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Albrja/mic 5805/cpapa implementation (#36)
Albrja/mic 5805/cpapa implementation No CPAP risk factor implementation - *Category*: Implemenation - *JIRA issue*: https://jira.ihme.washington.edu/browse/MIC-5805 - *Research reference*: https://vivarium-research.readthedocs.io/en/latest/models/intervention_models/neonatal/cpap_intervention.html#calibration-strategy Changes and notes -adds Intrapartum component to determine delivery facility type and CPAP availability for simulants -adds No CPAP risk effect component to modify preterm with rds CSMR pipeline ### Verification and Testing <!-- Details on how code was verified. Consider: plots, images, (small) csv files. -->
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,76 @@ | ||
| from __future__ import annotations | ||
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| from functools import partial | ||
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| import pandas as pd | ||
| from vivarium import Component | ||
| from vivarium.framework.engine import Builder | ||
| from vivarium.framework.event import Event | ||
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| from vivarium_gates_mncnh.constants import data_values | ||
| from vivarium_gates_mncnh.constants.data_keys import NO_CPAP_RISK | ||
| from vivarium_gates_mncnh.constants.data_values import COLUMNS, PIPELINES | ||
| from vivarium_gates_mncnh.utilities import get_location | ||
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| class NoCPAPRisk(Component): | ||
| """Component for CPAP intervention. This is essentially a risk effect.""" | ||
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| @property | ||
| def configuration_defaults(self) -> dict: | ||
| return { | ||
| self.name: { | ||
| "data_sources": { | ||
| "relative_risk": NO_CPAP_RISK.RELATIVE_RISK, | ||
| "paf": self.load_paf_data, | ||
| } | ||
| } | ||
| } | ||
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| @property | ||
| def columns_required(self) -> list[str]: | ||
| return [COLUMNS.CPAP_AVAILABLE] | ||
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| def __init__(self) -> None: | ||
| super().__init__() | ||
| self.preterm_csmr_target = PIPELINES.NEONATAL_PRETERM_BIRTH_WITH_RDS | ||
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| def setup(self, builder: Builder) -> None: | ||
| self.randomness = builder.randomness.get_stream(self.name) | ||
| self.location = get_location(builder) | ||
| self.preterm_with_rds_csmr = builder.value.get_value(self.preterm_csmr_target) | ||
| builder.value.register_value_modifier( | ||
| self.preterm_with_rds_csmr.name, | ||
| self.modify_preterm_with_rds_csmr, | ||
| required_resources=[ | ||
| self.preterm_with_rds_csmr.name, | ||
| COLUMNS.DELIVERY_FACILITY_TYPE, | ||
| COLUMNS.CPAP_AVAILABLE, | ||
| ], | ||
| ) | ||
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| ################## | ||
| # Helper nethods # | ||
| ################## | ||
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| def load_paf_data(self, builder: Builder) -> pd.Series: | ||
| data = builder.data.load(NO_CPAP_RISK.PAF) | ||
| data = data.rename(columns=data_values.CHILD_LOOKUP_COLUMN_MAPPER) | ||
| return data | ||
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| def modify_preterm_with_rds_csmr( | ||
| self, index: pd.Index, preterm_with_rds_csmr: pd.Series[float] | ||
| ) -> pd.Series[float]: | ||
| # No CPAP access is like a dichotomous risk factor, meaning those that have access to CPAP will | ||
| # not have their CSMR modify by no CPAP RR | ||
| pop = self.population_view.get(index) | ||
| no_cpap_idx = pop.index[pop[COLUMNS.CPAP_AVAILABLE] == False] | ||
| # NOTE: RR is relative risk for no CPAP | ||
