vivarium-public-health 2.3.2__py3-none-any.whl → 3.0.0__py3-none-any.whl

vivarium_public_health/metrics/disease.py

@@ -1,136 +0,0 @@
-"""
-================
-Disease Observer
-================
-
-This module contains tools for observing disease incidence and prevalence
-in the simulation.
-
-"""
-from typing import Any, Dict, List, Optional
-
-import pandas as pd
-from vivarium import Component
-from vivarium.framework.engine import Builder
-from vivarium.framework.event import Event
-from vivarium.framework.population import SimulantData
-
-from vivarium_public_health.utilities import to_years
-
-
-class DiseaseObserver(Component):
-    """Observes disease counts and person time for a cause.
-
-    By default, this observer computes aggregate disease state person time and
-    counts of disease events over the full course of the simulation. It can be
-    configured to add or remove stratification groups to the default groups
-    defined by a ResultsStratifier.
-
-    In the model specification, your configuration for this component should
-    be specified as, e.g.:
-
-    .. code-block:: yaml
-
-        configuration:
-            stratification:
-                cause_name:
-                    exclude:
-                        - "sex"
-                    include:
-                        - "sample_stratification"
-    """
-
-    CONFIGURATION_DEFAULTS = {
-        "stratification": {
-            "disease": {
-                "exclude": [],
-                "include": [],
-            }
-        }
-    }
-
-    ##############
-    # Properties #
-    ##############
-
-    @property
-    def configuration_defaults(self) -> Dict[str, Any]:
-        return {
-            "stratification": {
-                self.disease: self.CONFIGURATION_DEFAULTS["stratification"]["disease"]
-            }
-        }
-
-    @property
-    def columns_created(self) -> List[str]:
-        return [self.previous_state_column_name]
-
-    @property
-    def columns_required(self) -> Optional[List[str]]:
-        return [self.disease]
-
-    #####################
-    # Lifecycle methods #
-    #####################
-
-    def __init__(self, disease: str):
-        super().__init__()
-        self.disease = disease
-        self.current_state_column_name = self.disease
-        self.previous_state_column_name = f"previous_{self.disease}"
-
-    # noinspection PyAttributeOutsideInit
-    def setup(self, builder: Builder) -> None:
-        self.step_size = builder.time.step_size()
-        self.config = builder.configuration.stratification[self.disease]
-
-        disease_model = builder.components.get_component(f"disease_model.{self.disease}")
-
-        for state in disease_model.states:
-            builder.results.register_observation(
-                name=f"{state.state_id}_person_time",
-                pop_filter=f'alive == "alive" and {self.disease} == "{state.state_id}" and tracked==True',
-                aggregator=self.aggregate_state_person_time,
-                requires_columns=["alive", self.disease],
-                additional_stratifications=self.config.include,
-                excluded_stratifications=self.config.exclude,
-                when="time_step__prepare",
-            )
-
-        for transition in disease_model.transition_names:
-            filter_string = (
-                f'{self.previous_state_column_name} == "{transition.from_state}" '
-                f'and {self.disease} == "{transition.to_state}" '
-                f"and tracked==True "
-                f'and alive == "alive"'
-            )
-            builder.results.register_observation(
-                name=f"{transition}_event_count",
-                pop_filter=filter_string,
-                requires_columns=[self.previous_state_column_name, self.disease],
-                additional_stratifications=self.config.include,
-                excluded_stratifications=self.config.exclude,
-                when="collect_metrics",
-            )
-
-    ########################
-    # Event-driven methods #
-    ########################
-
-    def on_initialize_simulants(self, pop_data: SimulantData) -> None:
-        self.population_view.update(
-            pd.Series("", index=pop_data.index, name=self.previous_state_column_name)
-        )
-
-    def on_time_step_prepare(self, event: Event) -> None:
-        # This enables tracking of transitions between states
-        prior_state_pop = self.population_view.get(event.index)
-        prior_state_pop[self.previous_state_column_name] = prior_state_pop[self.disease]
-        self.population_view.update(prior_state_pop)
-
-    ###############
-    # Aggregators #
-    ###############
-
-    def aggregate_state_person_time(self, x: pd.DataFrame) -> float:
-        return len(x) * to_years(self.step_size())

