common_variables.py

from cohortextractor import filter_codes_by_category, patients, combine_codelists
from codelists import *
from datetime import datetime, timedelta


def generate_common_variables(index_date_variable, admission_variable):
    common_variables = dict(
        deregistered=patients.date_deregistered_from_all_supported_practices(
            date_format="YYYY-MM-DD"
        ),
        # Outcomes
        # Recent history of outcomes
        recent_dvt=patients.satisfying(
            "recent_dvt_gp OR recent_dvt_hospital",
            recent_dvt_gp=patients.with_these_clinical_events(
                filter_codes_by_category(vte_codes_gp, include=["dvt"]),
                between=[f"{index_date_variable} - 3 months", f"{index_date_variable}"],
            ),
            recent_dvt_hospital=patients.admitted_to_hospital(
                with_these_diagnoses=filter_codes_by_category(
                    vte_codes_hospital, include=["dvt"]
                ),
                between=[f"{index_date_variable} - 3 months", f"{index_date_variable}"],
            ),
        ),
        recent_pe=patients.satisfying(
            "recent_pe_gp OR recent_pe_hospital",
            recent_pe_gp=patients.with_these_clinical_events(
                filter_codes_by_category(vte_codes_gp, include=["pe"]),
                between=[f"{index_date_variable} - 3 months", f"{index_date_variable}"],
            ),
            recent_pe_hospital=patients.admitted_to_hospital(
                with_these_diagnoses=filter_codes_by_category(
                    vte_codes_hospital, include=["pe"]
                ),
                between=[f"{index_date_variable} - 3 months", f"{index_date_variable}"],
            ),
        ),
        recent_stroke=patients.satisfying(
            "recent_stroke_gp OR recent_stroke_hospital",
            recent_stroke_gp=patients.with_these_clinical_events(
                stroke,
                between=[f"{index_date_variable} - 3 months", f"{index_date_variable}"],
                return_expectations={"incidence": 0.05},
            ),
            recent_stroke_hospital=patients.admitted_to_hospital(
                with_these_diagnoses=stroke_hospital,
                between=[f"{index_date_variable} - 3 months", f"{index_date_variable}"],
            ),
        ),
        recent_mi=patients.satisfying(
            "recent_mi_gp OR recent_mi_hospital",
            recent_mi_gp=patients.with_these_clinical_events(
                mi_codes,
                between=[f"{index_date_variable} - 3 months", f"{index_date_variable}"],
                return_expectations={"incidence": 0.05},
            ),
            recent_mi_hospital=patients.admitted_to_hospital(
                with_these_diagnoses=filter_codes_by_category(
                    mi_codes_hospital, include=["1"]
                ),
                between=[f"{index_date_variable} - 3 months", f"{index_date_variable}"],
            ),
        ),
        recent_aki=patients.satisfying(
            "recent_aki_gp OR recent_aki_hospital",
            recent_aki_gp=patients.with_these_clinical_events(
                aki_gp,
                between=[f"{index_date_variable} - 3 months", f"{index_date_variable}"],
                return_expectations={"incidence": 0.05},
            ),
            recent_aki_hospital=patients.admitted_to_hospital(
                with_these_diagnoses=aki_codes,
                between=[f"{index_date_variable} - 3 months", f"{index_date_variable}"],
            ),
        ),
        recent_heart_failure=patients.satisfying(
            "recent_heart_failure_gp OR recent_heart_failure_hospital",
            recent_heart_failure_gp=patients.with_these_clinical_events(
                heart_failure_codes,
                between=[f"{index_date_variable} - 3 months", f"{index_date_variable}"],
                return_expectations={"incidence": 0.05},
            ),
            recent_heart_failure_hospital=patients.admitted_to_hospital(
                with_these_diagnoses=filter_codes_by_category(
                    heart_failure_codes_hospital, include=["1"]
                ),
                between=[f"{index_date_variable} - 3 months", f"{index_date_variable}"],
            ),
        ),
        previous_diabetes=patients.with_these_clinical_events(
            combine_codelists(
                diabetes_t1_codes, diabetes_t2_codes, diabetes_unknown_codes
            ),
            on_or_before=f"{index_date_variable}",
            return_expectations={"incidence": 0.05},
        ),
        # History of outcomes
        hist_dvt=patients.satisfying(
            "hist_dvt_gp OR hist_dvt_hospital",
            hist_dvt_gp=patients.with_these_clinical_events(
                filter_codes_by_category(vte_codes_gp, include=["dvt"]),
                on_or_before=f"{index_date_variable} - 1 days",
            ),
            hist_dvt_hospital=patients.admitted_to_hospital(
                with_these_diagnoses=filter_codes_by_category(
                    vte_codes_hospital, include=["dvt"]
                ),
                on_or_before=f"{index_date_variable} - 1 days",
