# 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",
