artifact updates

setup.py

@@ -43,8 +43,8 @@
         long_description = f.read()
 
     install_requirements = [
-        "gbd_mapping==4.0.0",
-        "vivarium==3.0.0",
+        "gbd_mapping>=4.0.0",
+        "vivarium>=3.0.0",
         "vivarium_public_health>=3.0.0,<4.0.0",
         "click",
         "jinja2",
@@ -58,8 +58,8 @@
 
     setup_requires = ["setuptools_scm"]
 
-    data_requirements = ["vivarium_inputs[data]==5.0.2"]
-    cluster_requirements = ["vivarium_cluster_tools==1.6.1"]
+    data_requirements = ["vivarium_inputs[data]>=5.0.2"]
+    cluster_requirements = ["vivarium_cluster_tools>=1.6.1"]
     test_requirements = ["pytest"]
     lint_requirements = ["black", "isort"]
 

src/vivarium_sodium_reduction/constants/data_keys.py

@@ -29,41 +29,194 @@ def log_name(self):
 POPULATION = __Population()
 
 
-# TODO - sample key group used to identify keys in model
-# For more information see the tutorial:
-# https://vivarium-inputs.readthedocs.io/en/latest/tutorials/pulling_data.html#entity-measure-data
-class __SomeDisease(NamedTuple):
+class __IschemicHeartDisease(NamedTuple):
+    # Keys that will be loaded into the artifact. must have a colon type declaration
+    PREVALENCE: TargetString = TargetString("cause.ischemic_heart_disease.prevalence")
+    INCIDENCE_RATE: TargetString = TargetString("cause.ischemic_heart_disease.incidence_rate")
+    DISABILITY_WEIGHT: TargetString = TargetString("cause.ischemic_heart_disease.disability_weight")
+    EMR: TargetString = TargetString("cause.ischemic_heart_disease.excess_mortality_rate")
+    CSMR: TargetString = TargetString("cause.ischemic_heart_disease.cause_specific_mortality_rate")
+    RESTRICTIONS: TargetString = TargetString("cause.ischemic_heart_disease.restrictions")
+
+    # Useful keys not for the artifact - distinguished by not using the colon type declaration
+
+    @property
+    def name(self):
+        return "ischemic_heart_disease"
+
+    @property
+    def log_name(self):
+        return "ischemic_heart_disease"
+
+
+IHD = __IschemicHeartDisease()
+
+
+class __IschemicStroke(NamedTuple):
+    # Keys that will be loaded into the artifact. must have a colon type declaration
+    PREVALENCE: TargetString = TargetString("cause.ischemic_stroke.prevalence")
+    INCIDENCE_RATE: TargetString = TargetString("cause.ischemic_stroke.incidence_rate")
+    DISABILITY_WEIGHT: TargetString = TargetString("cause.ischemic_stroke.disability_weight")
+    EMR: TargetString = TargetString("cause.ischemic_stroke.excess_mortality_rate")
+    CSMR: TargetString = TargetString("cause.ischemic_stroke.cause_specific_mortality_rate")
+    RESTRICTIONS: TargetString = TargetString("cause.ischemic_stroke.restrictions")
+
+    # Useful keys not for the artifact - distinguished by not using the colon type declaration
+
+    @property
+    def name(self):
+        return "ischemic_stroke"
+
+    @property
+    def log_name(self):
+        return "ischemic_stroke"
+
+
+ISCHEMIC_STROKE = __IschemicStroke()
+
+
+class __StomachCancer(NamedTuple):
+    # Keys that will be loaded into the artifact. must have a colon type declaration
+    PREVALENCE: TargetString = TargetString("cause.stomach_cancer.prevalence")
+    INCIDENCE_RATE: TargetString = TargetString("cause.stomach_cancer.incidence_rate")
+    DISABILITY_WEIGHT: TargetString = TargetString("cause.stomach_cancer.disability_weight")
+    EMR: TargetString = TargetString("cause.stomach_cancer.excess_mortality_rate")
+    CSMR: TargetString = TargetString("cause.stomach_cancer.cause_specific_mortality_rate")
+    RESTRICTIONS: TargetString = TargetString("cause.stomach_cancer.restrictions")
+
+    # Useful keys not for the artifact - distinguished by not using the colon type declaration
+
+    @property
+    def name(self):
+        return "stomach_cancer"
+
+    @property
+    def log_name(self):
+        return "stomach_cancer"
+
+
+STOMACH_CANCER = __StomachCancer()
+
+
+class __IntracerebralHemorrhage(NamedTuple):
+    # Keys that will be loaded into the artifact. must have a colon type declaration
+    PREVALENCE: TargetString = TargetString("cause.intracerebral_hemorrhage.prevalence")
+    INCIDENCE_RATE: TargetString = TargetString("cause.intracerebral_hemorrhage.incidence_rate")
+    DISABILITY_WEIGHT: TargetString = TargetString("cause.intracerebral_hemorrhage.disability_weight")
+    EMR: TargetString = TargetString("cause.intracerebral_hemorrhage.excess_mortality_rate")
+    CSMR: TargetString = TargetString("cause.intracerebral_hemorrhage.cause_specific_mortality_rate")
+    RESTRICTIONS: TargetString = TargetString("cause.intracerebral_hemorrhage.restrictions")
+
+    # Useful keys not for the artifact - distinguished by not using the colon type declaration
 
