between=[index_date, end_date],
returning="date_of_death",
date_format="YYYY-MM-DD",
return_expectations={
"incidence": 0.2,
},
),
death_category=patients.categorised_as(
{
"covid-death": "died_covid",
"non-covid-death": "(NOT died_covid) AND died_any",
"alive": "DEFAULT"
},
died_covid=patients.with_these_codes_on_death_certificate(
codes_ICD10_covid,
returning="binary_flag",
match_only_underlying_cause=False,
between=[index_date, end_date],
),
died_any=patients.died_from_any_cause(
between=[index_date, end_date],
returning="binary_flag",
),
return_expectations={
"category": {
"ratios": {
"alive": 0.8,
"covid-death": 0.1,
"non-covid-death": 0.1
}
},
"incidence": 1
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
},
),
died_ons_covid_flag_underlying=patients.
with_these_codes_on_death_certificate(
covid_identification,
on_or_after="2020-03-01",
match_only_underlying_cause=True,
return_expectations={
"date": {
"earliest": "2020-03-01"
},
"incidence": 0.1
include_day=True,
return_expectations={
"date": {
"earliest": "2020-02-01"
},
"rate": "exponential_increase"
},
),
# ons
died_ons_covid_flag_any=patients.with_these_codes_on_death_certificate(
covid_codelist,
on_or_after="2020-02-01",
match_only_underlying_cause=False,
return_expectations={
"date": {
"earliest": "2020-02-01"
},
"rate": "exponential_increase"
},
),
died_ons_confirmedcovid_flag_any=patients.
with_these_codes_on_death_certificate(
confirmed_covid_codelist,
on_or_after="2020-02-01",
match_only_underlying_cause=False,
return_expectations={
"date": {
"earliest": "2020-02-01"
},
"rate": "exponential_increase"
**date_X("codes_probable_covid_pos_test", n=n),
**date_X("codes_probable_covid_sequelae", n=n),
**date_X("codes_suspected_covid_advice", n=m),
**date_X("codes_suspected_covid_had_test", n=m),
**date_X("codes_suspected_covid_isolation", n=n),
**date_X("codes_suspected_covid_nonspecific", n=n),
**date_X("codes_suspected_covid", n=m),
**date_X("codes_covid_unrelated_to_case_status", n=m),
**date_X("codes_suspected_covid_had_antigen_test", n=n),
**sgss_X(n=n),
# Outcomes
died_ons_covid=patients.with_these_codes_on_death_certificate(
codes_covid_death,
returning="binary_flag",
on_or_after=from_date,
match_only_underlying_cause=False,
return_expectations={"date": {
"earliest": from_date
}},
),
died_ons_covid_underlying=patients.with_these_codes_on_death_certificate(
codes_covid_death,
returning="binary_flag",
on_or_after=from_date,
match_only_underlying_cause=True,
return_expectations={"date": {
"earliest": "2020-03-01"
}},
),
died_ons=patients.died_from_any_cause(
returning="binary_flag",
),
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},
),
stroke_ons=patients.with_these_codes_on_death_certificate(
stroke_hospital,
between=["index_date", "last_day_of_month(index_date)"],
return_expectations={"incidence": 0.05},
),
),
DVT=patients.satisfying(
"dvt_gp OR dvt_hospital OR dvt_ons",
dvt_gp=patients.with_these_clinical_events(
filter_codes_by_category(vte_codes_gp, include=["dvt"]),
between=["index_date", "last_day_of_month(index_date)"],
return_expectations={"incidence": 0.05},
),
dvt_hospital=patients.admitted_to_hospital(
with_these_diagnoses=filter_codes_by_category(vte_codes_hospital,
include=["dvt"]),
between=["index_date", "last_day_of_month(index_date)"],
return_expectations={"incidence": 0.05},
return_expectations={
"rate": "universal",
"int": {
"distribution": "population_ages"
},
},
),
sex=patients.sex(return_expectations={
"rate": "universal",
"category": {
"ratios": {
"M": 0.49,
"F": 0.51
}
},
}),
cardiac_disease=patients.with_these_clinical_events(
cardiac_disease_codes,
returning="binary_flag",
return_expectations={"incidence": 0.2},
),
# }
# Define output variable
covid_on_death_certificate=patients.with_these_codes_on_death_certificate(
covid_codes,
match_only_underlying_cause=False,
return_expectations={"incidence": 0.001},
),
)
