Indicators 46-61 (#51)

* indicators 46-61

* 62-63

* ind 63

---------

Co-authored-by: Patric Prado <pprado@caa.columbia.edu>

input/cql/HIVConceptsCustom.cql

@@ -71,4 +71,8 @@ code "viral load test": 'viral load test' from "missing concepts"
 code "delivery": 'delivery' from "missing concepts"
 code "tb treatment": 'tb treatment' from "missing concepts"
 code "ART medication": 'ART medication' from "missing concepts"
-code "DSD ART eligibility assessed" : 'DSD ART eligibility assessed' from "missing concepts"
+code "DSD ART eligibility assessed" : 'DSD ART eligibility assessed' from "missing concepts"
+code "syphilis test" : 'syphilis test' from "missing concepts"
+
+
+valueset "Antenatal care contact": 'http://fhir.org/guides/who/anc-cds/ValueSet/antenatal-care-contact'

input/cql/HIVConfig.cql

@@ -16,3 +16,6 @@ define "Intervention Interval":
 
 define "LTFU Days":
     28 days
+
+define "DSD Retention Interval":
+    12 months

input/cql/HIVElements.cql

@@ -2741,24 +2741,20 @@ define "Any STI syndrome diagnosed B.DE235 Observation":
 @activity: HIV.B23 Offer sexual and reproductive health services
 @description: Date of syphilis test
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "Syphilis test date B.DE249":
-  [Observation: Concepts."Syphilis test date - HIV.B.DE249"] O
-    where O.status in { 'final', 'amended', 'corrected' }
-define "Syphilis test date B.DE249 Value":
-  "Syphilis test date B.DE249" O
-  return O.value
+  [Procedure] P
+  where P.status = 'completed'
+  and P.code ~ ConceptsCustom."syphilis test"
 /* End of Syphilis test date B.DE249 */
 
 /*
 @dataElement: HIV.B.DE250 - Syphilis test result
 @activity: HIV.B23 Offer sexual and reproductive health services
 @description: Result from syphilis test
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "Syphilis test result B.DE250":
-  exists "Syphilis test result B.DE250 Observation"
-define "Syphilis test result B.DE250 Observation":
   [Observation: Concepts."Syphilis test result - HIV.B.DE250"] O
     where O.status in { 'final', 'amended', 'corrected' }
 /* End of Syphilis test result B.DE250 */
@@ -2768,14 +2764,9 @@ define "Syphilis test result B.DE250 Observation":
 @activity: HIV.B23 Offer sexual and reproductive health services
 @description: Test result is positive for syphilis
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "Positive B.DE251":
-  exists "Positive B.DE251 Condition"
-    or exists "Positive B.DE251 Observation"
-define "Positive B.DE251 Condition":
-  [Condition: Concepts."Positive - HIV.B.DE251"]
-define "Positive B.DE251 Observation":
-  "Syphilis test result B.DE250 Observation" O
+  "Syphilis test result B.DE250" O
     where O.status in { 'final', 'amended', 'corrected' }
       and O.value ~ Concepts."Positive - HIV.B.DE251"
 /* End of Positive B.DE251 */
@@ -2785,14 +2776,9 @@ define "Positive B.DE251 Observation":
 @activity: HIV.B23 Offer sexual and reproductive health services
 @description: Test result is negative for syphilis
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "Negative B.DE252":
-  exists "Negative B.DE252 Condition"
-    or exists "Negative B.DE252 Observation"
-define "Negative B.DE252 Condition":
-  [Condition: Concepts."Negative - HIV.B.DE252"]
-define "Negative B.DE252 Observation":
-  "Syphilis test result B.DE250 Observation" O
+  "Syphilis test result B.DE250" O
     where O.status in { 'final', 'amended', 'corrected' }
       and O.value ~ Concepts."Negative - HIV.B.DE252"
 /* End of Negative B.DE252 */
@@ -2802,14 +2788,9 @@ define "Negative B.DE252 Observation":
 @activity: HIV.B23 Offer sexual and reproductive health services
 @description: Test result is inconclusive
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "Inconclusive B.DE253":
-  exists "Inconclusive B.DE253 Condition"
-    or exists "Inconclusive B.DE253 Observation"
-define "Inconclusive B.DE253 Condition":
-  [Condition: Concepts."Inconclusive - HIV.B.DE253"]
-define "Inconclusive B.DE253 Observation":
-  "Syphilis test result B.DE250 Observation" O
+  "Syphilis test result B.DE250" O
     where O.status in { 'final', 'amended', 'corrected' }
       and O.value ~ Concepts."Inconclusive - HIV.B.DE253"
 /* End of Inconclusive B.DE253 */
@@ -10273,7 +10254,7 @@ define "Eligible for DSD ART":
 */
 
 define "Date DSD ART eligibility assessed":
-  [Procedure: CustomConcepts."DSD ART eligibility assessed"] P
+  [Procedure: ConceptsCustom."DSD ART eligibility assessed"] P
     where P.status in { 'completed' }
   return P.performed.toInterval()
 /* End of Date DSD ART eligibility assessed */
@@ -12219,7 +12200,7 @@ define "TB diagnostic test date":
 
 define "TB treatment start date":
   [MedicationStatement] MS
-    where exists(MS.reasonCode C where C ~ CustomConcepts."tb treatment")
+    where exists(MS.reasonCode C where C ~ ConceptsCustom."tb treatment")
     return (start of MS.effective.toInterval())
 /* End of TB treatment start date */
 
