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CHADSVASCPhenotype

CHADSVASCComponents dataclass

Database specific components of CHA2DS2-VASc score calculation.

This dataclass encapsulates all the database-specific definitions needed to calculate the CHA2DS2-VASc score, including codelists for diagnoses, filters for demographic characteristics, and domain names for data tables.

Attributes:

Name Type Description
codelist_heart_failure Codelist

Codelist containing codes for congestive heart failure diagnosis (C component, 1 point).
codelist_hypertension Codelist

Codelist containing codes for hypertension diagnosis (H component, 1 point).
codelist_diabetes Codelist

Codelist containing codes for diabetes mellitus diagnosis (D component, 1 point).
codelist_stroke_tia Codelist

Codelist containing codes for prior stroke or transient ischemic attack (S2 component, 2 points).
codelist_vascular_disease Codelist

Codelist containing codes for vascular disease (V component, 1 point). This includes prior myocardial infarction, peripheral artery disease, or aortic plaque.
filter_sex_female CategoricalFilter

CategoricalFilter to identify female patients (Sc component, 1 point). Should filter for the appropriate sex value (e.g., "F", "Female", or database-specific code).
domain_diagnosis str

Name of the domain/table containing diagnosis codes. Defaults to "CONDITION_OCCURRENCE_SOURCE" (OMOP CDM convention).
domain_sex str

Name of the domain/table containing patient demographics including sex. Defaults to "PERSON" (OMOP CDM convention).
Note

Age-based components (A and A2) are calculated automatically from the patient's birth date and do not require codelist configuration.

Component Summary
Type Number
Codelists 5
Categorical Filters 1
Domains 2
Source code in phenex/phenotypes/factory/chadsvasc.py 
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@dataclass
class CHADSVASCComponents:
    """
    Database specific components of CHA2DS2-VASc score calculation.

    This dataclass encapsulates all the database-specific definitions needed to
    calculate the CHA2DS2-VASc score, including codelists for diagnoses, filters
    for demographic characteristics, and domain names for data tables.

    Attributes:
        codelist_heart_failure: Codelist containing codes for congestive heart failure
            diagnosis (C component, 1 point).
        codelist_hypertension: Codelist containing codes for hypertension diagnosis
            (H component, 1 point).
        codelist_diabetes: Codelist containing codes for diabetes mellitus diagnosis
            (D component, 1 point).
        codelist_stroke_tia: Codelist containing codes for prior stroke or transient
            ischemic attack (S2 component, 2 points).
        codelist_vascular_disease: Codelist containing codes for vascular disease
            (V component, 1 point). This includes prior myocardial infarction,
            peripheral artery disease, or aortic plaque.
        filter_sex_female: CategoricalFilter to identify female patients
            (Sc component, 1 point). Should filter for the appropriate sex value
            (e.g., "F", "Female", or database-specific code).
        domain_diagnosis: Name of the domain/table containing diagnosis codes.
            Defaults to "CONDITION_OCCURRENCE_SOURCE" (OMOP CDM convention).
        domain_sex: Name of the domain/table containing patient demographics
            including sex. Defaults to "PERSON" (OMOP CDM convention).

    Note:
        Age-based components (A and A2) are calculated automatically from the
        patient's birth date and do not require codelist configuration.

    Component Summary:
        | Type                | Number |
        |---------------------|--------|
        | Codelists           | 5      |
        | Categorical Filters | 1      |
        | Domains             | 2      |
    """

    codelist_heart_failure: Codelist
    codelist_hypertension: Codelist
    codelist_diabetes: Codelist
    codelist_stroke_tia: Codelist
    codelist_vascular_disease: Codelist
    filter_sex_female: CategoricalFilter

    domain_diagnosis: str = "CONDITION_OCCURRENCE_SOURCE"
    domain_sex: str = "PERSON"

CHADSVASCPhenotype(components, relative_time_range, name='chadsvasc', value_filter=None)

Operational definition for CHADS-VASc as defined in Refining clinical risk stratification for predicting stroke and thromboembolism in atrial fibrillation using a novel risk factor-based approach: the euro heart survey on atrial fibrillation, Lip et. al.

