def medication_counts_and_dates(var_name, med_codelist_file, high_cost, needs_6m_12m=False):
"""
Generates dictionary of covariats for a medication including counts (or binary flags for high cost drugs) and dates
Takes a variable prefix and medication codelist filename (minus .csv)
Returns a dictionary suitable for unpacking into the main study definition
This will include all five of the items defined in the functions above
"""
definitions={}
if (med_codelist_file[0:5] == "cross"):
med_codelist_file = "crossimid-codelists/" + med_codelist_file
else:
med_codelist_file = "codelists/" + med_codelist_file
if (high_cost):
med_codelist=codelist_from_csv(med_codelist_file + ".csv", system="high_cost_drugs", column="olddrugname")
with_med_func=patients.with_high_cost_drugs
else:
med_codelist=codelist_from_csv(med_codelist_file + ".csv", system="snomed", column="snomed_id")
with_med_func=patients.with_these_medications
med_functions=[
("3m_0m", get_medication_for_dates, {"dates": ["2019-12-01", "2020-02-29"], "return_count": not high_cost}),
("6m_3m", get_medication_for_dates, {"dates": ["2019-09-01", "2020-11-30"], "return_count": not high_cost})
]
if (needs_6m_12m):
med_functions += [("12m_6m", get_medication_for_dates, {"dates": ["2019-03-01", "2020-08-31"], "return_count": not high_cost})]
for (suffix, fun, params) in med_functions:
definitions[var_name + "_" + suffix] = fun(med_codelist, with_med_func, **params)
return definitions
def medication_counts_and_dates(var_name, med_codelist_file):
"""
Generates dictionary of covariats for a medication including counts and dates
Takes a variable prefix and medication codelist filename (minus .csv)
Returns a dictionary suitable for unpacking into the main study definition
This will include all five of the items defined in the functions above
"""
definitions = {}
med_codelist = codelist_from_csv("codelists/" + med_codelist_file + ".csv",
system="snomed",
column="snomed_id")
med_functions = [("3m_0m", medication_count_3m_0m),
("6m_3m", medication_count_6m_3m),
("12m_6m", medication_count_12m_6m),
("earliest", medication_earliest),
("latest", medication_latest)]
for (suffix, fun) in med_functions:
definitions[var_name + "_" + suffix] = fun(med_codelist)
return definitions
from cohortextractor import codelist_from_csv
from config import codelist_path, codelist_system, codelist_code_column
# Change the path of the codelist to your chosen codelist
codelist = codelist_from_csv(
codelist_path,
system=codelist_system,
column=codelist_code_column,
)
ethnicity_codes = codelist_from_csv(
"codelists/opensafely-ethnicity.csv",
system="ctv3",
column="Code",
category_column="Grouping_6",
)
ld_codes = codelist_from_csv(
"codelists/opensafely-learning-disabilities.csv",
system="ctv3",
column="CTV3Code",
)
from cohortextractor import (
codelist_from_csv,
codelist,
)
# OUTCOME CODELISTS
covid_codelist = codelist_from_csv(
"codelists/opensafely-covid-identification.csv",
system="icd10",
column="icd10_code",
)
covid_identification_in_primary_care_case_codes_clinical = codelist_from_csv(
"codelists/opensafely-covid-identification-in-primary-care-probable-covid-clinical-code.csv",
system="ctv3",
column="CTV3ID",
)
covid_identification_in_primary_care_case_codes_test = codelist_from_csv(
"codelists/opensafely-covid-identification-in-primary-care-probable-covid-positive-test.csv",
system="ctv3",
column="CTV3ID",
)
covid_identification_in_primary_care_case_codes_seq = codelist_from_csv(
"codelists/opensafely-covid-identification-in-primary-care-probable-covid-sequelae.csv",
system="ctv3",
column="CTV3ID",
)
# Import functions
from cohortextractor import (
StudyDefinition,
patients,
codelist,
codelist_from_csv
)
# Import codelists
chronic_cardiac_disease_codes = codelist_from_csv(
"codelists/opensafely-chronic-cardiac-disease.csv", system="ctv3", column="CTV3ID"
)
chronic_liver_disease_codes = codelist_from_csv(
"codelists/opensafely-chronic-liver-disease.csv", system="ctv3", column="CTV3ID"
)
chronic_kidney_disease_codes = codelist_from_csv(