            ),
        ),
         hist_pe=patients.satisfying(
            "hist_pe_gp OR hist_pe_hospital",
           hist_pe_gp=patients.with_these_clinical_events(
                filter_codes_by_category(vte_codes_gp, include=["pe"]),
                on_or_before=f"{index_date_variable} - 1 days",
            ),
            hist_pe_hospital=patients.admitted_to_hospital(
                with_these_diagnoses=filter_codes_by_category(
                    vte_codes_hospital, include=["pe"]
                ),
                on_or_before=f"{index_date_variable} - 1 days",
            ),
        ),
         hist_stroke=patients.satisfying(
            "hist_stroke_gp OR hist_stroke_hospital",
            hist_stroke_gp=patients.with_these_clinical_events(
                stroke,
                on_or_before=f"{index_date_variable} - 1 days",
                return_expectations={"incidence": 0.05},
            ),
            hist_stroke_hospital=patients.admitted_to_hospital(
                with_these_diagnoses=stroke_hospital,
                on_or_before=f"{index_date_variable} - 1 days",
            ),
        ),
         hist_mi=patients.satisfying(
            "hist_mi_gp OR hist_mi_hospital",
            hist_mi_gp=patients.with_these_clinical_events(
                mi_codes,
               on_or_before=f"{index_date_variable} - 1 days",
            ),
            hist_mi_hospital=patients.admitted_to_hospital(
                with_these_diagnoses=filter_codes_by_category(
                    mi_codes_hospital, include=["1"]
                ),
               on_or_before=f"{index_date_variable} - 1 days",
            ),
        ),
         hist_aki=patients.satisfying(
            "hist_aki_gp OR hist_aki_hospital",
            hist_aki_gp=patients.with_these_clinical_events(
                aki_gp,
                on_or_before=f"{index_date_variable} - 1 days",
                return_expectations={"incidence": 0.05},
            ),
            hist_aki_hospital=patients.admitted_to_hospital(
                with_these_diagnoses=aki_codes,
                on_or_before=f"{index_date_variable} - 1 days",
            ),
        ),
         hist_heart_failure=patients.satisfying(
            "hist_heart_failure_gp OR hist_heart_failure_hospital",
            hist_heart_failure_gp=patients.with_these_clinical_events(
                heart_failure_codes,
                on_or_before=f"{index_date_variable} - 1 days",
                return_expectations={"incidence": 0.05},
            ),
            hist_heart_failure_hospital=patients.admitted_to_hospital(
                with_these_diagnoses=filter_codes_by_category(
                    heart_failure_codes_hospital, include=["1"]
                ),
                on_or_before=f"{index_date_variable} - 1 days",
            ),
        ),
        ## DVT
        dvt_gp=patients.with_these_clinical_events(
            filter_codes_by_category(vte_codes_gp, include=["dvt"]),
            return_first_date_in_period=True,
            date_format="YYYY-MM-DD",
            on_or_after=f"{index_date_variable} + 1 days",
            return_expectations={"date": {"earliest": "index_date"}},
        ),
        dvt_hospital=patients.admitted_to_hospital(
            returning="date_admitted",
            with_these_diagnoses=filter_codes_by_category(
                vte_codes_hospital, include=["dvt"]
            ),
            on_or_after=f"{index_date_variable} + 1 days",
            date_format="YYYY-MM-DD",
            find_first_match_in_period=True,
            return_expectations={"date": {"earliest": "index_date"}},
        ),
        dvt_in_hospital=patients.admitted_to_hospital(
            with_these_diagnoses=filter_codes_by_category(
                vte_codes_hospital, include=["dvt"]
            ),
            between=[f"{admission_variable}", f"{index_date_variable}"],
            return_expectations={"incidence": 0.1},
        ),
        dvt_ons=patients.with_these_codes_on_death_certificate(
            filter_codes_by_category(vte_codes_hospital, include=["dvt"]),
            returning="date_of_death",
            date_format="YYYY-MM-DD",
            match_only_underlying_cause=False,
            on_or_after=f"{index_date_variable} + 1 days",
            return_expectations={"date": {"earliest": "index_date"}},
        ),
        dvt=patients.satisfying("dvt_gp OR dvt_hospital OR dvt_ons"),
        dvt_no_gp=patients.satisfying("dvt_hospital OR dvt_ons"),
        dvt_cens_gp=patients.satisfying(
            "(dvt_gp AND NOT recent_dvt) OR dvt_hospital OR dvt_ons"
        ),
        # dvt_date=patients.minimum_of("dvt_gp", "dvt_hospital", "dvt_ons"),
        # PE
        pe_gp=patients.with_these_clinical_events(
            filter_codes_by_category(vte_codes_gp, include=["pe"]),
            return_first_date_in_period=True,
            date_format="YYYY-MM-DD",
            on_or_after=f"{index_date_variable} + 1 days",
            return_expectations={"date": {"earliest": "index_date"}},
        ),
        pe_hospital=patients.admitted_to_hospital(
            returning="date_admitted",
