return_expectations={
"date": {
"earliest": "2020-02-01"
},
"rate": "exponential_increase"
},
),
#SUS HOSPITAL ADMISSION
covid_admission_date=patients.admitted_to_hospital(
returning="date_admitted", # defaults to "binary_flag"
with_these_diagnoses=covid_codelist, # optional
on_or_after="2020-02-01",
find_first_match_in_period=True,
date_format="YYYY-MM-DD",
return_expectations={
"date": {
"earliest": "2020-02-01"
},
"incidence": 0.25
},
),
covid_admission_primary_diagnosis=patients.admitted_to_hospital(
returning="primary_diagnosis",
with_these_diagnoses=covid_codelist, # optional
on_or_after="2020-02-01",
find_first_match_in_period=True,
date_format="YYYY-MM-DD",
return_expectations={
"date": {
"earliest": "2020-02-01"
"General population": 0.8,
}
},
},
covid_positive=patients.with_test_result_in_sgss(
pathogen="SARS-CoV-2",
test_result="positive",
between=["2020-01-01", "last_day_of_month(index_date)"],
date_format="YYYY-MM-DD",
return_expectations={"date": {
"earliest": "index_date"
}},
),
covid_hospitalised=patients.admitted_to_hospital(
with_these_diagnoses=covid_codelist,
between=["2020-01-01", "last_day_of_month(index_date)"],
return_expectations={"incidence": 0.20},
),
),
stroke=patients.satisfying(
"stroke_gp OR stroke_hospital OR stroke_ons",
stroke_gp=patients.with_these_clinical_events(
stroke,
between=["index_date", "last_day_of_month(index_date)"],
return_expectations={"incidence": 0.05},
),
stroke_hospital=patients.admitted_to_hospital(
with_these_diagnoses=stroke_hospital,
between=["index_date", "last_day_of_month(index_date)"],
return_expectations={"incidence": 0.05},
),
"85-89": 0.05,
"90plus": 0.03,
"missing": 0.02,
}
},
},
age=patients.age_as_of("index_date", ),
),
# patients admitted to hospital with primary diagnoses included in cvd codelist
# filters out maternity-related admissions and transfers from other providers
cvd_emergency_elective=patients.admitted_to_hospital(
with_these_primary_diagnoses=cvd_codelist,
with_admission_method=[
"11", "12", "13", "21", "22", "23", "24", "25", "2A", "2B", "2C",
"2D", "28"
],
between=["index_date", "index_date + 6 days"],
return_expectations={"incidence": 0.1},
),
cvd_admission_method=patients.admitted_to_hospital(
with_these_primary_diagnoses=cvd_codelist,
with_admission_method=[
"11", "12", "13", "21", "22", "23", "24", "25", "2A", "2B", "2C",
"2D", "28"
],
between=["index_date", "index_date + 6 days"],
returning="admission_method",
return_expectations={
"incidence": 0.1,
"category": {
"1": 0.4,
"9": 0.1,
"": 0.1
}
},
},
),
# SUS HOSPITAL ADMISSION
covid_admission_date=patients.admitted_to_hospital(
returning="date_admitted",
with_these_diagnoses=covid_codelist,
on_or_after="sgss_pos_inrange",
find_first_match_in_period=True,
date_format="YYYY-MM-DD",
return_expectations={
"date": {
"earliest": "2020-11-16"
},
"incidence": 0.3
},
),
covid_discharge_date=patients.admitted_to_hospital(
returning="date_discharged",
with_these_diagnoses=covid_codelist,
on_or_after="sgss_pos_inrange",
find_first_match_in_period=True,
date_format="YYYY-MM-DD",
return_expectations={
"date": {
"earliest": "2020-11-16"