"codelists/opensafely-chronic_kidney_disease_codescsv", system="ctv3", column="CTV3ID"
)
hypertension_codes = codelist_from_csv(
"codelists/opensafely-hypertension_codes.csv", system="ctv3", column="CTV3ID"
)
chronic_diabetes_codes = codelist_from_csv(
"codelists/opensafely-chronic_diabetes_codes.csv", system="ctv3", column="CTV3ID"
)
chronic_respiratory_disease_disease_codes = codelist_from_csv(
"codelists/opensafely-chronic-respiratory_disease_codes.csv", system="ctv3", column="CTV3ID"
)
solid_organ_transplantation_codes = codelist_from_csv(
from cohortextractor import (
codelist_from_csv,
codelist,
)
# OUTCOME CODELISTS
covid_identification = codelist_from_csv(
"codelists/opensafely-covid-identification.csv",
system="icd10",
column="icd10_code",
)
covid_pos_primcare_code = codelist_from_csv(
"codelists/opensafely-covid-identification-in-primary-care-probable-covid-clinical-code.csv",
system="ctv3",
column="CTV3ID",
)
covid_pos_primcare_test = codelist_from_csv(
"codelists/opensafely-covid-identification-in-primary-care-probable-covid-positive-test.csv",
system="ctv3",
column="CTV3ID",
)
# MEDICATIONS - EXPOSURES
# DEMOGRAPHIC CODELIST
ethnicity_codes = codelist_from_csv(
"codelists/opensafely-ethnicity.csv",
system="ctv3",
column="Code",
from cohortextractor import (
codelist,
codelist_from_csv,
)
covid_codelist = codelist(["U071", "U072"], system="icd10")
confirmed_covid_codelist = codelist(["U071"], system="icd10")
suspected_covid_codelist = codelist(["U072"], system="icd10")
covid_primary_care_positive_test=codelist_from_csv(
"codelists/opensafely-covid-identification-in-primary-care-probable-covid-positive-test.csv",
system="ctv3",
column="CTV3ID",
)
covid_primary_care_code=codelist_from_csv(
"codelists/opensafely-covid-identification-in-primary-care-probable-covid-clinical-code.csv",
system="ctv3",
column="CTV3ID",
)
covid_primary_care_sequalae=codelist_from_csv(
"codelists/opensafely-covid-identification-in-primary-care-probable-covid-sequelae.csv",
system="ctv3",
column="CTV3ID",
)
covid_primary_care_exposure = codelist_from_csv(
"codelists/opensafely-covid-identification-in-primary-care-exposure-to-disease.csv",
from cohortextractor import (
codelist,
codelist_from_csv,
)
## measurement codes
codes_ICD10_covid = codelist_from_csv(
"codelists/opensafely-covid-identification.csv",
system="icd10",
column="icd10_code")
codes_cholesterol = codelist_from_csv(
"codelists-local/cholesterol-measurement.csv", system="ctv3", column="id")
codes_inr = codelist_from_csv(
"codelists-local/international-normalised-ratio-measurement.csv",
system="ctv3",
column="id")
from cohortextractor import (
codelist,
codelist_from_csv,
)
ethnicity_codes = codelist_from_csv(
"codelists/opensafely-ethnicity.csv",
system="ctv3",
column="Code",
category_column="Grouping_6",
)
dementia_codes = codelist_from_csv(
"codelists/opensafely-dementia-complete.csv",
system="ctv3",
column="code",
)
chronic_respiratory_disease_codes = codelist_from_csv(
"codelists/opensafely-chronic-respiratory-disease.csv",
system="ctv3",
column="CTV3ID",
)
chronic_cardiac_disease_codes = codelist_from_csv(
"codelists/opensafely-chronic-cardiac-disease.csv",
system="ctv3",
column="CTV3ID",
)
diabetes_codes = codelist_from_csv(
from cohortextractor import (
codelist,
codelist_from_csv,
)
covid_codelist = codelist(["U071", "U072"], system="icd10")
covidconf_codelist = codelist(["U071"], system="icd10")
aplastic_codes = codelist_from_csv(
"codelists/opensafely-aplastic-anaemia.csv", system="ctv3", column="CTV3ID"
)
hiv_codes = codelist_from_csv(
"codelists/opensafely-hiv.csv", system="ctv3", column="CTV3ID", category_column="CTV3ID"
)
hepc_codes = codelist_from_csv(
"codelists/opensafely-hepatitis-c.csv",
system="ctv3",
column="CTV3ID",
category_column="CTV3ID"
)
permanent_immune_codes = codelist_from_csv(
"codelists/opensafely-permanent-immunosuppression.csv",
system="ctv3",
column="CTV3ID",
)
temp_immune_codes = codelist_from_csv(
from cohortextractor import(
codelist,