@@ -12512,13 +12493,13 @@ define "Other E.DE70":
 @activity: HIV.E1 Capture or update mother's history
 @description: The date and time of the client's ANC contact (in the ANC DAK this is called 'Contact date')
 */
-// TODO: Replace placeholder with relevant CQL logic
+
+define "Antenatal care contact":
+  ["Encounter": type in ConceptsCustom."Antenatal care contact"]
+
 define "ANC contact date E.DE85":
-  [Observation: Concepts."ANC contact date - HIV.E.DE85"] O
-    where O.status in { 'final', 'amended', 'corrected' }
-define "ANC contact date E.DE85 Value":
-  "ANC contact date E.DE85" O
-  return O.value
+  "Antenatal care contact" E
+  return E.period.toInterval()
 /* End of ANC contact date E.DE85 */
 
 /*
@@ -14405,12 +14386,9 @@ define "At elevated risk for HIV acquisition PRV.DE1":
 @activity: HIV.B6 Capture or update client history
 @description: HIV prevention intervention that client accessed
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "HIV prevention intervention":
-  exists "HIV prevention intervention Observation"
-define "HIV prevention intervention Observation":
-  [Observation: Concepts."HIV prevention intervention"] O
-    where O.status in { 'final', 'amended', 'corrected' }
+  exists ("PrEP service") or exists("OAMT") or exists("NSP") or exists("STI services") or exists("VMMC") or exists("Other PRV.DE8")
 /* End of HIV prevention intervention */
 
 /*
@@ -14423,6 +14401,11 @@ define "PrEP service":
   [MedicationStatement] MS
     where exists(MS.reasonCode C where C ~ Concepts."PrEP for HIV prevention")
     sort by start of effective.toInterval()
+
+ define "PrEP service date":
+  [MedicationStatement] MS
+    where exists(MS.reasonCode C where C ~ Concepts."PrEP for HIV prevention")
+    return start of MS.effective.toInterval()   
 /* End of PrEP service */
 
 /*
@@ -14446,8 +14429,19 @@ define "OAMT statusHistory":
       EOC.statusHistory H
       where H.period is not null))
 
+define "OAMT status date":
+  [EpisodeOfCare] EOC
+    where exists(EOC.type T where T ~ Concepts."OAMT")
+    return start of EOC.period
 
-
+define "OAMT statusHistory date":
+    [EpisodeOfCare] EOC
+    where exists(EOC.type T where T ~ Concepts."OAMT") 
+    and (exists (
+      EOC.statusHistory H
+      where H.period is not null))
+    //return start of "OAMT statusHistory".statusHistory.period
+    //need to ask brynn
 
 /* End of OAMT */
 
@@ -14463,6 +14457,14 @@ define "NSP":
       such that DUS.reasonReference.references(D) 
         and D.status in { 'active' }
   where DUS.status = 'completed'
+
+  define "NSP date":
+  [DeviceUseStatement] DUS
+  with [Device: ConceptsCustom."needle-syringe"] D
+      such that DUS.reasonReference.references(D) 
+        and D.status in { 'active' }
+  where DUS.status = 'completed'
+  return start of DUS.timing.toInterval()
 /* End of NSP */
 
 /*
@@ -14475,6 +14477,12 @@ define "STI services":
   [Procedure] P
   where P.status = 'completed'
   and P.code ~ Concepts."STI testing and treatment services"
+
+define "STI services date":
+  [Procedure] P
+  where P.status = 'completed'
+  and P.code ~ Concepts."STI testing and treatment services"
+  return start of P.performed.toInterval()
 /* End of STI services */
 
 /*
@@ -14492,6 +14500,12 @@ define "VMMC":
   [Procedure] P
   where P.status = 'completed'
   and P.code ~ Concepts."Voluntary medical male circumcision VMMC"
+
+define "VMMC date":
+  [Procedure] P
+  where P.status = 'completed'
+  and P.code ~ Concepts."Voluntary medical male circumcision VMMC"
+  return start of P.performed.toInterval()
 /* End of VMMC */
 
 /*
@@ -14506,6 +14520,13 @@ define "Other PRV.DE8":
     and O.code ~ Concepts."HIV prevention intervention"
     and O.value ~ Concepts."Other - HIV.PRV.DE8"
     sort by start of effective.toInterval()
+
+define "Other PRV.DE8 date":
+  [Observation] O
+    where O.status in {'final', 'amended'}
+    and O.code ~ Concepts."HIV prevention intervention"
+    and O.value ~ Concepts."Other - HIV.PRV.DE8"
+  return start of O.effective.toInterval()
 
