vivarium-public-health 4.3.1__py3-none-any.whl → 4.3.3__py3-none-any.whl

vivarium_public_health/exposure/data_transformations.py

@@ -1,254 +0,0 @@
-"""
-=========================
-Risk Data Transformations
-=========================
-
-This module contains tools for handling raw risk exposure and relative
-risk data and performing any necessary data transformations.
-
-"""
-
-import numpy as np
-import pandas as pd
-from vivarium.framework.engine import Builder
-
-from vivarium_public_health.utilities import EntityString, TargetString
-
-#############
-# Utilities #
-#############
-
-
-def pivot_categorical(
-    builder: Builder,
-    risk: EntityString,
-    data: pd.DataFrame,
-    pivot_column: str = "parameter",
-    reset_index: bool = True,
-) -> pd.DataFrame:
-    """Pivots data that is long on categories to be wide."""
-    # todo remove dependency on artifact manager having exactly one value column
-    value_column = builder.data.value_columns()(f"{risk}.exposure")[0]
-    index_cols = [
-        column for column in data.columns if column not in [value_column, pivot_column]
-    ]
-    data = data.pivot_table(index=index_cols, columns=pivot_column, values=value_column)
-    if reset_index:
-        data = data.reset_index()
-    data.columns.name = None
-
-    return data
-
-
-##########################
-# Exposure data handlers #
-##########################
-
-
-def get_exposure_post_processor(builder, risk: str):
-    thresholds = builder.configuration[risk]["category_thresholds"]
-
-    if thresholds:
-        thresholds = [-np.inf] + thresholds + [np.inf]
-        categories = [f"cat{i}" for i in range(1, len(thresholds))]
-
-        def post_processor(exposure, _):
-            return pd.Series(
-                pd.cut(exposure, thresholds, labels=categories), index=exposure.index
-            ).astype(str)
-
-    else:
-        post_processor = None
-
-    return post_processor
-
-
-def load_exposure_data(builder: Builder, risk: EntityString) -> pd.DataFrame:
-    risk_component = builder.components.get_component(risk)
-    return risk_component.get_data(
-        builder, builder.configuration[risk_component.name]["data_sources"]["exposure"]
-    )
-
-
-###############################
-# Relative risk data handlers #
-###############################
-
-
-def rebin_relative_risk_data(
-    builder, risk: EntityString, relative_risk_data: pd.DataFrame
-) -> pd.DataFrame:
-    """Rebin relative risk data if necessary.
-
-    When the polytomous risk is rebinned, matching relative risk needs to be rebinned.
-    After rebinning, rr for both exposed and unexposed categories should be the weighted sum of relative risk
-    of the component categories where weights are relative proportions of exposure of those categories.
-    For example, if cat1, cat2, cat3 are exposed categories and cat4 is unexposed with exposure [0.1,0.2,0.3,0.4],
-    for the matching rr = [rr1, rr2, rr3, 1], rebinned rr for the rebinned cat1 should be:
-    (0.1 *rr1 + 0.2 * rr2 + 0.3* rr3) / (0.1+0.2+0.3)
-    """
-    if not risk in builder.configuration.to_dict():
-        return relative_risk_data
-
-    rebin_exposed_categories = set(builder.configuration[risk]["rebinned_exposed"])
-
-    if rebin_exposed_categories:
-        # todo make sure this works
-        exposure_data = load_exposure_data(builder, risk)
-        relative_risk_data = _rebin_relative_risk_data(
-            relative_risk_data, exposure_data, rebin_exposed_categories
-        )
-
-    return relative_risk_data
-
-
-def _rebin_relative_risk_data(
-    relative_risk_data: pd.DataFrame,
-    exposure_data: pd.DataFrame,
-    rebin_exposed_categories: set,
-) -> pd.DataFrame:
-    cols = list(exposure_data.columns.difference(["value"]))
-
-    relative_risk_data = relative_risk_data.merge(exposure_data, on=cols)
-    relative_risk_data["value_x"] = relative_risk_data.value_x.multiply(
-        relative_risk_data.value_y
-    )
-    relative_risk_data.parameter = relative_risk_data["parameter"].map(
-        lambda p: "cat1" if p in rebin_exposed_categories else "cat2"
-    )
-    relative_risk_data = relative_risk_data.groupby(cols).sum().reset_index()
-    relative_risk_data["value"] = relative_risk_data.value_x.divide(
-        relative_risk_data.value_y
-    ).fillna(0)
-    return relative_risk_data.drop(columns=["value_x", "value_y"])
-
-
-##############
-# Validators #
-##############
-
-
-def validate_distribution_data_source(builder: Builder, risk: EntityString) -> None:
-    """Checks that the exposure distribution specification is valid."""