codelist_from_csv,
)
covid_codelist = codelist(["U071", "U072"], system = "icd10")
# https://codelists.opensafely.org/codelist/opensafely/severe-and-profound-learning-disability-flags/44ef542a/
severe_and_profound_learning_disability_codes = codelist_from_csv(
"codelists/opensafely-severe-and-profound-learning-disability-flags-44ef542a.csv",
system = "ctv3",
column = "code",
)
# https://codelists.opensafely.org/codelist/opensafely/intellectual-disability-including-downs-syndrome/2020-08-27/
intellectual_disability_including_downs_syndrome_codes = codelist_from_csv(
"codelists/opensafely-intellectual-disability-including-downs-syndrome-2020-08-27.csv",
system="ctv3",
column="CTV3ID",
)
from cohortextractor import (
codelist_from_csv,
codelist,
)
# drug placeholder
ics_codes = codelist_from_csv(
"codelists/opensafely-high-dose-ics-inhalers.csv",
system="snomed",
column="id",
)
# OUTCOME CODELISTS
covid_identification = codelist_from_csv(
"codelists/opensafely-covid-identification.csv",
system="icd10",
column="icd10_code",
)
# DEMOGRAPHIC CODELIST
ethnicity_codes = codelist_from_csv(
"codelists/opensafely-ethnicity.csv",
system="ctv3",
column="Code",
category_column="Grouping_6",
)
# SMOKING CODELIST
clear_smoking_codes = codelist_from_csv(
"codelists/opensafely-smoking-clear.csv",
from cohortextractor import codelist, codelist_from_csv
stroke = codelist_from_csv(
"codelists/opensafely-incident-non-traumatic-stroke.csv",
system="ctv3",
column="CTV3ID",
)
stroke_hospital = codelist_from_csv(
"codelists/opensafely-stroke-secondary-care.csv",
system="icd10",
column="icd")
aki_codes = codelist(["N17", "N170", "N171", "N172", "N178", "N179"],
system="icd10")
mi_codes = codelist_from_csv(
"codelists/opensafely-myocardial-infarction-2.csv",
system="ctv3",
column="CTV3Code",
)
mi_codes_hospital = codelist_from_csv(
"codelists/opensafely-cardiovascular-secondary-care.csv",
system="icd10",
column="icd",
category_column="mi",
)
heart_failure_codes = codelist_from_csv(
"codelists/opensafely-heart-failure.csv",
system="ctv3",
column="CTV3ID",
)
heart_failure_codes_hospital = codelist_from_csv(
"codelists/opensafely-cardiovascular-secondary-care.csv",
system="icd10",
## LIBRARIES
# cohort extractor
from cohortextractor import (StudyDefinition, Measure, patients,
codelist_from_csv, codelist,
filter_codes_by_category, combine_codelists)
## CODELISTS
# All codelist are held within the codelist/ folder.
codes_diab = codelist_from_csv("codelists/opensafely-type-2-diabetes.csv",
system="ctv3",
column="CTV3ID")
## STUDY POPULATION
# Defines both the study population and points to the important covariates
index_date = "2020-01-01"
end_date = "2020-09-30"
study = StudyDefinition(
# Configure the expectations framework
default_expectations={
"date": {
"earliest": index_date,
"latest": end_date
},
"rate": "uniform",
},
index_date=index_date,
from cohortextractor import (
codelist,
codelist_from_csv,
)
adrenaline_pen = codelist_from_csv("codelists/opensafely-adrenaline-pens.csv",
system="snomed",
column="dmd_id")
chronic_cardiac_disease_codes = codelist_from_csv(
"codelists/opensafely-chronic-cardiac-disease.csv",
system="ctv3",
column="CTV3ID",
)
chemotherapy_or_radiotherapy_codes = codelist_from_csv(
"codelists/opensafely-chemotherapy-or-radiotherapy.csv",
system="ctv3",
column="CTV3ID",
)
cancer_excluding_lung_and_haematological_codes = codelist_from_csv(
"codelists/opensafely-cancer-excluding-lung-and-haematological.csv",
system="ctv3",
column="CTV3ID",
)
covid_primary_care_positive_test = codelist_from_csv(
"codelists/opensafely-covid-identification-in-primary-care-probable-covid-positive-test.csv",
system="ctv3",
column="CTV3ID",
)
## LIBRARIES
# cohort extractor
from cohortextractor import (StudyDefinition, patients, codelist_from_csv, codelist)
##CODE LIST
systolic_blood_pressure_codes = codelist(["2469."], system="ctv3")
ace_inhibitor_codes = codelist_from_csv("codelists/opensafely-ace-inhibitor-medications.csv",system="snomed",column="id")