 /* End of Other PRV.DE8 */
 
@@ -14514,13 +14535,11 @@ define "Other PRV.DE8":
 @activity: HIV.B6 Capture or update client history
 @description: Date the client accessed HIV prevention intervention
 */
-// TODO: Replace placeholder with relevant CQL logic
-define "Date accessed HIV prevention intervention":
-  [Observation: Concepts."Date accessed HIV prevention intervention"] O
-    where O.status in { 'final', 'amended', 'corrected' }
-define "Date accessed HIV prevention intervention Value":
-  "Date accessed HIV prevention intervention" O
-  return O.value
+
+define "Date accessed HIV prevention intervention": 
+  flatten{"PrEP service date", "NSP date", "STI services date", "VMMC date", "Other PRV.DE8 date","OAMT status date"}
+
+  //, "OAMT","NSP".timing,"STI services".performed,"VMMC".performed,"Other PRV.DE8".effective}
 /* End of Date accessed HIV prevention intervention */
 
 /*
@@ -14825,13 +14844,9 @@ define "Viral load test result SRV.DE13 Value":
 @activity: HIV.A2 Gather client details
 @description: The date and time of the client's visit
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "Visit date SRV.DE15":
-  [Observation: Concepts."Visit date - HIV.SRV.DE15"] O
-    where O.status in { 'final', 'amended', 'corrected' }
-define "Visit date SRV.DE15 Value":
-  "Visit date SRV.DE15" O
-  return O.value
+  [Encounter] E
 /* End of Visit date SRV.DE15 */
 
 /*
@@ -15023,5 +15038,3 @@ define "Reporting date Value":
  * Custom elements and logic for use DT and IND CQL Libraries
  */
 
-define "First On ART":
-  (First("On ART D.DE38"))

input/cql/HIVIND46Logic.cql

@@ -112,7 +112,7 @@ define "Initial Population":
 
 
 define "Numerator":
-  HIE."HIV-positive B.DE116"
+  HIE."Has HIV-positive Status"
   and 
   //I related the two because otherwise a positive observation could come from another test type and be counted. 
   exists(
@@ -130,7 +130,7 @@ define "Numerator":
  */
 
 define "Denominator":
-  HIE."HIV-positive B.DE116"
+  HIE."Has HIV-positive Status"
   and 
   exists(
     HE."TB diagnostic test category" P
@@ -147,21 +147,21 @@ define "Denominator":
  */
 
 define "Administrative Gender Stratifier":
-	HIC."By Administrative Gender Stratifier"
+	HIE."By Administrative Gender Stratifier"
 
 define "Age Stratifier":
-	HIC."By Age Stratifier"
+	HIE."By Age Stratifier"
 
 define "Geographic Region Stratifier":
-	HIC."By Geographic Region Stratifier"
+	HIE."By Geographic Region Stratifier"
 
 define "patientGroups Stratifier":
-	HIC."patientGroups"
+	HIE."patientGroups"
 
 define "Stratification":
- HIC."By Administrative Gender Stratifier".code 
-  + ':' + HIC."By Age Stratifier"
-+ ':' + HIC."By Geographic Region Stratifier"
-+ Combine(HIC.patientGroups, ':')
+ HIE."By Administrative Gender Stratifier".code 
+  + ':' + HIE."By Age Stratifier"
++ ':' + HIE."By Geographic Region Stratifier"
++ Combine(HIE.patientGroups, ':')
 
 //add Pregnant or breastfeeding women 

input/cql/HIVIND47Logic.cql

@@ -103,7 +103,7 @@ define "Initial Population":
  */
 
 define "Numerator":
-  HIE."HIV-positive B.DE116"
+  HIE."Has HIV-positive Status"
   and (start of HE."First On ART".effective.toInterval() during "Measurement Period")
   and HIE."Date of TB diagnosis"
 
@@ -116,7 +116,7 @@ define "Numerator":
  */
 
 define "Denominator":
-  HIE."HIV-positive B.DE116"
+  HIE."Has HIV-positive Status"
   and (start of HE."First On ART".effective.toInterval() during "Measurement Period")
 
 
@@ -127,21 +127,21 @@ define "Denominator":
  */
 
 define "Administrative Gender Stratifier":
-	HIC."By Administrative Gender Stratifier"
+	HIE."By Administrative Gender Stratifier"
 
 define "Age Stratifier":
-	HIC."By Age Stratifier"
+	HIE."By Age Stratifier"
 
 define "Geographic Region Stratifier":
-	HIC."By Geographic Region Stratifier"
+	HIE."By Geographic Region Stratifier"
 
 define "patientGroups Stratifier":
-	HIC."patientGroups"
+	HIE."patientGroups"
 
-//define "Stratification":
-// HIC."By Administrative Gender Stratifier".code 
-//  + ':' + HIC."By Age Stratifier"
-//+ ':' + HIC."By Geographic Region Stratifier"
-//+ Combine(HIC.patientGroups, ':')
+define "Stratification":
+ HIE."By Administrative Gender Stratifier".code 
+  + ':' + HIE."By Age Stratifier"
++ ':' + HIE."By Geographic Region Stratifier"
++ Combine(HIE.patientGroups, ':')
 
 //add Pregnant or breastfeeding women