vivarium-public-health 4.3.5__py3-none-any.whl → 4.3.7__py3-none-any.whl

vivarium_public_health/_version.py

@@ -1 +1 @@
-__version__ = "4.3.5"
+__version__ = "4.3.7"

vivarium_public_health/population/base_population.py

@@ -166,7 +166,7 @@ class BasePopulation(Component):
         demographic_proportions, year: int
     ) -> pd.DataFrame:
         reference_years = sorted(set(demographic_proportions.year_start))
-        ref_year_index = np.digitize(year, reference_years).item() - 1
+        ref_year_index = _find_bin_start_index(year, reference_years)
         return demographic_proportions[
             demographic_proportions.year_start == reference_years[ref_year_index]
         ]
@@ -235,15 +235,50 @@ class ScaledPopulation(BasePopulation):
             raise ValueError(
                 f"Scaling factor must be a pandas DataFrame. Provided value: {scaling_factor}"
             )
-        scaling_factor = scaling_factor.set_index(
-            [col for col in scaling_factor.columns if col != "value"]
+        start_year = builder.configuration.time.start.year
+        population_structure, scaling_factor = self._format_data_inputs(
+            population_structure, scaling_factor, start_year
         )
-        population_structure = population_structure.set_index(
-            [col for col in population_structure.columns if col != "value"]
+
+        return (population_structure * scaling_factor).reset_index()
+
+    def _format_data_inputs(
+        self, pop_structure: pd.DataFrame, scalar_data: pd.DataFrame, year: int
+    ) -> tuple[pd.DataFrame, pd.DataFrame]:
+        """Data cleaning function to check whether scalar_data and population structure are compatible for scaling
+        the population structure of a simulation."""
+
+        scaling_factor = scalar_data.set_index(
+            [col for col in scalar_data.columns if col != "value"]
         )
-        scaled_population_structure = (population_structure * scaling_factor).reset_index()
+        population_structure = pop_structure.set_index(
+            [col for col in pop_structure.columns if col != "value"]
+        )
+        if "year_start" not in scaling_factor.index.names:
+            return population_structure, scaling_factor
+
+        # Subset the population structure and scaling factors to the simulation
+        # start year. If the data does not contain the exact simulation start
+        # year, subset to the closest year less than the simulation start year.
+        pop_reference_years = sorted(
+            set(population_structure.index.get_level_values("year_start"))
+        )
+        pop_year_index = _find_bin_start_index(year, pop_reference_years)
+        population_structure = population_structure.loc[
+            population_structure.index.get_level_values("year_start")
+            == pop_reference_years[pop_year_index]
+        ]
 
-        return scaled_population_structure
+        scale_reference_years = sorted(
+            set(scaling_factor.index.get_level_values("year_start"))
+        )
+        scale_year_index = _find_bin_start_index(year, scale_reference_years)
+        scaling_factor = scaling_factor.loc[
+            scaling_factor.index.get_level_values("year_start")
+            == scale_reference_years[scale_year_index]
+        ]
+
+        return population_structure, scaling_factor
 
 
 class AgeOutSimulants(Component):
@@ -492,3 +527,31 @@ def _assign_demography_with_age_bounds(
     )
     register_simulants(simulants[list(key_columns)])
     return simulants
+
+
+def _find_bin_start_index(value: int, sorted_reference_values: list[int]) -> int:
+    """Finds the index of the closest reference value less than or equal to the provided value.
+
+    Parameters
+    ----------
+    value
+        The value for which to find the closest reference value.
+    sorted_reference_values
+        A sorted list of reference values.
+
+    Returns
+    -------
+        The index of the closest reference value less than or equal to the provided value.
+
+    Raises
+    ------
+        ValueError
+            If the provided value is less than the minimum reference value.
+    """
+    ref_value_index = np.digitize(value, sorted_reference_values).item() - 1
+    if ref_value_index < 0:
+        raise ValueError(
+            f"The provided value {value} is less than the minimum reference value "
+            f"{min(sorted_reference_values)}."
+        )
+    return ref_value_index

{vivarium_public_health-4.3.5.dist-info → vivarium_public_health-4.3.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vivarium_public_health
-Version: 4.3.5
+Version: 4.3.7
 Summary: Components for modelling diseases, risks, and interventions with ``vivarium``
 Home-page: https://github.com/ihmeuw/vivarium_public_health
 Author: The vivarium developers