vivarium_public_health/metrics/mortality.py

@@ -1,144 +0,0 @@
-"""
-==================
-Mortality Observer
-==================
-
-This module contains tools for observing cause-specific and
-excess mortality in the simulation, including "other causes".
-
-"""
-from typing import Callable, List, Optional
-
-import pandas as pd
-from vivarium import Component
-from vivarium.framework.engine import Builder
-
-from vivarium_public_health.disease import DiseaseState, RiskAttributableDisease
-
-
-class MortalityObserver(Component):
-    """An observer for cause-specific deaths and ylls (including "other causes").
-
-    By default, this counts cause-specific deaths and years of life lost over
-    the full course of the simulation. It can be configured to add or remove
-    stratification groups to the default groups defined by a
-    :class:ResultsStratifier. The aggregate configuration key can be set to
-    True to aggregate all deaths and ylls into a single observation and remove
-    the stratification by cause of death to improve runtime.
-
-    In the model specification, your configuration for this component should
-    be specified as, e.g.:
-
-    .. code-block:: yaml
-
-        configuration:
-            stratification:
-                mortality:
-                    exclude:
-                        - "sex"
-                    include:
-                        - "sample_stratification"
-
-    This observer needs to access the has_excess_mortality attribute of the causes
-    we're observing, but this attribute gets defined in the setup of the cause models.
-    As a result, the model specification should list this observer after causes.
-    """
-
-    CONFIGURATION_DEFAULTS = {
-        "stratification": {
-            "mortality": {
-                "exclude": [],
-                "include": [],
-                "aggregate": False,
-            }
-        }
-    }
-
-    def __init__(self):
-        super().__init__()
-        self.causes_of_death = ["other_causes"]
-        self.required_death_columns = ["alive", "exit_time"]
-        self.required_yll_columns = [
-            "alive",
-            "cause_of_death",
-            "exit_time",
-            "years_of_life_lost",
-        ]
-
-    ##############
-    # Properties #
-    ##############
-
-    @property
-    def columns_required(self) -> Optional[List[str]]:
-        return [
-            "alive",
-            "years_of_life_lost",
-            "cause_of_death",
-            "exit_time",
-        ]
-
-    #####################
-    # Lifecycle methods #
-    #####################
-
-    # noinspection PyAttributeOutsideInit
-    def setup(self, builder: Builder) -> None:
-        self.clock = builder.time.clock()
-        self.config = builder.configuration.stratification.mortality
-        cause_components = builder.components.get_components_by_type(
-            (DiseaseState, RiskAttributableDisease)
-        )
-        self.causes_of_death += [
-            cause.state_id for cause in cause_components if cause.has_excess_mortality
-        ]
-        if not self.config.aggregate:
-            for cause_of_death in self.causes_of_death:
-                self._register_mortality_observations(
-                    builder, cause_of_death, f'cause_of_death == "{cause_of_death}"'
-                )
-        else:
-            self._register_mortality_observations(builder, "all_causes")
-
-    ###################
-    # Private methods #
-    ###################
-
-    def _register_mortality_observations(
-        self, builder: Builder, cause: str, additional_pop_filter: str = ""
-    ) -> None:
-        pop_filter = (
-            'alive == "dead" and tracked == True'
-            if additional_pop_filter == ""
-            else f'alive == "dead" and tracked == True and {additional_pop_filter}'
-        )
-        builder.results.register_observation(
-            name=f"death_due_to_{cause}",
-            pop_filter=pop_filter,
-            aggregator=self.count_deaths,
-            requires_columns=self.required_death_columns,
-            additional_stratifications=self.config.include,
-            excluded_stratifications=self.config.exclude,
-            when="collect_metrics",
-        )
-        builder.results.register_observation(
-            name=f"ylls_due_to_{cause}",
-            pop_filter=pop_filter,
-            aggregator=self.calculate_ylls,
-            requires_columns=self.required_yll_columns,
-            additional_stratifications=self.config.include,
-            excluded_stratifications=self.config.exclude,
-            when="collect_metrics",
-        )
-
-    ###############
-    # Aggregators #
-    ###############
-
-    def count_deaths(self, x: pd.DataFrame) -> float:
-        died_of_cause = x["exit_time"] > self.clock()
-        return sum(died_of_cause)
-
-    def calculate_ylls(self, x: pd.DataFrame) -> float:
-        died_of_cause = x["exit_time"] > self.clock()
-        return x.loc[died_of_cause, "years_of_life_lost"].sum()