| no_cpap_rr = self.lookup_tables["relative_risk"](no_cpap_idx) | ||
| # NOTE: PAF is for no CPAP | ||
| paf = self.lookup_tables["paf"](index) | ||
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| # Modify the CSMR pipeline | ||
| modified_csmr = preterm_with_rds_csmr * (1 - paf) | ||
| modified_csmr.loc[no_cpap_idx] = modified_csmr * no_cpap_rr | ||
| return modified_csmr |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,80 @@ | ||
| 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 | ||
|
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||
| from vivarium_gates_mncnh.constants.data_keys import NO_CPAP_RISK | ||
| from vivarium_gates_mncnh.constants.data_values import ( | ||
| COLUMNS, | ||
| CPAP_ACCESS_PROBABILITIES, | ||
| DELIVERY_FACILITY_TYPE_PROBABILITIES, | ||
| DELIVERY_FACILITY_TYPES, | ||
| SIMULATION_EVENT_NAMES, | ||
| ) | ||
| from vivarium_gates_mncnh.utilities import get_location | ||
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| class Intrapartum(Component): | ||
| """This component functions to make key decisions about events in the intrapartum step of the model. | ||
| Specifically, it determines the delivery facility type and whether or not CPAP is available to the simulant.""" | ||
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| @property | ||
| def columns_created(self) -> list[str]: | ||
| return [ | ||
| COLUMNS.DELIVERY_FACILITY_TYPE, | ||
| COLUMNS.CPAP_AVAILABLE, | ||
| ] | ||
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| def setup(self, builder: Builder) -> None: | ||
| self._sim_step_name = builder.time.simulation_event_name() | ||
| self.randomness = builder.randomness.get_stream(self.name) | ||
| self.location = get_location(builder) | ||
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| def on_initialize_simulants(self, pop_data: SimulantData) -> None: | ||
| anc_data = pd.DataFrame( | ||
| { | ||
| COLUMNS.DELIVERY_FACILITY_TYPE: DELIVERY_FACILITY_TYPES.NONE, | ||
| COLUMNS.CPAP_AVAILABLE: False, | ||
| }, | ||
| index=pop_data.index, | ||
| ) | ||
| self.population_view.update(anc_data) | ||
|
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| def on_time_step(self, event: Event) -> None: | ||
| if self._sim_step_name() != SIMULATION_EVENT_NAMES.INTRAPARTUM: | ||
| return | ||
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| pop = self.population_view.get(event.index) | ||
| # Choose delivery facility type | ||
| delivery_facility_type = self.randomness.choice( | ||
| pop.index, | ||
| [ | ||
| DELIVERY_FACILITY_TYPES.HOME, | ||
| DELIVERY_FACILITY_TYPES.CEmONC, | ||
| DELIVERY_FACILITY_TYPES.BEmONC, | ||
| ], | ||
| p=list(DELIVERY_FACILITY_TYPE_PROBABILITIES[self.location].values()), | ||
| additional_key="delivery_facility_type", | ||
| ) | ||
| pop[COLUMNS.DELIVERY_FACILITY_TYPE] = delivery_facility_type | ||
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| # Determine if simulant had access to CPAP | ||
| facility_type_mapper = { | ||
| DELIVERY_FACILITY_TYPES.BEmONC: NO_CPAP_RISK.P_CPAP_BEmONC, | ||
| DELIVERY_FACILITY_TYPES.CEmONC: NO_CPAP_RISK.P_CPAP_CEmONC, | ||
| } | ||
| for facility_type in [ | ||
| DELIVERY_FACILITY_TYPES.BEmONC, | ||
| DELIVERY_FACILITY_TYPES.CEmONC, | ||
| ]: | ||
| facility_idx = pop.index[pop[COLUMNS.DELIVERY_FACILITY_TYPE] == facility_type] | ||
| cpap_access_probability = CPAP_ACCESS_PROBABILITIES[self.location][ | ||
| facility_type_mapper[facility_type] | ||
| ] | ||
| cpap_access_idx = self.randomness.filter_for_probability( | ||
| facility_idx, cpap_access_probability, f"cpap_access_{facility_type}" | ||
| ) | ||
| pop.loc[cpap_access_idx, COLUMNS.CPAP_AVAILABLE] = True | ||
|
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| self.population_view.update(pop) |
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