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Update variables_cohorts.py
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1. remove opa diagnosis for hospitable admission.
2. revise covid-19 severity variable by focusing on primary diagnosis only.
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@ZoeMZou
ZoeMZou committed Jan 15, 2025
1 parent b4a2cdf commit ed2a93b
Showing 1 changed file with 5 additions and 123 deletions.
128 changes: 5 additions & 123 deletions analysis/dataset_definition/variables_cohorts.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,9 +17,7 @@
vaccinations,
sgss_covid_all_tests,
apcs,
ec,
opa,
opa_diag,
ec,
clinical_events,
medications,
ons_deaths,
Expand All @@ -36,14 +34,12 @@
first_matching_event_clinical_snomed_between,
first_matching_med_dmd_between,
first_matching_event_apc_between,
first_matching_event_opa_between,
first_matching_event_ec_snomed_between,
matching_death_between,
last_matching_event_clinical_ctv3_before,
last_matching_event_clinical_snomed_before,
last_matching_med_dmd_before,
last_matching_event_apc_before,
last_matching_event_opa_before,
last_matching_event_ec_snomed_before,
matching_death_before,
filter_codes_by_category,
Expand Down Expand Up @@ -89,17 +85,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
.admission_date
)

tmp_exp_date_covid19_confirmed_opa = (
opa_diag.where(
((opa_diag.primary_diagnosis_code.is_in(covid_codes)) |
(opa_diag.secondary_diagnosis_code_1.is_in(covid_codes))) &
(opa_diag.appointment_date.is_on_or_between(index_date, end_date_exp))
)
.sort_by(opa_diag.appointment_date)
.first_for_patient()
.appointment_date
)

tmp_exp_covid19_confirmed_death = matching_death_between(covid_codes, index_date, end_date_exp)

tmp_exp_date_death = ons_deaths.date
Expand All @@ -112,7 +97,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
tmp_exp_date_covid19_confirmed_sgss,
tmp_exp_date_covid19_confirmed_snomed,
tmp_exp_date_covid19_confirmed_apc,
tmp_exp_date_covid19_confirmed_opa,
tmp_exp_date_covid19_confirmed_death
)

Expand All @@ -132,12 +116,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
).admission_date
)

tmp_out_date_pneumonia_opa= (
first_matching_event_opa_between(
pneumonia_icd10, index_date, end_date_out
).appointment_date
)

tmp_out_date_pneumonia_death= case(
when(
matching_death_between(pneumonia_icd10, index_date, end_date_out)
Expand All @@ -147,7 +125,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
out_date_pneumonia=minimum_of(
tmp_out_date_pneumonia_snomed,
tmp_out_date_pneumonia_apc,
tmp_out_date_pneumonia_opa,
tmp_out_date_pneumonia_death
)

Expand All @@ -165,12 +142,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
).admission_date
)

tmp_out_date_asthma_opa= (
first_matching_event_opa_between(
asthma_icd10, index_date, end_date_out
).appointment_date
)

tmp_out_date_asthma_death= case(
when(
matching_death_between(asthma_icd10, index_date, end_date_out)
Expand All @@ -180,7 +151,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
out_date_asthma=minimum_of(
tmp_out_date_asthma_snomed,
tmp_out_date_asthma_apc,
tmp_out_date_asthma_opa,
tmp_out_date_asthma_death
)

Expand All @@ -198,12 +168,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
).admission_date
)

tmp_out_date_copd_opa= (
first_matching_event_opa_between(
copd_icd10, index_date, end_date_out
).appointment_date
)

tmp_out_date_copd_death= case(
when(
matching_death_between(copd_icd10, index_date, end_date_out)
Expand All @@ -213,7 +177,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
out_date_copd=minimum_of(
tmp_out_date_copd_ctv3,
tmp_out_date_copd_apc,
tmp_out_date_copd_opa,
tmp_out_date_copd_death
)

Expand All @@ -231,12 +194,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
).admission_date
)

tmp_out_date_pulmonary_fibrosis_opa= (
first_matching_event_opa_between(
pulmonary_fibrosis_icd10, index_date, end_date_out
).appointment_date
)

tmp_out_date_pulmonary_fibrosis_death= case(
when(
matching_death_between(pulmonary_fibrosis_icd10, index_date, end_date_out)
Expand All @@ -246,7 +203,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
out_date_pulmonary_fibrosis=minimum_of(
tmp_out_date_pulmonary_fibrosis_snomed,
tmp_out_date_pulmonary_fibrosis_apc,
tmp_out_date_pulmonary_fibrosis_opa,
tmp_out_date_pulmonary_fibrosis_death
)