            with_these_diagnoses=filter_codes_by_category(
                vte_codes_hospital, include=["pe"]
            ),
            on_or_after=f"{index_date_variable} + 1 days",
            date_format="YYYY-MM-DD",
            find_first_match_in_period=True,
            return_expectations={"date": {"earliest": "index_date"}},
        ),
        pe_in_hospital=patients.admitted_to_hospital(
            with_these_diagnoses=filter_codes_by_category(
                vte_codes_hospital, include=["pe"]
            ),
            between=[f"{admission_variable}", f"{index_date_variable}"],
            return_expectations={"incidence": 0.1},
        ),
        pe_ons=patients.with_these_codes_on_death_certificate(
            filter_codes_by_category(vte_codes_hospital, include=["pe"]),
            returning="date_of_death",
            date_format="YYYY-MM-DD",
            match_only_underlying_cause=False,
            on_or_after=f"{index_date_variable} + 1 days",
            return_expectations={"date": {"earliest": "index_date"}},
        ),
        pe=patients.satisfying("pe_gp OR pe_hospital OR pe_ons"),
        pe_no_gp=patients.satisfying("pe_hospital OR pe_ons"),
        pe_cens_gp=patients.satisfying(
            "(pe_gp AND NOT recent_pe) OR pe_hospital OR pe_ons"
        ),
        # pe_date=patients.minimum_of("pe_gp", "pe_hospital", "pe_ons"),
        ## Stroke
        stroke_gp=patients.with_these_clinical_events(
            stroke,
            return_first_date_in_period=True,
            date_format="YYYY-MM-DD",
            on_or_after=f"{index_date_variable} + 1 days",
            return_expectations={"date": {"earliest": "index_date"}},
        ),
        stroke_hospital=patients.admitted_to_hospital(
            returning="date_admitted",
            with_these_diagnoses=stroke_hospital,
            on_or_after=f"{index_date_variable} + 1 days",
            date_format="YYYY-MM-DD",
            find_first_match_in_period=True,
            return_expectations={"date": {"earliest": "index_date"}},
        ),
        stroke_in_hospital=patients.admitted_to_hospital(
            with_these_diagnoses=stroke_hospital,
            between=[f"{admission_variable}", f"{index_date_variable}"],
            return_expectations={"incidence": 0.1},
        ),
        stroke_ons=patients.with_these_codes_on_death_certificate(
            stroke_hospital,
            returning="date_of_death",
            date_format="YYYY-MM-DD",
            match_only_underlying_cause=False,
            on_or_after=f"{index_date_variable} + 1 days",
            return_expectations={"date": {"earliest": "index_date"}},
        ),
        stroke=patients.satisfying("stroke_gp OR stroke_hospital OR stroke_ons"),
        stroke_no_gp=patients.satisfying("stroke_hospital OR stroke_ons"),
        stroke_cens_gp=patients.satisfying(
            "(stroke_gp AND NOT recent_stroke) OR stroke_hospital OR stroke_ons"
        ),
        # stroke_date=patients.minimum_of("stroke_gp", "stroke_hospital", "stroke_ons"),
        # Acute kidney injury
        aki_gp=patients.with_these_clinical_events(
            aki_gp,
            return_first_date_in_period=True,
            date_format="YYYY-MM-DD",
            on_or_after=f"{index_date_variable} + 1 days",
            return_expectations={"date": {"earliest": "index_date"}},
        ),
        aki_hospital=patients.admitted_to_hospital(
            returning="date_admitted",
            with_these_diagnoses=aki_codes,
            on_or_after=f"{index_date_variable} + 1 days",
            date_format="YYYY-MM-DD",
            find_first_match_in_period=True,
            return_expectations={"date": {"earliest": "index_date"}},
        ),
        aki_in_hospital=patients.admitted_to_hospital(
            with_these_diagnoses=aki_codes,
            between=[f"{admission_variable}", f"{index_date_variable}"],
            return_expectations={"incidence": 0.1},
        ),
        aki_ons=patients.with_these_codes_on_death_certificate(
            aki_codes,
            returning="date_of_death",
            date_format="YYYY-MM-DD",
            match_only_underlying_cause=False,
            on_or_after=f"{index_date_variable} + 1 days",
            return_expectations={"date": {"earliest": "index_date"}},
        ),
        aki=patients.satisfying("aki_hospital OR aki_ons OR aki_gp"),
        aki_no_gp=patients.satisfying("aki_hospital OR aki_ons"),
        aki_cens_gp=patients.satisfying(
            "(aki_gp AND NOT recent_aki) OR aki_hospital OR aki_ons"
        ),
        # MI
        mi_gp=patients.with_these_clinical_events(
            mi_codes,
            return_first_date_in_period=True,
            date_format="YYYY-MM-DD",
            on_or_after=f"{index_date_variable} + 1 days",
            return_expectations={"date": {"earliest": "index_date"}},
        ),
        mi_hospital=patients.admitted_to_hospital(
            returning="date_admitted",
            with_these_diagnoses=filter_codes_by_category(
                mi_codes_hospital, include=["1"]
            ),
            on_or_after=f"{index_date_variable} + 1 days",