+    @property
+    def name(self):
+        return "intracerebral_hemorrhage"
+
+    @property
+    def log_name(self):
+        return "intracerebral_hemorrhage"
+
+
+INTRACEREBRAL_HEMORRHAGE = __IntracerebralHemorrhage()
+
+
+class __SubarachnoidHemorrhage(NamedTuple):
     # Keys that will be loaded into the artifact. must have a colon type declaration
-    SOME_DISEASE_PREVALENCE: TargetString = TargetString("cause.some_disease.prevalence")
-    SOME_DISEASE_INCIDENCE_RATE: TargetString = TargetString(
-        "cause.some_disease.incidence_rate"
+    PREVALENCE: TargetString = TargetString("cause.subarachnoid_hemorrhage.prevalence")
+    INCIDENCE_RATE: TargetString = TargetString("cause.subarachnoid_hemorrhage.incidence_rate")
+    DISABILITY_WEIGHT: TargetString = TargetString("cause.subarachnoid_hemorrhage.disability_weight")
+    EMR: TargetString = TargetString("cause.subarachnoid_hemorrhage.excess_mortality_rate")
+    CSMR: TargetString = TargetString("cause.subarachnoid_hemorrhage.cause_specific_mortality_rate")
+    RESTRICTIONS: TargetString = TargetString("cause.subarachnoid_hemorrhage.restrictions")
+
+    # Useful keys not for the artifact - distinguished by not using the colon type declaration
+
+    @property
+    def name(self):
+        return "subarachnoid_hemorrhage"
+
+    @property
+    def log_name(self):
+        return "subarachnoid_hemorrhage"
+
+
+SUBARACHNOID_HEMORRHAGE = __SubarachnoidHemorrhage()
+
+
+class __HighSBP(NamedTuple):
+    DISTRIBUTION: TargetString = TargetString(
+        "risk_factor.high_systolic_blood_pressure.distribution"
     )
-    SOME_DISEASE_REMISSION_RATE: TargetString = TargetString(
-        "cause.some_disease.remission_rate"
+    EXPOSURE_MEAN: TargetString = TargetString(
+        "risk_factor.high_systolic_blood_pressure.exposure"
     )
-    DISABILITY_WEIGHT: TargetString = TargetString("cause.some_disease.disability_weight")
-    EMR: TargetString = TargetString("cause.some_disease.excess_mortality_rate")
-    CSMR: TargetString = TargetString("cause.some_disease.cause_specific_mortality_rate")
-    RESTRICTIONS: TargetString = TargetString("cause.some_disease.restrictions")
+    EXPOSURE_SD: TargetString = TargetString(
+        "risk_factor.high_systolic_blood_pressure.exposure_standard_deviation"
+    )
+    EXPOSURE_WEIGHTS: TargetString = TargetString(
+        "risk_factor.high_systolic_blood_pressure.exposure_distribution_weights"
+    )
+    RELATIVE_RISK: TargetString = TargetString(
+        "risk_factor.high_systolic_blood_pressure.relative_risk"
+    )
+    PAF: TargetString = TargetString(
+        "risk_factor.high_systolic_blood_pressure.population_attributable_fraction"
+    )
+    TMRED: TargetString = TargetString("risk_factor.high_systolic_blood_pressure.tmred")
 