-    exposure_type = builder.configuration[risk]["data_sources"]["exposure"]
-    rebin = builder.configuration[risk]["rebinned_exposed"]
-    category_thresholds = builder.configuration[risk]["category_thresholds"]
-
-    if risk.type == "alternative_risk_factor":
-        if exposure_type != "data" or rebin:
-            raise ValueError(
-                "Parameterized risk components are not available for alternative risks."
-            )
-
-        if not category_thresholds:
-            raise ValueError("Must specify category thresholds to use alternative risks.")
-
-    elif risk.type not in ["risk_factor", "coverage_gap"]:
-        raise ValueError(f"Unknown risk type {risk.type} for risk {risk.name}")
-
-
-def validate_relative_risk_data_source(builder, risk: EntityString, target: TargetString):
-    from vivarium_public_health.risks import RiskEffect
-
-    source_key = RiskEffect.get_name(risk, target)
-    source_config = builder.configuration[source_key]
-
-    provided_keys = set(
-        k
-        for k, v in source_config["distribution_args"].to_dict().items()
-        if isinstance(v, (int, float))
-    )
-
-    source_map = {
-        "data": set(),
-        "relative risk value": {"relative_risk"},
-        "normal distribution": {"mean", "se"},
-        "log distribution": {"log_mean", "log_se", "tau_squared"},
-    }
-
-    if provided_keys not in source_map.values():
-        raise ValueError(
-            f"The acceptable parameter options for specifying relative risk are: "
-            f"{source_map.values()}. You provided {provided_keys} for {source_key}."
-        )
-
-    source_type = [k for k, v in source_map.items() if provided_keys == v][0]
-
-    if source_type == "relative risk value":
-        if not 1 <= source_type <= 100:
-            raise ValueError(
-                "If specifying a single value for relative risk, it should be in the range [1, 100]. "
-                f"You provided {source_type} for {source_key}."
-            )
-    elif source_type == "normal distribution":
-        if source_config["mean"] <= 0 or source_config["se"] <= 0:
-            raise ValueError(
-                f"To specify parameters for a normal distribution for a risk effect, you must provide"
-                f"both mean and se above 0. This is not the case for {source_key}."
-            )
-    elif source_type == "log distribution":
-        if source_config["log_mean"] <= 0 or source_config["log_se"] <= 0:
-            raise ValueError(
-                f"To specify parameters for a log distribution for a risk effect, you must provide"
-                f"both log_mean and log_se above 0. This is not the case for {source_key}."
-            )
-        if source_config["tau_squared"] < 0:
-            raise ValueError(
-                f"To specify parameters for a log distribution for a risk effect, you must provide"
-                f"tau_squared >= 0. This is not the case for {source_key}."
-            )
-    else:
-        pass
-
-    return source_type
-
-
-def validate_relative_risk_rebin_source(
-    builder, risk: EntityString, target: TargetString, data: pd.DataFrame
-):
-    if data.index.size == 0:
-        raise ValueError(
-            f"Subsetting {risk} relative risk data to {target.name} {target.measure} "
-            "returned an empty DataFrame. Check your artifact."
-        )
-    if risk in builder.configuration.to_dict():
-        validate_rebin_source(builder, risk, data)
-
-
-def validate_rebin_source(builder, risk: EntityString, data: pd.DataFrame) -> None:
-
-    if not isinstance(data, pd.DataFrame):
-        return
-
-    rebin_exposed_categories = set(builder.configuration[risk]["rebinned_exposed"])
-
-    if rebin_exposed_categories and builder.configuration[risk]["category_thresholds"]:
-        raise ValueError(
-            f"Rebinning and category thresholds are mutually exclusive. "
-            f"You provided both for {risk.name}."
-        )
-
-    if rebin_exposed_categories and "polytomous" not in builder.data.load(
-        f"{risk}.distribution"
-    ):
-        raise ValueError(
-            f"Rebinning is only supported for polytomous risks. You provided "
-            f"rebinning exposed categoriesfor {risk.name}, which is of "
-            f"type {builder.data.load(f'{risk}.distribution')}."
-        )
-
-    invalid_cats = rebin_exposed_categories.difference(set(data.parameter))
-    if invalid_cats:
-        raise ValueError(
-            f"The following provided categories for the rebinned exposed "
-            f"category of {risk.name} are not found in the exposure data: "
-            f"{invalid_cats}."
-        )
-
-    if rebin_exposed_categories == set(data.parameter):
-        raise ValueError(
-            f"The provided categories for the rebinned exposed category of "
-            f"{risk.name} comprise all categories for the exposure data. "
-            f"At least one category must be left out of the provided categories "
-            f"to be rebinned into the unexposed category."
-        )