            date_format="YYYY-MM-DD",
            find_first_match_in_period=True,
            return_expectations={"date": {"earliest": "index_date"}},
        ),
        mi_in_hospital=patients.admitted_to_hospital(
            with_these_diagnoses=filter_codes_by_category(
                mi_codes_hospital, include=["1"]
            ),
            between=[f"{admission_variable}", f"{index_date_variable}"],
            return_expectations={"incidence": 0.1},
        ),
        mi_ons=patients.with_these_codes_on_death_certificate(
            filter_codes_by_category(mi_codes_hospital, include=["1"]),
            returning="date_of_death",
            date_format="YYYY-MM-DD",
            match_only_underlying_cause=False,
            on_or_after=f"{index_date_variable} + 1 days",
            return_expectations={"date": {"earliest": "index_date"}},
        ),
        mi=patients.satisfying("mi_gp OR mi_hospital OR mi_ons"),
        mi_no_gp=patients.satisfying("mi_hospital OR mi_ons"),
        mi_cens_gp=patients.satisfying(
            "(mi_gp AND NOT recent_mi) OR mi_hospital OR mi_ons"
        ),
        # Heart failure
        heart_failure_gp=patients.with_these_clinical_events(
            heart_failure_codes,
            return_first_date_in_period=True,
            date_format="YYYY-MM-DD",
            on_or_after=f"{index_date_variable} + 1 days",
            return_expectations={"date": {"earliest": "index_date"}},
        ),
        heart_failure_hospital=patients.admitted_to_hospital(
            returning="date_admitted",
            with_these_diagnoses=filter_codes_by_category(
                heart_failure_codes_hospital, include=["1"]
            ),
            on_or_after=f"{index_date_variable} + 1 days",
            date_format="YYYY-MM-DD",
            find_first_match_in_period=True,
            return_expectations={"date": {"earliest": "index_date"}},
        ),
        heart_failure_in_hospital=patients.admitted_to_hospital(
            with_these_diagnoses=filter_codes_by_category(
                heart_failure_codes_hospital, include=["1"]
            ),
            between=[f"{admission_variable}", f"{index_date_variable}"],
            return_expectations={"incidence": 0.1},
        ),
        heart_failure_ons=patients.with_these_codes_on_death_certificate(
            filter_codes_by_category(heart_failure_codes_hospital, include=["1"]),
            returning="date_of_death",
            date_format="YYYY-MM-DD",
            match_only_underlying_cause=False,
            on_or_after=f"{index_date_variable} + 1 days",
            return_expectations={"date": {"earliest": "index_date"}},
        ),
        heart_failure=patients.satisfying(
            "heart_failure_gp OR heart_failure_hospital OR heart_failure_ons"
        ),
        heart_failure_no_gp=patients.satisfying(
            "heart_failure_hospital OR heart_failure_ons"
        ),
        heart_failure_cens_gp=patients.satisfying(
            """
              (heart_failure_gp AND NOT recent_heart_failure)
            OR heart_failure_hospital OR heart_failure_ons
            """
        ),
        # Diabetes
        t1dm_gp=patients.with_these_clinical_events(
            diabetes_t1_codes,
            on_or_after=f"{index_date_variable} + 1 days",
            return_first_date_in_period=True,
            date_format="YYYY-MM-DD",
            return_expectations={"date": {"earliest": "index_date"}},
        ),
        t2dm_gp=patients.with_these_clinical_events(
            diabetes_t2_codes,
            on_or_after=f"{index_date_variable} + 1 days",
            return_first_date_in_period=True,
            date_format="YYYY-MM-DD",
            return_expectations={"date": {"earliest": "index_date"}},
        ),
        unknown_diabetes_gp=patients.with_these_clinical_events(
            diabetes_unknown_codes,
            on_or_after=f"{index_date_variable} + 1 days",
            return_first_date_in_period=True,
            date_format="YYYY-MM-DD",
            return_expectations={"date": {"earliest": "index_date"}},
        ),
        t1dm_hospital=patients.admitted_to_hospital(
            returning="date_admitted",
            with_these_diagnoses=diabetes_t1_codes_hospital,
            on_or_after=f"{index_date_variable} + 1 days",
            date_format="YYYY-MM-DD",
            find_first_match_in_period=True,
            return_expectations={"date": {"earliest": "index_date"}},
        ),
        t2dm_hospital=patients.admitted_to_hospital(
            returning="date_admitted",
            with_these_diagnoses=diabetes_t2_codes_hospital,
            on_or_after=f"{index_date_variable} + 1 days",
            date_format="YYYY-MM-DD",
            find_first_match_in_period=True,
            return_expectations={"date": {"earliest": "index_date"}},
        ),
        t2dm_in_hospital=patients.admitted_to_hospital(
            with_these_diagnoses=diabetes_t2_codes_hospital,
            between=[f"{admission_variable}", f"{index_date_variable}"],
            return_expectations={"incidence": 0.1},
        ),
