            f"{another_transition.name}": {
+                "rate_conversion_type": "exponential",
+            },
+        }
+    )
+
+    # Sets the configuration
+    with pytest.raises(ConfigurationError):
+        InteractiveContext(
+            components=[TestPopulation(), model],
+            configuration=base_config,
+            plugin_configuration=base_plugins,
+            setup=True,
+        )