"incidence": 0.01,
},
),
###############################################################################
# COVID VACCINATION
###############################################################################
# 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
find_first_match_in_period=True,
returning="date",
date_format="YYYY-MM-DD",
return_expectations={
"date": {
"earliest":
"2020-12-08", # first vaccine administered on the 8/12
"latest": "2021-01-31",
},
"incidence": 0.4
},
),
# SECOND DOSE COVID VACCINATION
covid_vacc_second_dose_date=patients.with_tpp_vaccination_record(
target_disease_matches="SARS-2 CORONAVIRUS",
on_or_after="covid_vacc_date + 19 days",
find_first_match_in_period=True,
returning="date",
date_format="YYYY-MM-DD",
return_expectations={
"ratios": {
"R": 0.3,
"O": 0.1,
"RO": 0.2,
"M": 0.4
}
}
},
),
# FLU VACCINATION STATUS
flu_vaccine_tpp_table=patients.with_tpp_vaccination_record(
target_disease_matches="INFLUENZA",
between=["2019-09-01", "2020-02-29"], # current flu season
returning="date",
find_first_match_in_period=True,
return_expectations={
"date": {
"earliest": "2019-09-01",
"latest": "2020-02-29"
}
},
),
flu_vaccine_med=patients.with_these_medications(
flu_med_codes,
between=["2019-09-01", "2020-02-29"], # current flu season
returning="date",
find_last_match_in_period=True,
include_month=True,
include_day=True,
return_expectations={
"date": {
"earliest": "2019-09-01",
"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
find_first_match_in_period=True,
returning="date",
date_format="YYYY-MM-DD",
return_expectations={
"date": {
"earliest":
"2020-12-08", # first vaccine administered on the 8/12
"latest": "2021-01-31",
},
"incidence": 0.1
},
),
### COVID test positive (SGSS)
first_pos_test_sgss=patients.with_test_result_in_sgss(
pathogen="SARS-CoV-2",
test_result="positive",
find_first_match_in_period=True,
returning="date",
date_format="YYYY-MM-DD",