arb_inhibitor_codes = codelist_from_csv("codelists/opensafely-angiotensin-ii-receptor-blockers-arbs.csv", system='snomed', column='id')
hf_codes = codelist_from_csv("codelists/opensafely-heart-failure.csv", system="ctv3", column="CTV3ID")
ckd_codes = codelist_from_csv("codelists/opensafely-chronic-kidney-disease.csv", system="ctv3", column="CTV3ID")
## STUDY POPULATION
study = StudyDefinition(
# define default dummy data behaviour
# Configure the expectations framework
default_expectations = {
"date": {"earliest": "1900-01-01", "latest": "today"},
"rate": "exponential_increase",
"incidence": 0.5,
"float": {"distribution": "normal", "mean": 80, "stddev": 10}},
# define the study index date
index_date = "2020-01-01",
# define the study population
population = patients.all(),
# define the study variables
from cohortextractor import (
codelist,
codelist_from_csv,
)
placeholder_event_codes = codelist_from_csv( #### USED AS A PLACEHOLDER
"codelists/opensafely-diabetes.csv",
system="ctv3",
column="CTV3ID")
placeholder_med_codes = codelist_from_csv(
"codelists/opensafely-asthma-inhaler-steroid-medication.csv",
system="snomed",
column="id",
)
ethnicity_codes = codelist_from_csv(
"codelists/opensafely-ethnicity.csv",
system="ctv3",
column="Code",
category_column="Grouping_6",
)
clear_smoking_codes = codelist_from_csv(
"codelists/opensafely-smoking-clear.csv",
system="ctv3",
column="CTV3Code",
category_column="Category",
)
unclear_smoking_codes = codelist_from_csv(
# Some covariates used in the study are created from codelists of clinical conditions or
# numerical values available on a patient's records.
# This script fetches all of the codelists identified in codelists.txt from OpenCodelists.
######################################
# --- IMPORT STATEMENTS ---
## Import code building blocks from cohort extractor package
from cohortextractor import (codelist, codelist_from_csv, combine_codelists)
## Ethnicity
ethnicity_codes = codelist_from_csv(
"codelists/primis-covid19-vacc-uptake-eth2001.csv",
system="snomed",
column="code",
category_column="grouping_16_id",
)
## BMI
bmi_codes = codelist_from_csv(
"codelists/primis-covid19-vacc-uptake-bmi.csv",
system="snomed",
column="code",
)
## Diabetes
diabetes_codes = codelist_from_csv(
"codelists/primis-covid19-vacc-uptake-diab.csv",
system="snomed",
column="code",
from cohortextractor import Measure, StudyDefinition, codelist_from_csv, patients
chronic_liver_disease_codes = codelist_from_csv(
"codelists/opensafely-chronic-liver-disease.csv",
system="ctv3",
column="CTV3ID")
study = StudyDefinition(
index_date="2020-02-01",
default_expectations={
"date": {
"earliest": "1900-01-01",
"latest": "index_date"
},
"rate": "exponential_increase",
},
population=patients.registered_with_one_practice_between(
"index_date - 1 year", "index_date"),
has_chronic_liver_disease=patients.with_these_clinical_events(
chronic_liver_disease_codes,
returning="binary_flag",
return_expectations={
"incidence": 1.0,
"date": {
"earliest": "1950-01-01",
"latest": "index_date"
},
},
),
stp=patients.registered_practice_as_of(
"index_date",
from cohortextractor import (
codelist,
codelist_from_csv,
)
# https://codelists.opensafely.org/codelist/opensafely/icd-10-chapter-ix/4868c7af/
cvd_codelist = codelist_from_csv(
"codelists/opensafely-icd-10-chapter-ix.csv",
system="icd10",
column="code",
)
# https://codelists.opensafely.org/codelist/opensafely/icd-10-chapter-x/2f59547a/
resp_codelist = codelist_from_csv(
"codelists/opensafely-icd-10-chapter-x.csv",
system="icd10",
column="code",
)
# https://codelists.opensafely.org/codelist/opensafely/icd-10-chapter-ii/77d4ee23/
cancer_codelist = codelist_from_csv(
"codelists/opensafely-icd-10-chapter-ii.csv",
system="icd10",
column="code",
)
#https://codelists.opensafely.org/codelist/opensafely/ethnicity/2020-04-27/
ethnicity_codes = codelist_from_csv(
"codelists/opensafely-ethnicity.csv",
# Risk groups
chd_code = codelist("CHD_COV_COD", system="snomed")
resp_code = codelist("RESP_COV_COD", system="snomed")