vivarium_public_health/metrics/risk.py

@@ -1,110 +0,0 @@
-"""
-==============
-Risk Observers
-==============
-
-This module contains tools for observing risk exposure during the simulation.
-
-"""
-from typing import Any, Dict, List, Optional
-
-import pandas as pd
-from vivarium import Component
-from vivarium.framework.engine import Builder
-
-from vivarium_public_health.utilities import to_years
-
-
-class CategoricalRiskObserver(Component):
-    """An observer for a categorical risk factor.
-
-    Observes category person time for a risk factor.
-
-    By default, this observer computes aggregate categorical person time
-    over the full course of the simulation. It can be configured to add or
-    remove stratification groups to the default groups defined by a
-    ResultsStratifier.
-
-    In the model specification, your configuration for this component should
-    be specified as, e.g.:
-
-    .. code-block:: yaml
-
-        configuration:
-            stratification:
-                risk_name:
-                    exclude:
-                        - "sex"
-                    include:
-                        - "sample_stratification"
-    """
-
-    CONFIGURATION_DEFAULTS = {
-        "stratification": {
-            "risk": {
-                "exclude": [],
-                "include": [],
-            }
-        }
-    }
-
-    ##############
-    # Properties #
-    ##############
-
-    @property
-    def configuration_defaults(self) -> Dict[str, Any]:
-        """
-        A dictionary containing the defaults for any configurations managed by
-        this component.
-        """
-        return {
-            "stratification": {
-                f"{self.risk}": self.CONFIGURATION_DEFAULTS["stratification"]["risk"]
-            }
-        }
-
-    @property
-    def columns_required(self) -> Optional[List[str]]:
-        return ["alive"]
-
-    #####################
-    # Lifecycle methods #
-    #####################
-
-    def __init__(self, risk: str):
-        """
-        Parameters
-        ----------
-        risk :
-        name of a risk
-
-        """
-        super().__init__()
-        self.risk = risk
-        self.exposure_pipeline_name = f"{self.risk}.exposure"
-
-    # noinspection PyAttributeOutsideInit
-    def setup(self, builder: Builder) -> None:
-        self.step_size = builder.time.step_size()
-        self.config = builder.configuration.stratification[self.risk]
-        self.categories = builder.data.load(f"risk_factor.{self.risk}.categories")
-
-        for category in self.categories:
-            builder.results.register_observation(
-                name=f"{self.risk}_{category}_person_time",
-                pop_filter=f'alive == "alive" and `{self.exposure_pipeline_name}`=="{category}" and tracked==True',
-                aggregator=self.aggregate_risk_category_person_time,
-                requires_columns=["alive"],
-                requires_values=[self.exposure_pipeline_name],
-                additional_stratifications=self.config.include,
-                excluded_stratifications=self.config.exclude,
-                when="time_step__prepare",
-            )
-
-    ###############
-    # Aggregators #
-    ###############
-
-    def aggregate_risk_category_person_time(self, x: pd.DataFrame) -> float:
-        return len(x) * to_years(self.step_size())