        t1dm_ons=patients.with_these_codes_on_death_certificate(
            diabetes_t1_codes_hospital,
            returning="date_of_death",
            date_format="YYYY-MM-DD",
            match_only_underlying_cause=False,
            on_or_after=f"{index_date_variable} + 1 days",
            return_expectations={"date": {"earliest": "index_date"}},
        ),
        t2dm_ons=patients.with_these_codes_on_death_certificate(
            diabetes_t2_codes_hospital,
            returning="date_of_death",
            date_format="YYYY-MM-DD",
            match_only_underlying_cause=False,
            on_or_after=f"{index_date_variable} + 1 days",
            return_expectations={"date": {"earliest": "index_date"}},
        ),
        oad_lastyear_meds=patients.with_these_medications(
            oad_med_codes,
            between=[
                f"{index_date_variable} - 1 year",
                f"{index_date_variable} + 1 days",
            ],
            return_expectations={"incidence": 0.05},
        ),
        insulin_lastyear_meds=patients.with_these_medications(
            insulin_med_codes,
            between=[
                f"{index_date_variable} - 1 year",
                f"{index_date_variable} + 1 days",
            ],
            return_expectations={"incidence": 0.05},
        ),
        type1_agg=patients.satisfying("t1dm_gp OR t1dm_hospital OR t1dm_ons"),
        type2_agg=patients.satisfying("t2dm_gp OR t2dm_hospital OR t2dm_ons"),
        t1dm=patients.satisfying(
            """
                (type1_agg AND NOT
                type2_agg)
            OR
                (((type1_agg AND type2_agg) OR
                (type1_agg AND unknown_diabetes_gp AND NOT type2_agg) OR
                (unknown_diabetes_gp AND NOT type1_agg AND NOT type2_agg))
                AND
                (insulin_lastyear_meds AND NOT
                oad_lastyear_meds))
            """,
            return_expectations={"incidence": 0.05},
        ),
        t2dm=patients.satisfying(
            """
                (type2_agg AND NOT
                type1_agg)
            OR
                (((type1_agg AND type2_agg) OR
                (type2_agg AND unknown_diabetes_gp AND NOT type1_agg) OR
                (unknown_diabetes_gp AND NOT type1_agg AND NOT type2_agg))
                AND
                (oad_lastyear_meds))
            """,
            return_expectations={"incidence": 0.05},
        ),
        died_date_ons=patients.died_from_any_cause(
            returning="date_of_death",
            date_format="YYYY-MM-DD",
            return_expectations={
                "date": {"earliest": "index_date"},
                "incidence": 0.1,
            },
        ),
        age=patients.age_as_of(
            f"{index_date_variable}",
            return_expectations={
                "rate": "universal",
                "int": {"distribution": "population_ages"},
            },
        ),
        sex=patients.sex(
            return_expectations={
                "rate": "universal",
                "category": {"ratios": {"M": 0.49, "F": 0.51}},
            }
        ),
        ethnicity=patients.with_these_clinical_events(
            ethnicity_codes,
            returning="category",
            find_last_match_in_period=True,
            on_or_before=f"{index_date_variable}",
            return_expectations={
                "category": {"ratios": {"1": 0.8, "5": 0.1, "3": 0.1}},
                "incidence": 0.75,
            },
        ),
        practice_id=patients.registered_practice_as_of(
            "index_date",
            returning="pseudo_id",
            return_expectations={
                "int": {"distribution": "normal", "mean": 1000, "stddev": 100},
                "incidence": 1,
            },
        ),
        bmi=patients.most_recent_bmi(
            on_or_before=f"{index_date_variable} - 1 day",
            minimum_age_at_measurement=16,
            include_measurement_date=True,
            include_month=True,
            return_expectations={
            "incidence": 0.98,
            "float": {"distribution": "normal", "mean": 35, "stddev": 10},
        },
        ),
        smoking_status=patients.categorised_as(
         {
            "S": "most_recent_smoking_code = 'S'",
            "E": """
                 most_recent_smoking_code = 'E' OR (
                   most_recent_smoking_code = 'N' AND ever_smoked
                 )
            """,
            "N": "most_recent_smoking_code = 'N' AND NOT ever_smoked",
            "M": "DEFAULT",
         },
         return_expectations={
             "category": {"ratios": {"S": 0.6, "E": 0.1, "N": 0.2, "M": 0.1}}
         },
         most_recent_smoking_code=patients.with_these_clinical_events(
             clear_smoking_codes,
             find_last_match_in_period=True,
             on_or_before=f"{index_date_variable} - 1 day",
             returning="category",
         ),
         ever_smoked=patients.with_these_clinical_events(
             filter_codes_by_category(clear_smoking_codes, include=["S", "E"]),
             on_or_before=f"{index_date_variable} - 1 day",
         ),
     ),
    
