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Viv3ckj/update ethnicity #28

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merged 5 commits into from
Oct 9, 2024
Merged

Viv3ckj/update ethnicity #28

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90a6e1d
Add ethnicity_from_sus codes for missing ethnicities
viv3ckj Oct 8, 2024
4d09d05
Modularize combined ethnicity query
milanwiedemann Oct 8, 2024
c2709c9
Merge pull request #29 from opensafely/milanwiedemann/idea-for-ethnic…
milanwiedemann Oct 8, 2024
b4d96b7
Merge branch 'viv3ckj/update-viz' into viv3ckj/update-measures
milanwiedemann Oct 8, 2024
ee35ab8
Merge branch 'viv3ckj/update-viz' into viv3ckj/update-measures
milanwiedemann Oct 9, 2024
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45 changes: 36 additions & 9 deletions analysis/measures_definition_pf_codes_conditions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
practice_registrations,
patients,
addresses,
ethnicity_from_sus,
)
from codelists import pharmacy_first_conditions_codelist, ethnicity_codelist

Expand All @@ -27,23 +28,49 @@

registration = practice_registrations.for_patient_on(INTERVAL.end_date)

latest_ethnicity_category_num = (
latest_ethnicity_from_codes_category_num = (
clinical_events.where(clinical_events.snomedct_code.is_in(ethnicity_codelist))
.where(clinical_events.date.is_on_or_before(INTERVAL.start_date))
.sort_by(clinical_events.date)
.last_for_patient()
.snomedct_code.to_category(ethnicity_codelist)
)

latest_ethnicity_category_desc = case(
when(latest_ethnicity_category_num == "1").then("White"),
when(latest_ethnicity_category_num == "2").then("Mixed"),
when(latest_ethnicity_category_num == "3").then("Asian or Asian British"),
when(latest_ethnicity_category_num == "4").then("Black or Black British"),
when(latest_ethnicity_category_num == "5").then("Chinese or Other Ethnic Groups"),
when(latest_ethnicity_category_num.is_null()).then("Missing"),
latest_ethnicity_from_codes = case(
when(latest_ethnicity_from_codes_category_num == "1").then("White"),
when(latest_ethnicity_from_codes_category_num == "2").then("Mixed"),
when(latest_ethnicity_from_codes_category_num == "3").then(
"Asian or Asian British"
),
when(latest_ethnicity_from_codes_category_num == "4").then(
"Black or Black British"
),
when(latest_ethnicity_from_codes_category_num == "5").then(
"Chinese or Other Ethnic Groups"
),
)

ethnicity_from_sus = case(
when(ethnicity_from_sus.code.is_in(["A", "B", "C"])).then("White"),
when(ethnicity_from_sus.code.is_in(["D", "E", "F", "G"])).then("Mixed"),
when(ethnicity_from_sus.code.is_in(["H", "J", "K", "L"])).then(
"Asian or Asian British"
),
when(ethnicity_from_sus.code.is_in(["M", "N", "P"])).then("Black or Black British"),
when(ethnicity_from_sus.code.is_in(["R", "S"])).then(
"Chinese or Other Ethnic Groups"
),
)

ethnicity_combined = case(
when(latest_ethnicity_from_codes.is_not_null()).then(latest_ethnicity_from_codes),
when(latest_ethnicity_from_codes.is_null() & ethnicity_from_sus.is_not_null()).then(
ethnicity_from_sus
),
otherwise="Missing",
)


# Age bands for age breakdown
age = patients.age_on(INTERVAL.start_date)
age_band = case(
Expand Down Expand Up @@ -85,7 +112,7 @@
"sex": patients.sex,
"imd": imd_quintile,
"region": latest_region,
"ethnicity": latest_ethnicity_category_desc,
"ethnicity": ethnicity_combined,
}

# Define the denominator as the number of patients registered
Expand Down