Merge branch 'mimic-time-series' into mimic

Author: myyong

config_story.yaml

@@ -103,6 +103,68 @@ src-stats:
               m.visit_occurrence_id,
               v.visit_start_datetime,
               v.visit_end_datetime) subquery;
+  - name: bp_sys_relative_change_stats
+    #For each patient + visit + BP type, sort measurements in time,
+    #compute |xₜ − xₜ₋₁| / xₜ₋₁ for each step,
+    #then average those within that visit.
+    #Finally, average that visit-level metric across the population.
+    query: >
+      WITH bp AS (
+          SELECT
+              p.person_id,
+              p.gender_concept_id,
+              v.visit_occurrence_id,
+              EXTRACT(YEAR FROM v.visit_start_datetime) - p.year_of_birth AS age,
+              m.measurement_concept_id,
+              m.value_as_number,
+              m.measurement_datetime
+          FROM mimic.person p
+          JOIN mimic.visit_occurrence v
+              ON p.person_id = v.person_id
+          JOIN mimic.measurement m
+              ON m.visit_occurrence_id = v.visit_occurrence_id
+          WHERE m.measurement_concept_id IN (21492239)  -- systolic
+      ),
+      bp_with_lag AS (
+          SELECT
+              bp.*,
+              LAG(value_as_number) OVER (
+                  PARTITION BY person_id, visit_occurrence_id, measurement_concept_id
+                  ORDER BY measurement_datetime
+              ) AS prev_value
+          FROM bp
+      ),
+      visit_level_rel_var AS (
+          SELECT
+              person_id,
+              gender_concept_id,
+              age,
+              visit_occurrence_id,
+              measurement_concept_id,
+              -- average relative change within this visit
+              AVG( ABS(value_as_number - prev_value)
+                   / NULLIF(prev_value, 0) ) AS avg_rel_var
+          FROM bp_with_lag
+          WHERE prev_value IS NOT NULL          -- skip first measurement in each visit
+          GROUP BY
+              person_id,
+              gender_concept_id,
+              age,
+              visit_occurrence_id,
+              measurement_concept_id
+      )
+      SELECT
+          gender_concept_id,
+          AVG(CASE WHEN measurement_concept_id = 21492239 AND age > 60
+                   THEN avg_rel_var END)::float4 AS avg_over_60_systolic_rel_var,
+          AVG(CASE WHEN measurement_concept_id = 21492239 AND age <= 60
+                   THEN avg_rel_var END)::float4  AS avg_under_60_systolic_rel_var,
+          STDDEV(CASE WHEN measurement_concept_id = 21492239 AND age > 60
+                      THEN avg_rel_var END)::float4  AS stddev_over_60_systolic_rel_var,
+          STDDEV(CASE WHEN measurement_concept_id = 21492239 AND age <= 60
+                      THEN avg_rel_var END)::float4 AS stddev_under_60_systolic_rel_var
+      FROM visit_level_rel_var
+      GROUP BY gender_concept_id;
 tables:
   person:
     num_rows_per_pass: 0