diff --git a/mimic-iv/concepts_postgres/comorbidity/first_day_lab.sql b/mimic-iv/concepts_postgres/comorbidity/first_day_lab.sql deleted file mode 100644 index 54ec040f..00000000 --- a/mimic-iv/concepts_postgres/comorbidity/first_day_lab.sql +++ /dev/null @@ -1,167 +0,0 @@ -DROP TABLE IF EXISTS .first_day_lab; CREATE TABLE .first_day_lab AS -WITH cbc AS -( - SELECT - ie.stay_id - , MIN(hematocrit) as hematocrit_min - , MAX(hematocrit) as hematocrit_max - , MIN(hemoglobin) as hemoglobin_min - , MAX(hemoglobin) as hemoglobin_max - , MIN(platelet) as platelets_min - , MAX(platelet) as platelets_max - , MIN(wbc) as wbc_min - , MAX(wbc) as wbc_max - FROM mimiciv_icu.icustays ie - LEFT JOIN mimiciv_derived.complete_blood_count le - ON le.subject_id = ie.subject_id - AND le.charttime >= DATETIME_SUB(ie.intime, INTERVAL '6' HOUR) - AND le.charttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY) - GROUP BY ie.stay_id -) -, chem AS -( - SELECT - ie.stay_id - , MIN(albumin) AS albumin_min, MAX(albumin) AS albumin_max - , MIN(globulin) AS globulin_min, MAX(globulin) AS globulin_max - , MIN(total_protein) AS total_protein_min, MAX(total_protein) AS total_protein_max - , MIN(aniongap) AS aniongap_min, MAX(aniongap) AS aniongap_max - , MIN(bicarbonate) AS bicarbonate_min, MAX(bicarbonate) AS bicarbonate_max - , MIN(bun) AS bun_min, MAX(bun) AS bun_max - , MIN(calcium) AS calcium_min, MAX(calcium) AS calcium_max - , MIN(chloride) AS chloride_min, MAX(chloride) AS chloride_max - , MIN(creatinine) AS creatinine_min, MAX(creatinine) AS creatinine_max - , MIN(glucose) AS glucose_min, MAX(glucose) AS glucose_max - , MIN(sodium) AS sodium_min, MAX(sodium) AS sodium_max - , MIN(potassium) AS potassium_min, MAX(potassium) AS potassium_max - FROM mimiciv_icu.icustays ie - LEFT JOIN mimiciv_derived.chemistry le - ON le.subject_id = ie.subject_id - AND le.charttime >= DATETIME_SUB(ie.intime, INTERVAL '6' HOUR) - AND le.charttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY) - GROUP BY ie.stay_id -) -, diff AS -( - SELECT - ie.stay_id - , MIN(basophils_abs) AS basophils_abs_min, MAX(basophils_abs) AS basophils_abs_max - , MIN(eosinophils_abs) AS eosinophils_abs_min, MAX(eosinophils_abs) AS eosinophils_abs_max - , MIN(lymphocytes_abs) AS lymphocytes_abs_min, MAX(lymphocytes_abs) AS lymphocytes_abs_max - , MIN(monocytes_abs) AS monocytes_abs_min, MAX(monocytes_abs) AS monocytes_abs_max - , MIN(neutrophils_abs) AS neutrophils_abs_min, MAX(neutrophils_abs) AS neutrophils_abs_max - , MIN(atypical_lymphocytes) AS atypical_lymphocytes_min, MAX(atypical_lymphocytes) AS atypical_lymphocytes_max - , MIN(bands) AS bands_min, MAX(bands) AS bands_max - , MIN(immature_granulocytes) AS immature_granulocytes_min, MAX(immature_granulocytes) AS immature_granulocytes_max - , MIN(metamyelocytes) AS metamyelocytes_min, MAX(metamyelocytes) AS metamyelocytes_max - , MIN(nrbc) AS nrbc_min, MAX(nrbc) AS nrbc_max - FROM mimiciv_icu.icustays ie - LEFT JOIN mimiciv_derived.blood_differential le - ON le.subject_id = ie.subject_id - AND le.charttime >= DATETIME_SUB(ie.intime, INTERVAL '6' HOUR) - AND le.charttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY) - GROUP BY ie.stay_id -) -, coag AS -( - SELECT - ie.stay_id - , MIN(d_dimer) AS d_dimer_min, MAX(d_dimer) AS d_dimer_max - , MIN(fibrinogen) AS fibrinogen_min, MAX(fibrinogen) AS fibrinogen_max - , MIN(thrombin) AS thrombin_min, MAX(thrombin) AS thrombin_max - , MIN(inr) AS inr_min, MAX(inr) AS inr_max - , MIN(pt) AS pt_min, MAX(pt) AS pt_max - , MIN(ptt) AS ptt_min, MAX(ptt) AS ptt_max - FROM mimiciv_icu.icustays ie - LEFT JOIN mimiciv_derived.coagulation le - ON le.subject_id = ie.subject_id - AND le.charttime >= DATETIME_SUB(ie.intime, INTERVAL '6' HOUR) - AND