Expand Down Expand Up @@ -287,40 +243,20 @@ def generate_variables(index_date, end_date_exp, end_date_out):
.exists_for_patient()
)

tmp_sub_bin_priorcovid19_confirmed_opa = (
opa_diag.where(
((opa_diag.primary_diagnosis_code.is_in(covid_codes)) | (opa_diag.secondary_diagnosis_code_1.is_in(covid_codes))) &
(opa_diag.appointment_date.is_before(index_date))
)
.exists_for_patient()
)

## 2. Covid-19 severity

### SUS
### SUS (primary diagnosis only)

tmp_sub_date_severecovid19_apc = (
sub_date_covid19_hospital = (
apcs.where(
((apcs.primary_diagnosis.is_in(covid_codes)) | (apcs.secondary_diagnosis.is_in(covid_codes))) &
(apcs.primary_diagnosis.is_in(covid_codes)) &
(apcs.admission_date.is_on_or_after(index_date))
)
.sort_by(apcs.admission_date)
.first_for_patient()
.admission_date
)

tmp_sub_date_severecovid19_opa = (
opa_diag.where(
((opa_diag.primary_diagnosis_code.is_in(covid_codes)) | (opa_diag.secondary_diagnosis_code_1.is_in(covid_codes))) &
(opa_diag.appointment_date.is_on_or_after(index_date))
)
.sort_by(opa_diag.appointment_date)
.first_for_patient()
.appointment_date
)

sub_date_covid19_hospital = minimum_of(tmp_sub_date_severecovid19_apc, tmp_sub_date_severecovid19_opa)

## 3. Smoking status

tmp_most_recent_smoking_cat = (
Expand Down Expand Up @@ -353,7 +289,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
tmp_exp_date_covid19_confirmed_sgss=tmp_exp_date_covid19_confirmed_sgss,
tmp_exp_date_covid19_confirmed_snomed=tmp_exp_date_covid19_confirmed_snomed,
tmp_exp_date_covid19_confirmed_apc=tmp_exp_date_covid19_confirmed_apc,
tmp_exp_date_covid19_confirmed_opa=tmp_exp_date_covid19_confirmed_opa,
tmp_exp_date_death=tmp_exp_date_death,
tmp_exp_covid19_confirmed_death=tmp_exp_covid19_confirmed_death,
tmp_exp_date_covid19_confirmed_death=tmp_exp_date_covid19_confirmed_death,
Expand Down Expand Up @@ -384,9 +319,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
).exists_for_patient()) |
(first_matching_event_apc_between(
asthma_icd10, index_date-days(730), index_date-days(1)
).exists_for_patient()) |
(first_matching_event_opa_between(
asthma_icd10, index_date-days(730), index_date-days(1)
).exists_for_patient())
),

Expand All @@ -397,9 +329,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
).exists_for_patient()) |
(last_matching_event_apc_before(
copd_icd10, index_date
).exists_for_patient()) |
(last_matching_event_opa_before(
copd_icd10, index_date
).exists_for_patient())
),

Expand Down Expand Up @@ -466,9 +395,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
).exists_for_patient()) |
(last_matching_event_apc_before(
bmi_obesity_icd10, index_date
).exists_for_patient()) |
(last_matching_event_opa_before(
bmi_obesity_icd10, index_date
).exists_for_patient())
),

Expand Down Expand Up @@ -497,9 +423,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
).exists_for_patient()) |
(last_matching_event_apc_before(
ami_icd10 + ami_prior_icd10, index_date
).exists_for_patient()) |
(last_matching_event_opa_before(
ami_icd10 + ami_prior_icd10, index_date
).exists_for_patient())
),

Expand All @@ -513,9 +436,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
).exists_for_patient()) |
(last_matching_event_apc_before(
dementia_icd10 + dementia_vascular_icd10, index_date
).exists_for_patient()) |
(last_matching_event_opa_before(
dementia_icd10 + dementia_vascular_icd10, index_date
).exists_for_patient())
),

