WIP Sentinel Events model

Scripts/REPORTING/HIVCaseSurveillance/load_cs_sentinel_events

@@ -0,0 +1,185 @@
+IF OBJECT_ID(N'[HIVCaseSurveillance].[dbo].[CsSentinelEvents]', N'U') IS NOT NULL 
+    DROP TABLE [HIVCaseSurveillance].[dbo].[CsSentinelEvents];
+begin
+ with  MFL_partner_agency_combination as (
+    select 
+        distinct MFL_Code,
+         SDP,
+        SDP_Agency as Agency 
+    from ODS.dbo.All_EMRSites 
+ ),
+ confirmed_reported_cases_and_art as (
+        select 
+                ctpatients.PatientKey,
+                ctpatients.Gender,
+                art.AgeLastVisit,
+                art.Agegroupkey,
+                ctpatients.sitecode,
+                case when  confirmed_date.Date is not null Then 1 Else 0 End as NewCaseReported,
+                Case when art_date.Date is not null then 1 Else 0 End as LinkedToART,
+                case when art_date.Date is null Then 1 Else 0 End as NotLinkedOnART,
+                  confirmed_date.Date as DateConfirmedPositive,
+                eomonth(confirmed_date.Date) as CohortYearMonth,
+                case 
+                    when art_date.Date < confirmed_date.Date then confirmed_date.Date
+                    else art_date.Date
+                end as StartARTDate,
+                DATEDIFF(year,ctpatients.DOB,confirmed_date.Date) as AgeatDiagnosis             
+        from NDWH.dbo.DimPatient as ctpatients
+            left join  NDWH.dbo.FACTART as art on ctpatients.patientkey=art.PatientKey
+            left join NDWH.dbo.DimDate as confirmed_date on confirmed_date.DateKey = ctpatients.DateConfirmedHIVPositiveKey
+            left join NDWH.dbo.DimDate as art_date on art_date.DateKey = art.StartARTDateKey
+            left join NDWH.dbo.DimAgeGroup as age on age.AgeGroupKey=art.AgeGroupKey
+
+            where DateConfirmedHIVPositiveKey is not null
+
+ ) ,
+
+ BaselineCD4s As (
+    SELECT
+    PatientKey,
+    BaselineCD4,
+    BaselineCD4Date
+    from NDWH.dbo.FactCD4
+    where BaselineCD4 is not null
+ ),
+ OtherCD4s As (
+   Select 
+   Patientkey,
+   OtherCD4s,
+   OtherCD4sDate,
+   OtherCD4Percent,
+   OtherCD4PercentDate
+  from NDWH.dbo.FactCD4
+
+ ),
+ BaselineWHO As (
+    Select 
+     Patientkey,
+    WHOStageATART,
+    AgeAtARTStart
+    from  NDWH.dbo.FactARTBaselines
+ ),
+ Viralloads As (
+  SELECT 
+    ROW_NUMBER() OVER (PARTITION BY viralloads.patientkey ORDER BY  OrderedbyDate.[Date] ASC) AS [Rank],
+    viralloads.Patientkey,
+    SiteCode,
+    OrderedbyDate.[Date] As OrderedbyDate ,
+    ReportedbyDate.Date As ReportedbyDate ,
+    viralloads.TestName,
+    viralloads.TestResult,
+    fac.FacilityKey
+FROM 
+    NDWH.dbo.FactOrderedViralLoads as viralloads
+    LEFT join NDWH.dbo.DimFacility fac on fac.FacilityKey = viralloads.FacilityKey
+    LEFT JOIN NDWH.dbo.DimAgency agency on agency.AgencyKey = viralloads.AgencyKey
+    LEFT JOIN NDWH.dbo.DimPatient pat on pat.PatientKey = viralloads.PatientKey
+    LEFT JOIN NDWH.dbo.DimPartner partner on partner.PartnerKey = viralloads.PartnerKey