ckd_code = codelist("CKD_COV_COD", system="snomed")
cld_code = codelist("CLD_COD", system="snomed")
diab_code = codelist("DIAB_COD", system="snomed")
immdx_code = codelist("IMMDX_COV_COD", system="snomed")
cns_code = codelist("CNS_COV_COD", system="snomed")
spln_code = codelist("SPLN_COV_COD", system="snomed")
obesity_code = codelist("SEV_OBESITY", system="snomed")
learndis_code = codelist("LEARNDIS_COD", system="snomed")
mental_code = codelist("SEV_MENTAL_COD", system="snomed")
clinical_riskgroup_codes = codelist_from_csv(
"codelists-local/clinical-riskgroup-disease.csv",
system="snomed",
column="code",
)
all_riskgroup_codes = codelist_from_csv(
"codelists-local/all-riskgroup-disease.csv",
system="snomed",
column="code",
)
# Covid shielding
shield_code = codelist("SHIELD_COD", system="snomed")
# Household member of shielding patient
hhld_code = codelist("HHLD_IMDEF", system="snomed")
from cohortextractor import (
StudyDefinition,
Measure,
patients,
codelist,
codelist_from_csv,
)
chronic_cardiac_disease_codes = codelist_from_csv(
"codelists/opensafely-chronic-cardiac-disease.csv",
system="ctv3",
column="CTV3ID")
chronic_liver_disease_codes = codelist_from_csv(
"codelists/opensafely-chronic-liver-disease.csv",
system="ctv3",
column="CTV3ID")
salbutamol_codes = codelist_from_csv(
"codelists/opensafely-asthma-inhaler-salbutamol-medication.csv",
system="snomed",
column="id",
)
systolic_blood_pressure_codes = codelist(["2469."], system="ctv3")
diastolic_blood_pressure_codes = codelist(["246A."], system="ctv3")
study = StudyDefinition(
index_date="2020-02-01",
# Configure the expectations framework
default_expectations={
"date": {
"earliest": "1900-01-01",
"latest": "index_date"
from cohortextractor import codelist, codelist_from_csv
codes_antigen_negative = codelist_from_csv(
"codelists/opensafely-covid-identification-in-primary-care-antigen-test-negative.csv",
system="ctv3",
column="CTV3ID",
)
codes_exposure_to_disease = codelist_from_csv(
"codelists/opensafely-covid-identification-in-primary-care-exposure-to-disease.csv",
system="ctv3",
column="CTV3ID",
)
codes_historic_covid = codelist_from_csv(
"codelists/opensafely-covid-identification-in-primary-care-historic-case.csv",
system="ctv3",
column="CTV3ID",
)
codes_potential_historic_covid = codelist_from_csv(
"codelists/opensafely-covid-identification-in-primary-care-potential-historic-case.csv",
system="ctv3",
column="CTV3ID",
)
codes_probable_covid = codelist_from_csv(
"codelists/opensafely-covid-identification-in-primary-care-probable-covid-clinical-code.csv",
system="ctv3",
column="CTV3ID",
)
## LIBRARIES
# cohort extractor
from cohortextractor import (StudyDefinition, Measure, patients,
codelist_from_csv, codelist,
filter_codes_by_category, combine_codelists)
## CODELISTS
# All codelist are held within the codelist/ folder.
codes_ICD10_covid = codelist_from_csv(
"codelists/opensafely-covid-identification.csv",
system="icd10",
column="icd10_code")
## STUDY POPULATION
# Defines both the study population and points to the important covariates
index_date = "2020-01-01"
end_date = "2020-09-30"
study = StudyDefinition(
# Configure the expectations framework
default_expectations={
"date": {
"earliest": index_date,
"latest": end_date
},
"rate": "uniform",
},
index_date=index_date,
## LIBRARIES
# cohort extractor
from cohortextractor import (StudyDefinition, Measure, patients,
codelist_from_csv, codelist,
filter_codes_by_category, combine_codelists)
## CODELISTS
# All codelist are held within the codelist/ folder.
codes_cholesterol = codelist_from_csv(
"codelists-local/cholesterol-measurement.csv", system="ctv3", column="id")
codes_inr = codelist_from_csv(
"codelists-local/international-normalised-ratio-measurement.csv",
system="ctv3",
column="id")
# dictionary of STP codes (for dummy data)
from dictionaries import dict_stp
## STUDY POPULATION
index_date = "2020-01-01"
study = StudyDefinition(
# Configure the expectations framework
default_expectations={
"date": {
"earliest": index_date,
"latest": "today"
},