le.charttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY) - GROUP BY ie.stay_id -) -, enz AS -( - SELECT - ie.stay_id - - , MIN(alt) AS alt_min, MAX(alt) AS alt_max - , MIN(alp) AS alp_min, MAX(alp) AS alp_max - , MIN(ast) AS ast_min, MAX(ast) AS ast_max - , MIN(amylase) AS amylase_min, MAX(amylase) AS amylase_max - , MIN(bilirubin_total) AS bilirubin_total_min, MAX(bilirubin_total) AS bilirubin_total_max - , MIN(bilirubin_direct) AS bilirubin_direct_min, MAX(bilirubin_direct) AS bilirubin_direct_max - , MIN(bilirubin_indirect) AS bilirubin_indirect_min, MAX(bilirubin_indirect) AS bilirubin_indirect_max - , MIN(ck_cpk) AS ck_cpk_min, MAX(ck_cpk) AS ck_cpk_max - , MIN(ck_mb) AS ck_mb_min, MAX(ck_mb) AS ck_mb_max - , MIN(ggt) AS ggt_min, MAX(ggt) AS ggt_max - , MIN(ld_ldh) AS ld_ldh_min, MAX(ld_ldh) AS ld_ldh_max - FROM mimiciv_icu.icustays ie - LEFT JOIN mimiciv_derived.enzyme le - ON le.subject_id = ie.subject_id - AND le.charttime >= DATETIME_SUB(ie.intime, INTERVAL '6' HOUR) - AND le.charttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY) - GROUP BY ie.stay_id -) -SELECT -ie.subject_id -, ie.stay_id --- complete blood count -, hematocrit_min, hematocrit_max -, hemoglobin_min, hemoglobin_max -, platelets_min, platelets_max -, wbc_min, wbc_max --- chemistry -, albumin_min, albumin_max -, globulin_min, globulin_max -, total_protein_min, total_protein_max -, aniongap_min, aniongap_max -, bicarbonate_min, bicarbonate_max -, bun_min, bun_max -, calcium_min, calcium_max -, chloride_min, chloride_max -, creatinine_min, creatinine_max -, glucose_min, glucose_max -, sodium_min, sodium_max -, potassium_min, potassium_max --- blood differential -, basophils_abs_min, basophils_abs_max -, eosinophils_abs_min, eosinophils_abs_max -, lymphocytes_abs_min, lymphocytes_abs_max -, monocytes_abs_min, monocytes_abs_max -, neutrophils_abs_min, neutrophils_abs_max -, atypical_lymphocytes_min, atypical_lymphocytes_max -, bands_min, bands_max -, immature_granulocytes_min, immature_granulocytes_max -, metamyelocytes_min, metamyelocytes_max -, nrbc_min, nrbc_max --- coagulation -, d_dimer_min, d_dimer_max -, fibrinogen_min, fibrinogen_max -, thrombin_min, thrombin_max -, inr_min, inr_max -, pt_min, pt_max -, ptt_min, ptt_max --- enzymes and bilirubin -, alt_min, alt_max -, alp_min, alp_max -, ast_min, ast_max -, amylase_min, amylase_max -, bilirubin_total_min, bilirubin_total_max -, bilirubin_direct_min, bilirubin_direct_max -, bilirubin_indirect_min, bilirubin_indirect_max -, ck_cpk_min, ck_cpk_max -, ck_mb_min, ck_mb_max -, ggt_min, ggt_max -, ld_ldh_min, ld_ldh_max -FROM mimiciv_icu.icustays ie -LEFT JOIN cbc - ON ie.stay_id = cbc.stay_id -LEFT JOIN chem - ON ie.stay_id = chem.stay_id -LEFT JOIN diff - ON ie.stay_id = diff.stay_id -LEFT JOIN coag - ON ie.stay_id = coag.stay_id -LEFT JOIN enz - ON ie.stay_id = enz.stay_id -; diff --git a/mimic-iv/concepts_postgres/measurement/kdigo_uo.sql b/mimic-iv/concepts_postgres/measurement/kdigo_uo.sql deleted file mode 100644 index 645a970d..00000000 --- a/mimic-iv/concepts_postgres/measurement/kdigo_uo.sql +++ /dev/null @@ -1,2 +0,0 @@ -DROP TABLE IF EXISTS kdigo_uo; CREATE TABLE kdigo_uo AS -DROP TABLE IF EXISTS kdigo_uo; CREATE TABLE kdigo_uo AS diff --git a/mimic-iv/concepts_postgres/postgres-make-concepts.sql b/mimic-iv/concepts_postgres/postgres-make-concepts.sql index 3bbed1e3..de4ec2a9 100644 --- a/mimic-iv/concepts_postgres/postgres-make-concepts.sql +++ b/mimic-iv/concepts_postgres/postgres-make-concepts.sql @@ -49,6 +49,7 @@ SET search_path TO mimiciv_derived, mimiciv_hosp, mimiciv_icu, mimiciv_ed; -- medication \i medication/acei.sql \i medication/antibiotic.sql +\i medication/arb.sql \i medication/dobutamine.sql \i medication/dopamine.sql \i medication/epinephrine.sql