        stp=patients.registered_practice_as_of(
            "index_date",
            returning="stp_code",
            return_expectations={
                "rate": "universal",
                "category": {
                    "ratios": {
                        "STP1": 0.1,
                        "STP2": 0.1,
                        "STP3": 0.1,
                        "STP4": 0.1,
                        "STP5": 0.1,
                        "STP6": 0.1,
                        "STP7": 0.1,
                        "STP8": 0.1,
                        "STP9": 0.1,
                        "STP10": 0.1,
                    }
                },
            },
        ),
        region=patients.registered_practice_as_of(
            "index_date",
            returning="nuts1_region_name",
            return_expectations={
                "rate": "universal",
                "category": {
                    "ratios": {
                        "North East": 0.1,
                        "North West": 0.1,
                        "Yorkshire and The Humber": 0.1,
                        "East Midlands": 0.1,
                        "West Midlands": 0.1,
                        "East": 0.1,
                        "London": 0.2,
                        "South East": 0.1,
                        "South West": 0.1,
                    },
                },
            },
        ),
        imd=patients.address_as_of(
            "index_date",
            returning="index_of_multiple_deprivation",
            round_to_nearest=100,
            return_expectations={
                "rate": "universal",
                "category": {
                    "ratios": {
                        "100": 0.1,
                        "200": 0.1,
                        "300": 0.1,
                        "400": 0.1,
                        "500": 0.1,
                        "600": 0.1,
                        "700": 0.1,
                        "800": 0.1,
                        "900": 0.1,
                        "1000": 0.1,
                    }
                },
            },
        ),

