# STUDY POPULATION
population=patients.registered_with_one_practice_between(
"2019-02-01", "2020-02-01"),
dereg_date=patients.date_deregistered_from_all_supported_practices(
on_or_before="2020-12-01",
date_format="YYYY-MM",
return_expectations={"date": {
"earliest": "2020-02-01"
}},
),
# OUTCOMES,
primary_care_case=patients.with_these_clinical_events(
combine_codelists(
covid_primary_care_code,
covid_primary_care_positive_test,
covid_primary_care_sequalae,
),
returning="date",
find_first_match_in_period=True,
date_format="YYYY-MM-DD",
return_expectations={"rate": "exponential_increase"},
),
primary_care_historic_case=patients.with_these_clinical_events(
combine_codelists(
covid_primary_care_historic_case,
covid_primary_care_potential_historic_case,
),
returning="date",
date_format="YYYY-MM-DD",
find_first_match_in_period=True,
},
"incidence": 0.95,
},
),
# CANCER - 3 TYPES
cancer_haem=patients.with_these_clinical_events(
haem_cancer_codes,
return_first_date_in_period=True,
include_month=True,
return_expectations={"date": {
"latest": "2019-01-31"
}},
),
cancer_nonhaem=patients.with_these_clinical_events(
combine_codelists(lung_cancer_codes, other_cancer_codes),
return_first_date_in_period=True,
include_month=True,
return_expectations={"date": {
"latest": "2019-01-31"
}},
),
#### PERMANENT
permanent_immunodeficiency=patients.with_these_clinical_events(
combine_codelists(hiv_codes, permanent_immune_codes,
sickle_cell_codes),
on_or_before="2019-01-31",
return_last_date_in_period=True,
include_month=True,
return_expectations={"date": {
),
covid_icu_date=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"
},
"incidence": 0.8
},
),
covid_tpp_probable=patients.with_these_clinical_events(
combine_codelists(
covid_identification_in_primary_care_case_codes_clinical,
covid_identification_in_primary_care_case_codes_test,
covid_identification_in_primary_care_case_codes_seq),
return_first_date_in_period=True,
include_day=True,
return_expectations={
"date": {
"earliest": "2020-02-01"
},
"incidence": 0.6
},
),
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,
"latest": "2020-02-29"
}},
),
# CURRENT ASTHMA
asthma=patients.with_these_clinical_events(
current_asthma_codes,
on_or_before="2020-02-29",
return_first_date_in_period=True,
include_month=True,
return_expectations={"date": {
"latest": "2020-02-29"
}},
),
# CANCER - 3 TYPES
cancer=patients.with_these_clinical_events(
combine_codelists(lung_cancer_codes, haem_cancer_codes,
other_cancer_codes),
on_or_before="2020-02-29",
return_first_date_in_period=True,
include_month=True,
return_expectations={"date": {
"latest": "2020-02-29"
}},
),
# IMMUNOSUPPRESSION
#### PERMANENT
permanent_immunodeficiency=patients.with_these_clinical_events(
combine_codelists(
hiv_codes,
permanent_immune_codes,
sickle_cell_codes,
organ_transplant_codes,
),
pneumococcal_vaccine=patients.satisfying(
"""
pneumococcal_vaccine_tpp_table OR
pneumococcal_vaccine_med OR
pneumococcal_vaccine_clinical
""", ),
### EXACERBATION
# count
exacerbation_count=patients.with_these_medications(
oral_steroid_med_codes,
between=["2019-03-01", "2020-02-29"],
ignore_days_where_these_clinical_codes_occur=combine_codelists(
sle_codes,
interstital_lung_codes,
ra_codes,
ms_codes,
temporal_arteritis_codes,
),
returning="number_of_episodes",
episode_defined_as="series of events each <= 14 days apart",
return_expectations={
"int": {
"distribution": "normal",
"mean": 2,
"stddev": 1
},
"incidence": 0.2,
},
),
# # binary flag
},
),
### STATIN USE
statin=patients.with_these_medications(
statin_med_codes,
between=["2019-11-01", "2020-02-29"],
return_last_date_in_period=True,
include_month=True,
return_expectations={
"date": {"earliest": "2019-11-01", "latest": "2020-02-29"}
},
),
### EXACERBATIONS
## count
exacerbation_count=patients.with_these_clinical_events(
combine_codelists(copd_infection_codes, lrti_codes),
between=["2019-03-01", "2020-02-29"],
ignore_days_where_these_codes_occur=copd_review_rescue_codes,
returning="number_of_episodes",
episode_defined_as="series of events each <= 14 days apart",
return_expectations={
"int": {"distribution": "normal", "mean": 4, "stddev": 2},
"incidence": 0.2,
},
),
# binary flag
exacerbations=patients.satisfying(
"""
exacerbation_count > 0
""",
),
on_or_after="2020-02-01",
returning="date_of_death",
include_month=True,
include_day=True,
return_expectations={
"date": {
"earliest": "2020-08-01"
},
"incidence": 0.5
},
),
### Primary care COVID cases
covid_tpp_probable=patients.with_these_clinical_events(
combine_codelists(
covid_identification_in_primary_care_case_codes_clinical,
covid_identification_in_primary_care_case_codes_test,
covid_identification_in_primary_care_case_codes_seq),
return_first_date_in_period=True,
include_day=True,
return_expectations={
"date": {
"earliest": "2020-10-20"
},
"incidence": 0.2
},
),
# Any COVID vaccination (first dose)
covid_vacc_date=patients.with_tpp_vaccination_record(
target_disease_matches="SARS-2 CORONAVIRUS",
on_or_after="2020-12-01", # check all december to date