vivarium_public_health/testing/mock_artifact.py

@@ -1,145 +0,0 @@
-"""
-==================
-Mock Data Artifact
-==================
-
-This module contains a mock version of the artifact manager for use with
-testing vivarium_public_health components.
-
-"""
-import pandas as pd
-from vivarium.framework.artifact import ArtifactManager
-from vivarium.testing_utilities import build_table
-
-from vivarium_public_health.testing.utils import make_age_bins, make_uniform_pop_data
-
-MOCKERS = {
-    "cause": {
-        "prevalence": 0,
-        "cause_specific_mortality_rate": 0,
-        "excess_mortality_rate": 0,
-        "remission_rate": 0,
-        "incidence_rate": 0.001,
-        "disability_weight": pd.DataFrame({"value": [0]}),
-        "restrictions": lambda *args, **kwargs: {"yld_only": False},
-    },
-    "risk_factor": {
-        "distribution": lambda *args, **kwargs: "ensemble",
-        "exposure": 120,
-        "exposure_standard_deviation": 15,
-        "relative_risk": build_table(
-            [1.5, "continuous", "test_cause", "incidence_rate"],
-            1990,
-            2017,
-            (
-                "age",
-                "sex",
-                "year",
-                "value",
-                "parameter",
-                "affected_entity",
-                "affected_measure",
-            ),
-        ),
-        "population_attributable_fraction": build_table(
-            [1, "test_cause_1", "incidence_rate"],
-            1990,
-            2017,
-            ("age", "sex", "year", "value", "cause", "affected_measure"),
-        ),
-        "tmred": lambda *args, **kwargs: {
-            "distribution": "uniform",
-            "min": 80,
-            "max": 100,
-            "inverted": False,
-        },
-        "exposure_parameters": lambda *args, **kwargs: {
-            "scale": 1,
-            "max_rr": 10,
-            "max_val": 200,
-            "min_val": 0,
-        },
-        "ensemble_weights": lambda *args, **kwargs: pd.DataFrame({"norm": 1}, index=[0]),
-    },
-    "sequela": {
-        "prevalence": 0,
-        "cause_specific_mortality_rate": 0,
-        "excess_mortality_rate": 0,
-        "remission_rate": 0,
-        "incidence_rate": 0.001,
-        "disability_weight": pd.DataFrame({"value": [0]}),
-    },
-    "etiology": {
-        "population_attributable_fraction": build_table(
-            [1, "incidence_rate"],
-            1990,
-            2017,
-            ("age", "sex", "year", "value", "affected_measure"),
-        ),
-    },
-    "healthcare_entity": {
-        "cost": build_table(
-            [0, "outpatient_visits"],
-            1990,
-            2017,
-            ("age", "sex", "year", "value", "healthcare_entity"),
-        ),
-        "utilization_rate": 0,
-    },
-    # FIXME: this is a hack to get the MockArtifact to use the correct value
-    "population.location": "Kenya",
-    "population": {
-        "age_bins": make_age_bins(),
-        "structure": make_uniform_pop_data(),
-        "theoretical_minimum_risk_life_expectancy": (
-            build_table(98.0, 1990, 1990)
-            .query('sex=="Female"')
-            .filter(["age_start", "age_end", "value"])
-        ),
-    },
-}
-
-
-class MockArtifact:
-    def __init__(self):
-        self.mocks = MOCKERS.copy()
-
-    def load(self, entity_key):
-        if entity_key in self.mocks:
-            return self.mocks[entity_key]
-
-        entity_type, *_, entity_measure = entity_key.split(".")
-        assert entity_type in self.mocks
-        assert entity_measure in self.mocks[entity_type]
-        value = self.mocks[entity_type][entity_measure]
-
-        if callable(value):
-            value = value(entity_key)
-        elif not isinstance(value, (pd.DataFrame, pd.Series)):
-            value = build_table(value, 1990, 2018)
-
-        return value
-
-    def write(self, entity_key, data):
-        self.mocks[entity_key] = data
-
-
-class MockArtifactManager(ArtifactManager):
-    def __init__(self):
-        self.artifact = self._load_artifact(None)
-
-    @property
-    def name(self):
-        return "mock_artifact_manager"
-
-    def setup(self, builder):
-        pass
-
-    def load(self, entity_key, *args, **kwargs):
-        return self.artifact.load(entity_key)
-
-    def write(self, entity_key, data):
-        self.artifact.write(entity_key, data)
-
-    def _load_artifact(self, _):
-        return MockArtifact()

vivarium_public_health/testing/utils.py

@@ -1,71 +0,0 @@
-"""
-=================
-Testing Utilities
-=================
-
-This module contains data generation tools for testing vivarium_public_health
-components.
-
-"""
-from itertools import product
-
-import numpy as np
-import pandas as pd
-
-
-def make_uniform_pop_data(age_bin_midpoint=False):
-    age_bins = [(b.age_start, b.age_end) for b in make_age_bins().itertuples()]
-    sexes = ("Male", "Female")
-    years = zip(range(1990, 2018), range(1991, 2019))
-    locations = (1, 2)
-
-    age_bins, sexes, years, locations = zip(*product(age_bins, sexes, years, locations))
-    mins, maxes = zip(*age_bins)
-    year_starts, year_ends = zip(*years)
-
-    pop = pd.DataFrame(
-        {
-            "age_start": mins,
-            "age_end": maxes,
-            "sex": sexes,
-            "year_start": year_starts,
-            "year_end": year_ends,
-            "location": locations,
-            "value": 100 * (np.array(maxes) - np.array(mins)),
-        }
-    )
-    if age_bin_midpoint:  # used for population tests
-        pop["age"] = pop.apply(lambda row: (row["age_start"] + row["age_end"]) / 2, axis=1)
-    return pop
-
-
-def make_age_bins():
-    idx = pd.MultiIndex.from_tuples(
-        [
-            (0.0, 0.01917808, "Early Neonatal"),
-            (0.01917808, 0.07671233, "Late Neonatal"),
-            (0.07671233, 1.0, "Post Neonatal"),
-            (1.0, 5.0, "1 to 4"),
-            (5.0, 10.0, "5 to 9"),
-            (10.0, 15.0, "10 to 14"),
-            (15.0, 20.0, "15 to 19"),
-            (20.0, 25.0, "20 to 24"),
-            (25.0, 30.0, "25 to 29"),
-            (30.0, 35.0, "30 to 34"),
-            (35.0, 40.0, "35 to 39"),
-            (40.0, 45.0, "40 to 44"),
-            (45.0, 50.0, "45 to 49"),
-            (50.0, 55.0, "50 to 54"),
-            (55.0, 60.0, "55 to 59"),
-            (60.0, 65.0, "60 to 64"),
-            (65.0, 70.0, "65 to 69"),
-            (70.0, 75.0, "70 to 74"),
-            (75.0, 80.0, "75 to 79"),
-            (80.0, 85.0, "80 to 84"),
-            (85.0, 90.0, "85 to 89"),
-            (90.0, 95.0, "90 to 94"),
-            (95.0, 125.0, "95 plus"),
-        ],
-        names=["age_start", "age_end", "age_group_name"],
-    )
-    return pd.DataFrame(index=idx).reset_index()