            # diabetes
    
    diabetes=patients.with_these_clinical_events(
        diabetes_codes,
        on_or_before=f"{index_date_variable} - 1 day",
        return_expectations={"incidence": 0.05},
    ),
    
    hba1c_percentage=patients.with_these_clinical_events(
        hba1c_old_codes,
        find_last_match_in_period=True,
        between=[f"{index_date_variable}  - 2 years", f"{index_date_variable}  - 1 day"],
        returning="numeric_value",
        include_date_of_match=True,
        include_month=True,
        return_expectations={
            "float": {"distribution": "normal", "mean": 5, "stddev": 2},
            "incidence": 0.98,
        },
    ),
    
    hba1c_mmol_per_mol=patients.with_these_clinical_events(
        hba1c_new_codes,
        find_last_match_in_period=True,
        between=[f"{index_date_variable}  - 2 years", f"{index_date_variable} - 1 day"],
        returning="numeric_value",
        include_date_of_match=True,
        include_month=True,
        return_expectations={
            "float": {"distribution": "normal", "mean": 40.0, "stddev": 20},
            "incidence": 0.98,
        },
    ),
    
        chronic_cardiac_disease=patients.with_these_clinical_events(
        chronic_cardiac_disease_codes,
        on_or_before=f"{index_date_variable}  - 1 day",
        return_expectations={"incidence": 0.05},
    ),
    

        af=patients.with_these_clinical_events(
            af_codes,
            on_or_before=f"{index_date_variable}",
            return_expectations={"incidence": 0.05},
        ),
        anticoag_rx=patients.with_these_medications(
            combine_codelists(doac_codes, warfarin_codes),
            between=[f"{index_date_variable} - 3 months", f"{index_date_variable}"],
            return_expectations={
                "date": {
                    "earliest": "index_date - 3 months",
                    "latest": "index_date",
                }
            },
        ),
        creatinine=patients.with_these_clinical_events(
            creatinine_codes,
            find_last_match_in_period=True,
            on_or_before=f"{index_date_variable} - 1 day",
            returning="numeric_value",
            include_date_of_match=True,
            include_month=True,
            return_expectations={
                "float": {"distribution": "normal", "mean": 60.0, "stddev": 15},
                "date": {"earliest": "2019-02-28", "latest": "2020-02-29"},
                "incidence": 0.95,
            },
        ),

    hypertension=patients.with_these_clinical_events(
        hypertension_codes,
        on_or_before=f"{index_date_variable} - 1 day",
        return_expectations={"incidence": 0.05},
    ),
    bp_sys=patients.mean_recorded_value(
        systolic_blood_pressure_codes,
        on_most_recent_day_of_measurement=True,
        on_or_before=f"{index_date_variable}- 1 day",
        include_measurement_date=True,
        include_month=True,
        return_expectations={
            "float": {"distribution": "normal", "mean": 80, "stddev": 10},
            "date": {"latest": "2020-02-29"},
            "incidence": 0.95,
        },
    ),
    
    bp_dias=patients.mean_recorded_value(
        diastolic_blood_pressure_codes,
        on_most_recent_day_of_measurement=True,
        on_or_before=f"{index_date_variable} - 1 day",
        return_expectations={
            "float": {"distribution": "normal", "mean": 120, "stddev": 10},
            "date": {"latest": "2020-02-29"},
            "incidence": 0.95,
        },
    ),
    
        dialysis=patients.with_these_clinical_events(
            dialysis_codes,
            on_or_before=f"{index_date_variable}",
            return_first_date_in_period=True,
            include_month=True,
        ),

