Add comorbidity suspecting logic for HCC 37 - Diabetes with Chronic C…

…omplications (#426)

* Add new value sets seed

* Add new comorbidity model

* Add list rollup model

* Update seed name

* Rename column

* Fix hcc

* Update dbt docs

* Add function to cast string to resolve redshift error

* Bump package version

* Refactor comorbidity table

* update dbt docs

dbt_project.yml

@@ -1,5 +1,5 @@
 name: 'the_tuva_project'
-version: '0.7.12'
+version: '0.7.13'
 config-version: 2
 require-dbt-version: ">=1.3.0"
 

models/hcc_suspecting/final/hcc_suspecting__list.sql

@@ -10,21 +10,52 @@ with hcc_history_suspects as (
         , data_source
         , hcc_code
         , hcc_description
-        , 'Prior coding history' as reason
+        , cast('Prior coding history' as {{ dbt.type_string() }}) as reason
         , icd_10_cm_code
             || case
                 when last_billed is not null then ' last billed on ' || last_billed
                 when last_billed is null and last_recorded is not null then ' last recorded on ' || last_recorded
                 else ' (missing recorded and billing dates) '
           end as contributing_factor
+        , coalesce(last_billed, last_recorded) as condition_date
     from {{ ref('hcc_suspecting__int_patient_hcc_history') }}
     where current_year_billed = false
 
 )
 
+, comorbidity_suspects as (
+
+    select distinct
+          patient_id
+        , data_source
+        , hcc_code
+        , hcc_description
+        , cast('Comorbidity suspect' as {{ dbt.type_string() }}) as reason
+        , condition_1_concept_name
+            || ' ('
+            || condition_1_code
+            || ' on '
+            || condition_1_recorded_date
+            || ')'
+            || ' and '
+            || condition_2_concept_name
+            || ' ('
+            || condition_2_code
+            || ' on '
+            || condition_2_recorded_date
+            || ')'
+          as contributing_factor
+        , condition_1_recorded_date as condition_date
+    from {{ ref('hcc_suspecting__int_comorbidity_suspects') }}
+    where current_year_billed = false
+
+)
+
 , unioned as (
 
     select * from hcc_history_suspects
+    union all
+    select * from comorbidity_suspects
 
 )
 
@@ -37,6 +68,7 @@ with hcc_history_suspects as (
         , cast(hcc_description as {{ dbt.type_string() }}) as hcc_description
         , cast(reason as {{ dbt.type_string() }}) as reason
         , cast(contributing_factor as {{ dbt.type_string() }}) as contributing_factor
+        , cast(condition_date as date) as condition_date
     from unioned
 
 )
@@ -48,5 +80,6 @@ select
     , hcc_description
     , reason
     , contributing_factor
+    , condition_date
     , '{{ var('tuva_last_run')}}' as tuva_last_run
 from add_data_types

models/hcc_suspecting/final/hcc_suspecting__list_rollup.sql

@@ -0,0 +1,61 @@
+{{ config(
+     enabled = var('hcc_suspecting_enabled',var('claims_enabled',var('clinical_enabled',var('tuva_marts_enabled',False)))) | as_bool
+   )
+}}
+
+with list as (
+
+    select
+          patient_id
+        , data_source
+        , hcc_code
+        , hcc_description
+        , reason
+        , contributing_factor
+        , condition_date
+        , row_number() over (
+            partition by
+                  patient_id
+                , hcc_code
+            order by condition_date desc
+          ) as row_num
+    from {{ ref('hcc_suspecting__list') }}
+
+)
+
+, list_dedupe as (
+
+    select
+          patient_id
+        , hcc_code
+        , hcc_description
+        , reason
+        , contributing_factor
+        , condition_date as latest_condition_date
+    from list
+    where row_num = 1
+
+)
+
+, add_data_types as (
+
+    select
+          cast(patient_id as {{ dbt.type_string() }}) as patient_id
+        , cast(hcc_code as {{ dbt.type_string() }}) as hcc_code
+        , cast(hcc_description as {{ dbt.type_string() }}) as hcc_description
+        , cast(reason as {{ dbt.type_string() }}) as reason
+        , cast(contributing_factor as {{ dbt.type_string() }}) as contributing_factor
+        , cast(latest_condition_date as date) as latest_condition_date
+    from list_dedupe
+
+)
+
+select
+      patient_id
+    , hcc_code
+    , hcc_description
+    , reason
+    , contributing_factor
+    , latest_condition_date
+    , '{{ var('tuva_last_run')}}' as tuva_last_run
+from add_data_types