vivarium_public_health-2.3.2.dist-info/RECORD

@@ -1,49 +0,0 @@
-vivarium_public_health/__about__.py,sha256=RgWycPypKZS80TpSX7o41cREnG8PfguNHDHLuLyl820,487
-vivarium_public_health/__init__.py,sha256=tomMOl3PI7O8GdxDWGBiBjT0Bwd31GpyQTYTzwIv108,361
-vivarium_public_health/_version.py,sha256=J4CRnpR3v72FGOMp8gqSua_XWZpAfXuqgVWiQFB-gTY,22
-vivarium_public_health/utilities.py,sha256=_X9sZQ7flsi2sVWQ9zrf8GJw8QwZsPZm3NUjx1gu7bM,2555
-vivarium_public_health/disease/__init__.py,sha256=RuuiRcvAJfX9WQGt_WZZjxN7Cu3E5rMTmuaRS-UaFPM,419
-vivarium_public_health/disease/model.py,sha256=9Ru3mg3UUp3h1W0y-1xkWjQBgxqSq-LXM0ByiEcNmGA,8332
-vivarium_public_health/disease/models.py,sha256=uiB2qUlxBsPPPmHJ8Cgot_T1ItZ8RYSNVOBtxtn93Y0,3478
-vivarium_public_health/disease/special_disease.py,sha256=gl8aK0z6afCxiCZxgJafLe4xmbR91zk3079hsi2pUAw,14751
-vivarium_public_health/disease/state.py,sha256=wTSiWKXgJ4k9kr0p8oC3gAHil0-zQPOifNoBftHnTRw,24837
-vivarium_public_health/disease/transition.py,sha256=Or5nucRzeGG-UuE_CGkPZ9qE35-Ed9I9LWHj4rjknCc,5334
-vivarium_public_health/metrics/__init__.py,sha256=bWAvvdCm_7RPIazo12qFohA2x5-_EV6ceV8IhKS37sk,209
-vivarium_public_health/metrics/disability.py,sha256=zm0vAG00wj44CHjYGdT2_pebgARa3XXIerrR06t80rc,3984
-vivarium_public_health/metrics/disease.py,sha256=_WQYjd6FRrxRs1Oj8NR9ZmcbXVvsHqX_hods10hwHzU,4546
-vivarium_public_health/metrics/mortality.py,sha256=B1AX-N4aO1Jd2NEJ_yMC1NHaDr4pEXmQxNm5kXoLz8w,4826
-vivarium_public_health/metrics/risk.py,sha256=ANwgwpasX-5t0OHMQysV8p_cM86NL2bV6za1FM0JR88,3201
-vivarium_public_health/metrics/stratification.py,sha256=_ChQy8yeP09wFKne4UPPiUEfCKDM6UGfHl4moKCjoNQ,4612
-vivarium_public_health/mslt/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-vivarium_public_health/mslt/delay.py,sha256=4JiSID5bt2xB1DQR1FX1f0NV947HKtwfk-D32C54kbg,22581
-vivarium_public_health/mslt/disease.py,sha256=JWe_A6X5NyDcTXf-HIeSSUv0DCwj27aIwRXVWzjXCVQ,15683
-vivarium_public_health/mslt/intervention.py,sha256=q6-ZHYFuV9o7WKlHMpiFAsEH2fYzwOayY120eDAOQ5U,10335
-vivarium_public_health/mslt/magic_wand_components.py,sha256=7sy_7fa0R5pk5XPdt9-AfK005JV3em4Tvu4L4xeg4g0,3980
-vivarium_public_health/mslt/observer.py,sha256=Z0aWLrlSjxLuYqzXarNunJ2Xqei4R9nX03dnE6uvr4o,13940
-vivarium_public_health/mslt/population.py,sha256=R5Z7aBf63LDbasPVMMI0HTh41FIL_OAhYk0qQWf_-lU,7285
-vivarium_public_health/plugins/__init__.py,sha256=oBW_zfgG_LbwfgTDjUe0btfy9FaDvAbtXho1zQFnz0Y,76
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