def test_patients_died_from_any_cause():
session = make_session()
session.add_all(
[
# Not dead
Patient(),
# Died after date cutoff
Patient(ONSDeath=[ONSDeaths(dod="2021-01-01")]),
# Died
Patient(ONSDeath=[ONSDeaths(dod="2020-02-01")]),
]
)
session.commit()
study = StudyDefinition(
population=patients.all(),
died=patients.died_from_any_cause(on_or_before="2020-06-01"),
date_died=patients.died_from_any_cause(
on_or_before="2020-06-01",
returning="date_of_death",
include_month=True,
include_day=True,
),
)
results = study.to_dicts()
assert [i["died"] for i in results] == ["0", "0", "1"]
assert [i["date_died"] for i in results] == ["", "", "2020-02-01"]
def test_make_df_from_binary_default_outcome():
study = StudyDefinition(
population=patients.all(),
died=patients.died_from_any_cause(return_expectations={"incidence": 0.1}),
)
population_size = 10000
result = study.make_df_from_expectations(population_size)
assert len(result[~pd.isnull(result.died)]) == 0.1 * population_size
}},
),
died_ons_covid_flag_underlying=patients.
with_these_codes_on_death_certificate(
covid_codelist,
on_or_after="2020-03-01",
match_only_underlying_cause=True,
return_expectations={"date": {
"earliest": "2020-03-01"
}},
),
died_date_ons=patients.died_from_any_cause(
on_or_after="2020-03-01",
returning="date_of_death",
include_month=True,
include_day=True,
return_expectations={"date": {
"earliest": "2020-03-01"
}},
),
## DEMOGRAPHIC INFORMATION
age=patients.age_as_of(
"2020-02-29",
return_expectations={
"rate": "universal",
"int": {
"distribution": "population_ages"
},
},
),
sex=patients.sex(return_expectations={
),
died_date_cpns=patients.with_death_recorded_in_cpns(
on_or_before="2020-06-01",
returning="date_of_death",
include_month=True,
include_day=True,
),
died_ons_covid_flag_any=patients.with_these_codes_on_death_certificate(
covid_codelist, on_or_before="2020-06-01", match_only_underlying_cause=False
),
died_ons_covid_flag_underlying=patients.with_these_codes_on_death_certificate(
covid_codelist, on_or_before="2020-06-01", match_only_underlying_cause=True
),
died_date_ons=patients.died_from_any_cause(
on_or_before="2020-06-01",
returning="date_of_death",
include_month=True,
include_day=True,
),
# The rest of the lines define the covariates with associated GitHub issues
# https://github.com/ebmdatalab/tpp-sql-notebook/issues/33
age=patients.age_as_of("2020-02-01"),
# https://github.com/ebmdatalab/tpp-sql-notebook/issues/46
sex=patients.sex(),
# https://github.com/ebmdatalab/tpp-sql-notebook/issues/52
imd=patients.address_as_of(
"2020-02-01", returning="index_of_multiple_deprivation", round_to_nearest=100
),