        # respiratory
    
       chronic_respiratory_disease=patients.with_these_clinical_events(
            chronic_respiratory_disease_codes,
            on_or_before=f"{index_date_variable} - 1 day",
            return_expectations={"incidence": 0.05},
        ),
    
        asthma=patients.categorised_as(
            {
            "0": "DEFAULT",
            "1": """
            (
              recent_asthma_code OR (
                asthma_code_ever AND NOT
                copd_code_ever
              )
            ) AND (
              prednisolone_last_year = 0 OR 
              prednisolone_last_year > 4
            )
            """,
            "2": """
            (
              recent_asthma_code OR (
                asthma_code_ever AND NOT
                copd_code_ever
              )
            ) AND
            prednisolone_last_year > 0 AND
            prednisolone_last_year < 5
            
            """,
            },
        return_expectations={
            "category": {"ratios": {"0": 0.8, "1": 0.1, "2": 0.1}},
        },
        recent_asthma_code=patients.with_these_clinical_events(
            asthma_codes,
            between=[f"{index_date_variable} - 3 years", f"{index_date_variable} - 1 days"],
        ),
        asthma_code_ever=patients.with_these_clinical_events(asthma_codes),
        copd_code_ever=patients.with_these_clinical_events(
            chronic_respiratory_disease_codes
        ),
        prednisolone_last_year=patients.with_these_medications(
            prednisolone_codes,
            between=[f"{index_date_variable} - 1 years", f"{index_date_variable} - 1 days"],
            returning="number_of_matches_in_period",
        ),
    ),
    
    # cancer
    

    lung_cancer=patients.with_these_clinical_events(
        lung_cancer_codes, return_first_date_in_period=True, include_month=True,
    ),
    haem_cancer=patients.with_these_clinical_events(
        haem_cancer_codes, return_first_date_in_period=True, include_month=True,
    ),
    other_cancer=patients.with_these_clinical_events(
        other_cancer_codes, return_first_date_in_period=True, include_month=True,
    ),
    
    # immuno
    
    organ_transplant=patients.with_these_clinical_events(
        organ_transplant_codes,
        on_or_before=f"{index_date_variable} - 1 day",
        return_expectations={"incidence": 0.05},
    ),
    dysplenia=patients.with_these_clinical_events(
        spleen_codes,
        on_or_before=f"{index_date_variable} - 1 day",
        return_expectations={"incidence": 0.05},
    ),
    sickle_cell=patients.with_these_clinical_events(
        sickle_cell_codes,
        on_or_before=f"{index_date_variable} - 1 day",
        return_expectations={"incidence": 0.05},
    ),
    aplastic_anaemia=patients.with_these_clinical_events(
        aplastic_codes, return_last_date_in_period=True, include_month=True,
    ),
    hiv=patients.with_these_clinical_events(
        hiv_codes,
        on_or_before=f"{index_date_variable} - 1 day",
        return_expectations={"incidence": 0.05},
    ),
    permanent_immunodeficiency=patients.with_these_clinical_events(
        permanent_immune_codes,
        on_or_before=f"{index_date_variable} - 1 day",
        return_expectations={"incidence": 0.05},
    ),
    temporary_immunodeficiency=patients.with_these_clinical_events(
        temp_immune_codes, return_last_date_in_period=True, include_month=True,
    ),
    
    ra_sle_psoriasis=patients.with_these_clinical_events(
        ra_sle_psoriasis_codes,
        on_or_before=f"{index_date_variable} - 1 day",
        return_expectations={"incidence": 0.05},
    ),
    
    
    # neuro
    
    other_neuro=patients.with_these_clinical_events(
        other_neuro_codes,
        on_or_before=f"{index_date_variable} - 1 day",
        return_expectations={"incidence": 0.05},
    ),
    dementia=patients.with_these_clinical_events(
        dementia_codes,
        on_or_before=f"{index_date_variable} - 1 day",
        return_expectations={"incidence": 0.05},
    ),
    
    
    # gastro
    
    chronic_liver_disease=patients.with_these_clinical_events(
        chronic_liver_disease_codes,
        on_or_before=f"{index_date_variable} - 1 day",
        return_expectations={"incidence": 0.05},
    ),

    )
    return common_variables