#' Function to get ICD data for calculating elixhauser scores
#' Updated: 2021-10-01
#' @param drug_concept_id A string
#' @param biomarker_concept_id A string
#' @param table_name A string
#' @param table_type A string, either c("covariates", "drugs", "biomarkers", "icds")
#' @param ancestor_table A string, eg, "antihypertensive_drugs_ancestor_tbl_20210308151236"
#' @param conn A variable
#' @export
netezza_query_icds <- function(drug_concept_id, biomarker_concept_id, table_name, table_type, ancestor_table, conn,...) {
sql_query <- glue::glue("
(
WITH pw_codesets AS
(
SELECT s3.codeset_id, s3.concept_id, s3.concept_name
FROM (
(SELECT 1 as codeset_id, s1.concept_id, s1.concept_name
FROM (
SELECT t1.concept_id, t1.concept_name
FROM (SELECT * FROM v_concept WHERE domain_id = 'Drug') t1
INNER JOIN (SELECT * FROM v_concept_ancestor WHERE ancestor_concept_id = {drug_concept_id}) t2
ON (t1.concept_id = t2.DESCENDANT_CONCEPT_ID)
GROUP BY t1.concept_id, t1.concept_name
) s1)
UNION DISTINCT
(SELECT 2 as codeset_id, s2.concept_id, s2.concept_name
FROM (
SELECT t1.concept_id, t1.concept_name
FROM (SELECT * FROM v_concept WHERE domain_id = 'Measurement') t1
INNER JOIN (SELECT * FROM v_concept_ancestor WHERE ancestor_concept_id = {biomarker_concept_id}) t2
ON (t1.concept_id = t2.DESCENDANT_CONCEPT_ID)
GROUP BY t1.concept_id, t1.concept_name
) s2)) s3
),
pw_index_date AS
(
SELECT s1.person_id,
{drug_concept_id} as drug_concept_id,
s1.drug_exposure_start_date
FROM (
(SELECT s2.person_id, s2.drug_concept_id, s3.concept_name as drug_concept_name, s2.drug_exposure_start_date
FROM (SELECT * FROM v_drug_exposure) s2
INNER JOIN (SELECT concept_id, concept_name FROM pw_codesets WHERE codeset_id = 1) s3
ON (s2.drug_concept_id = s3.concept_id))
) s1
),
pw_obsperiod AS
(
SELECT s1.person_id,
s1.drug_concept_id,
min(s1.drug_exposure_start_date) as first_drug_exposure,
max(s1.drug_exposure_start_date) as last_drug_exposure
FROM (
(SELECT s2.person_id, s2.drug_concept_id, s2.drug_exposure_start_date
FROM (SELECT * FROM pw_index_date) s2
INNER JOIN (SELECT * FROM v_visit_occurrence WHERE visit_concept_id = 9202) s3
ON (s2.person_id = s3.person_id AND s2.drug_exposure_start_date = s3.visit_start_date))
) s1
GROUP BY s1.person_id, s1.drug_concept_id
),
pw_start_end AS
(
SELECT s1.person_id,
s1.drug_concept_id,
add_months(s1.first_drug_exposure, -12) as start_date,
add_months(s1.first_drug_exposure, 12) as end_date
FROM (SELECT * FROM pw_obsperiod) s1
),
pw_icds AS
(
SELECT s1.person_id, s2.concept_code, s1.condition_date, s2.vocabulary_id
FROM (SELECT person_id,
condition_source_concept_id,
condition_source_value,
condition_start_date as condition_date
FROM V_CONDITION_OCCURRENCE
) s1
INNER JOIN (SELECT * FROM pw_elixhauser_codes) s2
ON (s1.condition_source_concept_id = s2.concept_id)
GROUP BY s1.person_id, s2.concept_code, s1.condition_date, s2.vocabulary_id
),
pw_icds_selected AS
(
SELECT s1.person_id, s1.condition_date, s1.concept_code, s1.vocabulary_id
FROM (SELECT * FROM pw_icds) s1
INNER JOIN (SELECT * FROM pw_start_end) s2
ON (s1.person_id = s2.person_id AND
s1.condition_date >= s2.start_date AND
s1.condition_date <= s2.end_date)
GROUP BY s1.person_id, s1.condition_date, s1.concept_code, s1.vocabulary_id
),
pw_icds_op AS
(
SELECT s1.person_id, s1.concept_code, s1.condition_date, s1.vocabulary_id
FROM (
SELECT s2.person_id, s2.concept_code, s2.condition_date, s2.vocabulary_id
FROM (SELECT * FROM pw_icds_selected) s2
INNER JOIN (SELECT * FROM v_visit_occurrence WHERE visit_concept_id = 9202) s3
ON (s2.person_id = s3.person_id AND s2.condition_date = s3.visit_start_date)
GROUP BY s2.person_id, s2.concept_code, s2.condition_date, s2.vocabulary_id
) s1
)
select * from pw_icds_op);", .con = conn)
return(sql_query)
}
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