Expand All @@ -526,9 +446,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
).exists_for_patient()) |
(last_matching_event_apc_before(
liver_disease_icd10, index_date
).exists_for_patient()) |
(last_matching_event_opa_before(
liver_disease_icd10, index_date
).exists_for_patient())
),

Expand All @@ -539,9 +456,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
).exists_for_patient()) |
(last_matching_event_apc_before(
ckd_icd10, index_date
).exists_for_patient()) |
(last_matching_event_opa_before(
ckd_icd10, index_date
).exists_for_patient())
),

Expand All @@ -552,9 +466,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
).exists_for_patient()) |
(last_matching_event_apc_before(
cancer_icd10, index_date
).exists_for_patient()) |
(last_matching_event_opa_before(
cancer_icd10, index_date
).exists_for_patient())
),

Expand All @@ -571,9 +482,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
).exists_for_patient()) |
(last_matching_event_apc_before(
hypertension_icd10, index_date
).exists_for_patient()) |
(last_matching_event_opa_before(
hypertension_icd10, index_date
).exists_for_patient())
),

Expand All @@ -587,9 +495,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
).exists_for_patient()) |
(last_matching_event_apc_before(
diabetes_icd10, index_date
).exists_for_patient()) |
(last_matching_event_opa_before(
diabetes_icd10, index_date
).exists_for_patient())
),

Expand All @@ -600,9 +505,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
).exists_for_patient()) |
(last_matching_event_apc_before(
depression_icd10, index_date
).exists_for_patient()) |
(last_matching_event_opa_before(
depression_icd10, index_date
).exists_for_patient())
),

Expand All @@ -613,9 +515,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
).exists_for_patient()) |
(last_matching_event_apc_before(
pneumonia_icd10, index_date
).exists_for_patient()) |
(last_matching_event_opa_before(
pneumonia_icd10, index_date
).exists_for_patient())
),

Expand All @@ -626,9 +525,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
).exists_for_patient()) |
(last_matching_event_apc_before(
asthma_icd10, index_date
).exists_for_patient()) |
(last_matching_event_opa_before(
asthma_icd10, index_date
).exists_for_patient())
),

Expand All @@ -639,9 +535,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
).exists_for_patient()) |
(last_matching_event_apc_before(
pulmonary_fibrosis_icd10, index_date
).exists_for_patient()) |
(last_matching_event_opa_before(
pulmonary_fibrosis_icd10, index_date
).exists_for_patient())
),

Expand All @@ -652,9 +545,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
).exists_for_patient()) |
(last_matching_event_apc_before(
copd_icd10, index_date
).exists_for_patient()) |
(last_matching_event_opa_before(
copd_icd10, index_date
).exists_for_patient())
),

Expand All @@ -665,9 +555,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
).exists_for_patient()) |
(last_matching_event_apc_before(
stroke_isch_icd10, index_date
).exists_for_patient()) |
(last_matching_event_opa_before(
stroke_isch_icd10, index_date
).exists_for_patient())
),

Expand All @@ -677,12 +564,10 @@ def generate_variables(index_date, end_date_exp, end_date_out):
tmp_sub_bin_priorcovid19_confirmed_sgss=tmp_sub_bin_priorcovid19_confirmed_sgss,
tmp_sub_bin_priorcovid19_confirmed_snomed=tmp_sub_bin_priorcovid19_confirmed_snomed,
tmp_sub_bin_priorcovid19_confirmed_apc=tmp_sub_bin_priorcovid19_confirmed_apc,
tmp_sub_bin_priorcovid19_confirmed_opa=tmp_sub_bin_priorcovid19_confirmed_opa,
sub_bin_covid19_confirmed_history=(
tmp_sub_bin_priorcovid19_confirmed_sgss |
tmp_sub_bin_priorcovid19_confirmed_snomed |
tmp_sub_bin_priorcovid19_confirmed_apc |
tmp_sub_bin_priorcovid19_confirmed_opa
tmp_sub_bin_priorcovid19_confirmed_apc
),

## Covid_19 severity
Expand Down Expand Up @@ -735,9 +620,6 @@ def generate_variables(index_date, end_date_exp, end_date_out):
(last_matching_event_apc_before(
prostate_cancer_icd10, index_date
).exists_for_patient()) |
(last_matching_event_opa_before(
prostate_cancer_icd10, index_date
).exists_for_patient()) |
(matching_death_before(
prostate_cancer_icd10, index_date
))
Expand Down

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