-    # Useful keys not for the artifact - distinguished by not using the colon type declaration
-    RAW_DISEASE_PREVALENCE = TargetString("sequela.raw_disease.prevalence")
-    RAW_DISEASE_INCIDENCE_RATE = TargetString("sequela.raw_disease.incidence_rate")
+    @property
+    def name(self):
+        return "high_sbp"
+
+    @property
+    def log_name(self):
+        return self.name.replace("_", " ")
+
+
+SBP = __HighSBP()
+
+
+class __HighSodium(NamedTuple):
+    DISTRIBUTION: TargetString = TargetString(
+        "risk_factor.diet_high_in_sodium.distribution"
+    )
+    EXPOSURE_MEAN: TargetString = TargetString(
+        "risk_factor.diet_high_in_sodium.exposure"
+    )
+    EXPOSURE_SD: TargetString = TargetString(
+        "risk_factor.diet_high_in_sodium.exposure_standard_deviation"
+    )
+    EXPOSURE_WEIGHTS: TargetString = TargetString(
+        "risk_factor.diet_high_in_sodium.exposure_distribution_weights"
+    )
+    RELATIVE_RISK: TargetString = TargetString(
+        "risk_factor.diet_high_in_sodium.relative_risk"
+    )
+    PAF: TargetString = TargetString(
+        "risk_factor.diet_high_in_sodium.population_attributable_fraction"
+    )
+    TMRED: TargetString = TargetString("risk_factor.diet_high_in_sodium.tmred")
 
     @property
     def name(self):
-        return "some_disease"
+        return "high_sodium"
 
     @property
     def log_name(self):
-        return "some disease"
+        return self.name.replace("_", " ")
+
 
+SODIUM = __HighSodium()
 
-SOME_DISEASE = __SomeDisease()
 
 MAKE_ARTIFACT_KEY_GROUPS = [
     POPULATION,
-    # TODO: list all key groups here
-    # SOME_DISEASE
+    IHD,
+    ISCHEMIC_STROKE,
+    STOMACH_CANCER,
+    INTRACEREBRAL_HEMORRHAGE,
+    SUBARACHNOID_HEMORRHAGE,
+    SBP,
+    SODIUM,
 ]

src/vivarium_sodium_reduction/constants/metadata.py

@@ -16,7 +16,7 @@
 MAKE_ARTIFACT_SLEEP = 10
 
 LOCATIONS = [
-    # TODO - project locations here
+    "United States of America",
 ]
 
 ARTIFACT_INDEX_COLUMNS = [

src/vivarium_sodium_reduction/constants/models.py

@@ -1,39 +1,12 @@
 from vivarium_sodium_reduction.constants import data_keys
 
 
-class TransitionString(str):
-    def __new__(cls, value):
-        # noinspection PyArgumentList
-        obj = str.__new__(cls, value.lower())
-        obj.from_state, obj.to_state = value.split("_TO_")
-        return obj
-
-
 ###########################
 # Disease Model variables #
 ###########################
 
-# TODO input details of model states and transitions
-SOME_MODEL_NAME = data_keys.SOME_DISEASE.name
-SUSCEPTIBLE_STATE_NAME = f"susceptible_to_{SOME_MODEL_NAME}"
-FIRST_STATE_NAME = "first_state"
-SECOND_STATE_NAME = "second_state"
-SOME_DISEASE_MODEL_STATES = (SUSCEPTIBLE_STATE_NAME, FIRST_STATE_NAME, SECOND_STATE_NAME)
-SOME_DISEASE_MODEL_TRANSITIONS = (
-    TransitionString(f"{SUSCEPTIBLE_STATE_NAME}_TO_{FIRST_STATE_NAME}"),
-    TransitionString(f"{FIRST_STATE_NAME}_TO_{SECOND_STATE_NAME}"),
-    TransitionString(f"{SECOND_STATE_NAME}_TO_{FIRST_STATE_NAME}"),
-)
-
-STATE_MACHINE_MAP = {
-    SOME_MODEL_NAME: {
-        "states": SOME_DISEASE_MODEL_STATES,
-        "transitions": SOME_DISEASE_MODEL_TRANSITIONS,
-    },
-}
-
-
-STATES = tuple(state for model in STATE_MACHINE_MAP.values() for state in model["states"])
-TRANSITIONS = tuple(
-    state for model in STATE_MACHINE_MAP.values() for state in model["transitions"]
-)
+# TODO input details of model states
+#SOME_MODEL_NAME = data_keys.SOME_DISEASE.name
+#SUSCEPTIBLE_STATE_NAME = f"susceptible_to_{SOME_MODEL_NAME}"
+#FIRST_STATE_NAME = "first_state"
+#SECOND_STATE_NAME = "second_state"