This is a database agnostic implementation. Database specific components are specified by various CHADSVASCComponents.

Parameters:

Name Type Description Default
components CHADSVASCComponents

Database specific definitions of codelists, categorical filters, and domains. See documentation for CHADSVASCComponents for more details.

 required
relative_time_range RelativeTimeRangeFilter

Required specificiation of a relative time range which defines the date at which the score will be calculated (i.e. calculated at the anchor date)

 required
name Optional[str]

Optional override of default name 'chadsvasc'.

 'chadsvasc'
value_filter Optional[ValueFilter]

Optional filtering of persons by the calculated chadsvasc value

 None
Source code in phenex/phenotypes/factory/chadsvasc.py 
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def CHADSVASCPhenotype(
    components: CHADSVASCComponents,
    relative_time_range: RelativeTimeRangeFilter,
    name: Optional[str] = "chadsvasc",
    value_filter: Optional[ValueFilter] = None,
) -> ScorePhenotype:
    """
    Operational definition for CHADS-VASc as defined in [*Refining clinical risk stratification for predicting stroke and thromboembolism in atrial fibrillation using a novel risk factor-based approach: the euro heart survey on atrial fibrillation*,  Lip et. al](https://pubmed.ncbi.nlm.nih.gov/19762550/).

    This is a database agnostic implementation. Database specific components are specified by various CHADSVASCComponents.

    Parameters:
        components: Database specific definitions of codelists, categorical filters, and domains. See documentation for CHADSVASCComponents for more details.
        relative_time_range: Required specificiation of a relative time range which defines the date at which the score will be calculated (i.e. calculated at the anchor date)
        name: Optional override of default name 'chadsvasc'.
        value_filter: Optional filtering of persons by the calculated chadsvasc value
    """

    # --- Create individual components ---
    pt_chf = CodelistPhenotype(
        name=f"{name}_heart_failure",
        domain=components.domain_diagnosis,
        codelist=components.codelist_heart_failure,
        relative_time_range=relative_time_range,
    )
    pt_hypertension = CodelistPhenotype(
        name=f"{name}_hypertension",
        domain=components.domain_diagnosis,
        codelist=components.codelist_hypertension,
        relative_time_range=relative_time_range,
    )
    pt_age_ge_75 = AgePhenotype(
        name=f"{name}_agege75",
        value_filter=ValueFilter(
            min_value=GreaterThanOrEqualTo(75),
        ),
    )
    pt_diabetes = CodelistPhenotype(
        name=f"{name}_diabetes",
        domain=components.domain_diagnosis,
        codelist=components.codelist_diabetes,
        relative_time_range=relative_time_range,
    )
    pt_stroke_tia = CodelistPhenotype(
        name=f"{name}_stroke_tia",
        domain=components.domain_diagnosis,
        codelist=components.codelist_stroke_tia,
        relative_time_range=relative_time_range,
    )
    pt_vascular_disease = CodelistPhenotype(
        name=f"{name}_vascular_disease",
        domain=components.domain_diagnosis,
        codelist=components.codelist_vascular_disease,
        relative_time_range=relative_time_range,
    )
    pt_age_ge65_l75 = AgePhenotype(
        name=f"{name}_age_ge65_l75",
        value_filter=ValueFilter(
            min_value=GreaterThanOrEqualTo(65), max_value=LessThan(75)
        ),
    )
    pt_female = CategoricalPhenotype(
        name=f"{name}_sex_female",
        categorical_filter=components.filter_sex_female,
        domain=components.domain_sex,
    )

    return ScorePhenotype(
        expression=(
            pt_chf  # 1 point
            + pt_hypertension  # 1 point
            + (2 * pt_age_ge_75)  # 2 points
            + pt_diabetes  # 1 point
            + (2 * pt_stroke_tia)  # 2 points
            + pt_vascular_disease  # 1 point
            + pt_age_ge65_l75  # 1 point
            + pt_female  # 1 point
        ),
        name=name,
        value_filter=value_filter,
    )