# This line defines the study population population=patients.satisfying( """ has_follow_up AND (age >=18 AND age <= 110) AND (sex = "M" OR sex = "F") """, has_follow_up=patients.registered_with_one_practice_between( "2019-02-28", "2020-02-29")), # Outcomes icu_date_admitted=patients.admitted_to_icu( on_or_after="2020-03-01", include_day=True, returning="date_admitted", find_first_match_in_period=True, return_expectations={ "date": { "earliest": "2020-03-01" }, "incidence": 0.1 }, ), died_ons_covid_flag_any=patients.with_these_codes_on_death_certificate( covid_identification, on_or_after="2020-03-01", match_only_underlying_cause=False, return_expectations={ "date": { "earliest": "2020-03-01" }, "incidence": 0.1 },
find_first_match_in_period=True, return_expectations={ "date": { "earliest": "2020-02-01" }, "rate": "exponential_increase" }, ), # ICU attendance and ventilation any_resp_support_flag=patients.admitted_to_icu( on_or_after="2020-02-01", find_first_match_in_period=True, returning="had_respiratory_support", return_expectations={ "date": { "earliest": "2020-02-01" }, "rate": "exponential_increase" }, ), basic_resp_support_flag=patients.admitted_to_icu( on_or_after="2020-02-01", find_first_match_in_period=True, returning="had_basic_respiratory_support", return_expectations={ "date": { "earliest": "2020-02-01" }, "rate": "exponential_increase" },
"ratios": { "10": 0.5, "20": 0.5 } }, "incidence": 0.4, }, ), # ICU ADMISSION icu_admission_date=patients.admitted_to_icu( on_or_after="sgss_pos_inrange", find_first_match_in_period=True, returning="date_admitted", date_format="YYYY-MM-DD", return_expectations={ "date": { "earliest": "2020-11-16" }, "incidence": 0.2 }, ), ### DEMOGRAPHIC COVARIATES # AGE age=patients.age_as_of( "sgss_pos_inrange", return_expectations={ "rate": "universal", "int": { "distribution": "population_ages" },
saba_single OR ics_single OR low_med_dose_ics OR low_med_dose_ics_multiple_ingredient OR low_med_dose_ics_single_ingredient OR high_dose_ics_multiple_ingredient OR high_dose_ics_single_ing OR high_dose_ics """), ), ## OUTCOMES (at least one outcome or covariate is required) icu_date_admitted=patients.admitted_to_icu( on_or_after="2020-03-01", include_day=True, returning="date_admitted", return_expectations={"date": { "earliest": "2020-03-01" }}, ), died_date_cpns=patients.with_death_recorded_in_cpns( on_or_after="2020-03-01", returning="date_of_death", include_month=True, include_day=True, return_expectations={"date": { "earliest": "2020-03-01" }}, ), died_ons_covid_flag_any=patients.with_these_codes_on_death_certificate( covid_codelist, on_or_after="2020-03-01",
returning="date_arrived", date_format="YYYY-MM-DD", find_first_match_in_period=True, return_expectations={ "date": { "earliest": "2020-02-01" }, "rate": "exponential_increase", }, ), icu_date_admitted=patients.admitted_to_icu( on_or_after="2020-02-01", include_day=True, returning="date_admitted", find_first_match_in_period=True, return_expectations={ "date": { "earliest": "2020-02-01" }, "rate": "exponential_increase", }, ), died_date_cpns=patients.with_death_recorded_in_cpns( on_or_after="2020-02-01", returning="date_of_death", include_month=True, include_day=True, return_expectations={ "date": { "earliest": "2020-02-01" }, "rate": "exponential_increase",