models/hcc_suspecting/hcc_suspecting_models.yml

@@ -10,8 +10,9 @@ models:
       tags: hcc_suspecting
       materialized: table
     description: >
-      This final model displays the list of suspecting conditions per patient 
-      with the reason and contributing factors.
+      This final model displays the list of suspecting conditions per patient, 
+      data_source, hcc, and diagnosis code with the reason and contributing 
+      factors.
     columns:
       - name: patient_id
         description: Unique ID for the patient.
@@ -32,6 +33,39 @@ models:
       - name: contributing_factor
         description: >
           Description of the contributing factor(s) for the suspecting condition.
+      - name: condition_date
+        description: Date when the condition was recorded or billed.
+      - name: tuva_last_run
+        description: The date the model was run.
+
+  - name: hcc_suspecting__list_rollup
+    config:
+      schema: |
+        {%- if var('tuva_schema_prefix',None) != None -%}{{var('tuva_schema_prefix')}}_hcc_suspecting{% else %}hcc_suspecting{%- endif -%}
+      alias: list_rollup
+      tags: hcc_suspecting
+      materialized: table
+    description: >
+      This final model displays the list of suspecting conditions per patient 
+      and hcc with the latest contributing factor rolled up.
+    columns:
+      - name: patient_id
+        description: Unique ID for the patient.
+      - name: hcc_code
+        description: >
+          HCC code from the latest CMS HCC model available in the mart.
+        meta:
+          terminology: https://github.com/tuva-health/tuva/blob/main/seeds/value_sets/hcc_suspecting/hcc_suspecting__hcc_descriptions.csv
+      - name: hcc_description
+        description: >
+          HCC description from the latest CMS HCC model available in the mart.
+      - name: reason
+        description: Standardized reason for the suspecting condition.
+      - name: contributing_factor
+        description: >
+          Description of the contributing factor(s) for the suspecting condition.
+      - name: latest_condition_date
+        description: Date when the condition was recorded or billed.
       - name: tuva_last_run
         description: The date the model was run.
 
@@ -91,6 +125,42 @@ models:
       - name: tuva_last_run
         description: The date the model was run.
 
+  - name: hcc_suspecting__int_comorbidity_suspects
+    config:
+      schema: |
+        {%- if var('tuva_schema_prefix',None) != None -%}{{var('tuva_schema_prefix')}}_hcc_suspecting{% else %}hcc_suspecting{%- endif -%}
+      alias: _int_comorbidity_suspects
+      tags: hcc_suspecting
+      materialized: table
+    description: Comorbidity suspecting conditions.
+    columns:
+      - name: patient_id
+        description: Unique ID for the patient.
+      - name: data_source
+        description: >
+          User-configured field that indicates the data source (e.g. typically 
+          named after the payer and state "BCBS Tennessee").
+      - name: hcc_code
+        description: >
+          HCC code from the latest CMS HCC model available in the mart.
+        meta:
+          terminology: https://github.com/tuva-health/tuva/blob/main/seeds/value_sets/hcc_suspecting/hcc_suspecting__hcc_descriptions.csv
+      - name: hcc_description
+        description: >
+          HCC description from the latest CMS HCC model available in the mart.
+      - name: reason
+        description: Standardized reason for the suspecting condition.
+      - name: contributing_factor
+        description: >
+          Description of the contributing factor(s) for the suspecting condition.
+      - name: condition_date
+        description: Date when the condition was recorded or billed.
+      - name: current_year_billed
+        description: >
+          Flag indicating that the HCC has been billed during the payment year.
+      - name: tuva_last_run
+        description: The date the model was run.
+
   - name: hcc_suspecting__int_patient_hcc_history
     config:
       schema: |
@@ -134,8 +204,8 @@ models:
           condition_type <> 'problem').
       - name: current_year_billed
         description: >
-          Flag indicating that the ICD-10-CM code mapped to the HCC was billed
-          during the payment year.
+          Flag indicating that the ICD-10-CM code mapped to the HCC has been
+          billed during the payment year.
       - name: tuva_last_run
         description: The date the model was run.