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study_definition_delivery.py
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study_definition_delivery.py
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# Import functions
from cohortextractor import (
StudyDefinition,
patients,
codelist_from_csv,
codelist,
filter_codes_by_category,
combine_codelists,
)
# Import codelists
from codelists import *
from study_definition_delivery_common import common_variables, index_date
# Specify study definition
study = StudyDefinition(
index_date=index_date,
# ETHNICITY IN 16 CATEGORIES
ethnicity_16=patients.with_these_clinical_events(
ethnicity_codes_16,
returning="category",
find_last_match_in_period=True,
include_date_of_match=False,
return_expectations={
"category": {
"ratios": {
"1": 0.0625,
"2": 0.0625,
"3": 0.0625,
"4": 0.0625,
"5": 0.0625,
"6": 0.0625,
"7": 0.0625,
"8": 0.0625,
"9": 0.0625,
"10": 0.0625,
"11": 0.0625,
"12": 0.0625,
"13": 0.0625,
"14": 0.0625,
"15": 0.0625,
"16": 0.0625,
}
},
"incidence": 0.75,
},
),
# ETHNICITY IN 6 CATEGORIES
ethnicity=patients.with_these_clinical_events(
ethnicity_codes,
returning="category",
find_last_match_in_period=True,
include_date_of_match=False,
return_expectations={
"category": {"ratios": {"1": 0.2, "2": 0.2, "3": 0.2, "4": 0.2, "5": 0.2}},
"incidence": 0.75,
},
),
# fill missing ethnicity from SUS
ethnicity_6_sus=patients.with_ethnicity_from_sus(
returning="group_6",
use_most_frequent_code=True,
return_expectations={
"category": {"ratios": {"1": 0.2, "2": 0.2, "3": 0.2, "4": 0.2, "5": 0.2}},
"incidence": 0.4,
},
),
ethnicity_16_sus=patients.with_ethnicity_from_sus(
returning="group_16",
use_most_frequent_code=True,
return_expectations={
"category": {
"ratios": {
"1": 0.0625,
"2": 0.0625,
"3": 0.0625,
"4": 0.0625,
"5": 0.0625,
"6": 0.0625,
"7": 0.0625,
"8": 0.0625,
"9": 0.0625,
"10": 0.0625,
"11": 0.0625,
"12": 0.0625,
"13": 0.0625,
"14": 0.0625,
"15": 0.0625,
"16": 0.0625,
}
},
"incidence": 0.4,
},
),
# CLINICAL CO-MORBIDITIES WORK IN PROGRESS IN COLLABORATION WITH NHSX
# https://github.com/opensafely/vaccine-eligibility/blob/master/analysis/study_definition.py
chronic_cardiac_disease=patients.with_these_clinical_events(
chronic_cardiac_disease_codes,
on_or_before=index_date,
returning="binary_flag",
return_expectations={
"incidence": 0.01,
},
),
current_copd=patients.with_these_clinical_events(
current_copd_codes,
on_or_before=index_date,
returning="binary_flag",
return_expectations={
"incidence": 0.01,
},
),
# dementia
dementia=patients.with_these_clinical_events(
dementia_codes,
on_or_before=index_date,
returning="binary_flag",
return_expectations={
"incidence": 0.01,
},
),
dialysis=patients.with_these_clinical_events(
dialysis_codes,
on_or_before=index_date,
returning="binary_flag",
return_expectations={
"incidence": 0.01,
},
),
solid_organ_transplantation=patients.with_these_clinical_events(
solid_organ_transplantation_codes,
on_or_before=index_date,
returning="binary_flag",
return_expectations={
"incidence": 0.01,
},
),
chemo_or_radio=patients.with_these_clinical_events(
chemotherapy_or_radiotherapy_codes,
on_or_before=index_date,
returning="binary_flag",
return_expectations={
"incidence": 0.01,
},
),
intel_dis_incl_downs_syndrome=patients.with_these_clinical_events(
intellectual_disability_including_downs_syndrome_codes,
on_or_before=index_date,
returning="binary_flag",
return_expectations={
"incidence": 0.01,
},
),
lung_cancer=patients.with_these_clinical_events(
lung_cancer_codes,
on_or_before=index_date,
returning="binary_flag",
return_expectations={
"incidence": 0.01,
},
),
cancer_excl_lung_and_haem=patients.with_these_clinical_events(
cancer_excluding_lung_and_haematological_codes,
on_or_before=index_date,
returning="binary_flag",
return_expectations={
"incidence": 0.01,
},
),
haematological_cancer=patients.with_these_clinical_events(
haematological_cancer_codes,
on_or_before=index_date,
returning="binary_flag",
return_expectations={
"incidence": 0.01,
},
),
bone_marrow_transplant=patients.with_these_clinical_events(
bone_marrow_transplant_codes,
between=["index_date - 6 months", index_date],
returning="binary_flag",
return_expectations={
"incidence": 0.01,
},
),