{vivarium_public_health-4.3.5.dist-info → vivarium_public_health-4.3.7.dist-info}/RECORD

@@ -1,6 +1,6 @@
 vivarium_public_health/__about__.py,sha256=RgWycPypKZS80TpSX7o41cREnG8PfguNHDHLuLyl820,487
 vivarium_public_health/__init__.py,sha256=GDeeP-7OlCBwPuv_xQoB1wNmvCaFsqfTB7qnnYApm0w,1343
-vivarium_public_health/_version.py,sha256=NYrliYxjsS6KdKfQAwEvUhfqJXk87BHG-YA6Q3DTUIY,22
+vivarium_public_health/_version.py,sha256=jiLY_6kRRuH71R8uwkvkgOzPZ0hPgjpzzaC6-JM7Fyk,22
 vivarium_public_health/utilities.py,sha256=QNXQ6fhAr1HcV-GwKw7wQLz6QyuNxqNvMA-XujKjTgs,3035
 vivarium_public_health/disease/__init__.py,sha256=VUJHDLlE6ngo2qHNQUtZ8OWH5H_T7_ao-xsYKDkRmHw,443
 vivarium_public_health/disease/exceptions.py,sha256=vb30IIV82OiDf2cNZCs_E2rF6mdDDHbnZSND60no5CU,97
@@ -20,7 +20,7 @@ vivarium_public_health/plugins/__init__.py,sha256=oBW_zfgG_LbwfgTDjUe0btfy9FaDvA
 vivarium_public_health/plugins/parser.py,sha256=WoUisq0d-PfJtSzKYZ6C-s-fYdQpNiRBE14vKaYE27Y,32921
 vivarium_public_health/population/__init__.py,sha256=x_9rB93q64Krw-kbBDI1-_U_JsPO1_QrL03AwiFlwXI,243
 vivarium_public_health/population/add_new_birth_cohorts.py,sha256=x6A60GE_F3I8AgLABNJ-2ziiUj52lAd66uX5yc2vIDI,9038
-vivarium_public_health/population/base_population.py,sha256=Wu797AL13KRLhXkYni_XocJBLfhfvCVgGeas08U3tCM,18898
+vivarium_public_health/population/base_population.py,sha256=IqQFVZiw-bSDX1MHjwn6pmQYoJksKNwi0OQo_uHZyDM,21399
 vivarium_public_health/population/data_transformations.py,sha256=YHbwfb40EPbXsPW-Rk1s5d61rP8fqgDtMELB7OJG3mo,22662
 vivarium_public_health/population/mortality.py,sha256=Mtv45FENNY0GlPIoVd3d3pRq01aEh4cjzNXIgEe6hMo,10364
 vivarium_public_health/results/__init__.py,sha256=rKUZGlRXJgEyFY4a_WJeg3XnC0l34S5guYZ0N9JJS4E,319
@@ -43,8 +43,8 @@ vivarium_public_health/treatment/__init__.py,sha256=wONElu9aJbBYwpYIovYPYaN_GYfV
 vivarium_public_health/treatment/magic_wand.py,sha256=zg4I48G-l9fC6-qjvApbM1zNACJimZlX9ZZ9fdHKwvc,1985
 vivarium_public_health/treatment/scale_up.py,sha256=_bsf9c_yVc7-q_-yBcXimISTUfYzPps1auH0uEf7sfQ,7048
 vivarium_public_health/treatment/therapeutic_inertia.py,sha256=ZIHnpuszZwA_BkS53JbSLvpcnX_bqG2knwCUyUgkA9M,2362
-vivarium_public_health-4.3.5.dist-info/licenses/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
-vivarium_public_health-4.3.5.dist-info/METADATA,sha256=AqoR7HJE8HzNFk3525wVzzu_SHktWYfVa6GO0leCXs4,3877
-vivarium_public_health-4.3.5.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-vivarium_public_health-4.3.5.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
-vivarium_public_health-4.3.5.dist-info/RECORD,,
+vivarium_public_health-4.3.7.dist-info/licenses/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
+vivarium_public_health-4.3.7.dist-info/METADATA,sha256=M7KR6H7eH4yPNByDLXOPWBLjKrdytboajMaN28u9MxU,3877
+vivarium_public_health-4.3.7.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+vivarium_public_health-4.3.7.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
+vivarium_public_health-4.3.7.dist-info/RECORD,,