# cystic_fibrosis=patients.with_these_clinical_events(
# cystic_fibrosis_codes,
# on_or_before=index_date,
# returning="binary_flag",
# return_expectations={"incidence": 0.01,},
# ),
# sickle_cell_disease=patients.with_these_clinical_events(
# sickle_cell_disease_codes,
# on_or_before=index_date,
# returning="binary_flag",
# return_expectations={"incidence": 0.01,},
# ),
# permanant_immunosuppression=patients.with_these_clinical_events(
# permanent_immunosuppression_codes,
# on_or_before=index_date,
# returning="binary_flag",
# return_expectations={"incidence": 0.01,},
# ),
# temporary_immunosuppression=patients.with_these_clinical_events(
# temporary_immunosuppression_codes,
# on_or_before=index_date,
# returning="binary_flag",
# return_expectations={"incidence": 0.01,},
# ),
#
psychosis_schiz_bipolar=patients.with_these_clinical_events(
psychosis_schizophrenia_bipolar_affective_disease_codes,
on_or_before=index_date,
returning="binary_flag",
return_expectations={
"incidence": 0.01,
},
),
# https://github.com/opensafely/codelist-development/issues/4
# asplenia=patients.with_these_clinical_events(
# asplenia_codes,
# on_or_before=index_date,
# returning="binary_flag",
# return_expectations={"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": index_date,
},
"incidence": 0.9,
},
),
# 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={
"date": {
"earliest": "2020-12-29", # first reported second dose administered on the 29/12
"latest": index_date,
},
"incidence": 0.8,
},
),
# BOOSTER (3rd) DOSE COVID VACCINATION
## Booster dose scehdule is 6 months from 2nd dose. However, for now, we will use an 8 week interval,
## to ensure that anyone having a third dose within the primary course (immunosuppressed, from 1st Sept)
## are not shown as due/missing a booster dose.
## however those with third doses will also eventually become eligible for booster so this may need to be revisited
covid_vacc_third_dose_date=patients.with_tpp_vaccination_record(
target_disease_matches="SARS-2 CORONAVIRUS",
on_or_after="covid_vacc_second_dose_date + 56 days",
find_first_match_in_period=True,
returning="date",
date_format="YYYY-MM-DD",
return_expectations={
"date": {
"earliest": "2021-09-24", # first booster dose recorded
"latest": index_date,
},
"incidence": 0.1,
},
),
# COVID VACCINATION - Pfizer BioNTech
covid_vacc_pfizer_date=patients.with_tpp_vaccination_record(
product_name_matches="COVID-19 mRNA Vaccine Comirnaty 30micrograms/0.3ml dose conc for susp for inj MDV (Pfizer)",
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": index_date,
},
"incidence": 0.7,
},
),
# COVID VACCINATION - Oxford AZ
covid_vacc_oxford_date=patients.with_tpp_vaccination_record(
product_name_matches="COVID-19 Vaccine Vaxzevria 0.5ml inj multidose vials (AstraZeneca)",
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": "2020-01-04", # first vaccine administered on the 4/1
"latest": index_date,
},
"incidence": 0.7,
},
),
# COVID VACCINATION - Moderna
covid_vacc_moderna_date=patients.with_tpp_vaccination_record(
product_name_matches="COVID-19 mRNA Vaccine Spikevax (nucleoside modified) 0.1mg/0.5mL dose disp for inj MDV (Moderna)",
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": "2020-04-01", # expected from early april
"latest": index_date,
},
"incidence": 0.4,
},
),
## BRAND OF THIRD/BOOSTER DOSES
# BOOSTER (3rd) DOSE COVID VACCINATION - Pfizer
covid_vacc_third_dose_pfizer_date=patients.with_tpp_vaccination_record(
product_name_matches="COVID-19 mRNA Vaccine Comirnaty 30micrograms/0.3ml dose conc for susp for inj MDV (Pfizer)",
on_or_after="covid_vacc_second_dose_date + 56 days",
find_first_match_in_period=True,
returning="date",
date_format="YYYY-MM-DD",
return_expectations={
"date": {
"earliest": "2021-09-24", # first booster dose recorded
"latest": index_date,
},
"incidence": 0.25,
},
),
# BOOSTER (3rd) DOSE COVID VACCINATION - Oxford AZ
covid_vacc_third_dose_oxford_date=patients.with_tpp_vaccination_record(
product_name_matches="COVID-19 Vaccine Vaxzevria 0.5ml inj multidose vials (AstraZeneca)",
on_or_after="covid_vacc_second_dose_date + 56 days",
find_first_match_in_period=True,
returning="date",
date_format="YYYY-MM-DD",
return_expectations={
"date": {
"earliest": "2021-09-24", # first booster dose recorded
"latest": index_date,
},
"incidence": 0.10,
},
),
# BOOSTER (3rd) DOSE COVID VACCINATION - Moderna
covid_vacc_third_dose_moderna_date=patients.with_tpp_vaccination_record(
product_name_matches="COVID-19 mRNA Vaccine Spikevax (nucleoside modified) 0.1mg/0.5mL dose disp for inj MDV (Moderna)",
on_or_after="covid_vacc_second_dose_date + 56 days",
find_first_match_in_period=True,
returning="date",
date_format="YYYY-MM-DD",
return_expectations={
"date": {
"earliest": "2021-09-24", # first booster dose recorded
"latest": index_date,
},
"incidence": 0.25,
},
),
**common_variables
)