+
+    left join NDWH.dbo.DimDate as  ReportedbyDate on ReportedbyDate.DateKey = viralloads.ReportedbyDateKey
+    LEFT JOIN NDWH.dbo.DimDate as Orderedbydate on Orderedbydate.DateKey = viralloads.OrderedbyDateKey
+ ),
+ InitialViralLoads As (
+    SELECT
+    Viralloads.patientkey,
+    Viralloads.Facilitykey,
+    Viralloads.Testresult,
+  CASE 
+    WHEN (Isnumeric(Testresult) = 1 AND Cast(Replace(Testresult, ',', '') AS Float) < 200.00)
+         OR Testresult IN ('undetectable', 'NOT DETECTED', '0 copies/ml', 'LDL', 'Less than Low Detectable Level') 
+    THEN 1 Else 0
+    End As IsSuppressedInitialViralload
+
+    from Viralloads
+    where Rank=1
+ ),
+ FirstFollowupViralloads As (
+    SELECT
+    Patientkey,
+    Facilitykey,
+    Testresult,
+      CASE 
+    WHEN (Isnumeric(Testresult) = 1 AND Cast(Replace(Testresult, ',', '') AS Float) < 200.00)
+         OR Testresult IN ('undetectable', 'NOT DETECTED', '0 copies/ml', 'LDL', 'Less than Low Detectable Level') 
+    THEN 1 Else 0 End As IsSuppressedFirstFollowupViralloads
+    from Viralloads
+    where Rank=2
+ ),
+  SecondFollowupViralloads As (
+    SELECT
+    Patientkey,
+    Facilitykey,
+    Testresult,
+      CASE 
+    WHEN (Isnumeric(Testresult) = 1 AND Cast(Replace(Testresult, ',', '') AS Float) < 200.00)
+         OR Testresult IN ('undetectable', 'NOT DETECTED', '0 copies/ml', 'LDL', 'Less than Low Detectable Level') 
+    THEN 1 Else 0 End As IsSuppressedSecondFollowupViralloads
+    from Viralloads
+    where Rank=3
+ ),
+ThirdFollowupViralloads As (
+    SELECT
+    Patientkey,
+    Facilitykey,
+    Testresult,
+     CASE 
+    WHEN (Isnumeric(Testresult) = 1 AND Cast(Replace(Testresult, ',', '') AS Float) < 200.00)
+         OR Testresult IN ('undetectable', 'NOT DETECTED', '0 copies/ml', 'LDL', 'Less than Low Detectable Level') 
+    THEN 1 Else 0 End As IsSuppressedThirdFollowupViralloads
+    from Viralloads
+    where Rank=4
+)
+ select 
+    confirmed_reported_cases_and_art.PatientKey,
+    Gender,
+    AgeLastVisit,
+    SiteCode,
+    SDP as PartnerName,
+    AgencyName,
+    NewCaseReported,
+    LinkedToART,
+    NotLinkedOnART,
+    DateConfirmedPositive,
+    CohortYearMonth,
+    StartARTDate,
+    AgeatDiagnosis,
+    case when BaselineCD4 is not null Then 1 Else 0 End as WithBaselineCD4,
+    case when BaselineCD4 is  null Then 1 Else 0 End as WithoutBaselineCD4,
+    case when  BaselineCD4 is not null and Try_CONVERT(FLOAT, BaselineCD4) < 200 Then 1 Else 0 End as CD4Lessthan200,
+    case when  BaselineCD4 is not null and Try_CONVERT(FLOAT, BaselineCD4) >= 200 Then 1 Else 0 End as CD4Morethan200,
+CASE 
+    WHEN 
+       (ISNUMERIC(OtherCD4s) = 1 AND TRY_CONVERT(float, OtherCD4s) IS NOT NULL AND TRY_CONVERT(float, OtherCD4s) < 200)
+        OR 
+        (AgeatDiagnosis <= 5 AND ISNUMERIC(OtherCD4Percent) = 1 AND TRY_CONVERT(float, OtherCD4Percent) IS NOT NULL AND TRY_CONVERT(float, OtherCD4Percent) < 25)
+    THEN 1 
+    ELSE 0 
+  END AS TreatmentFailure,
+    WHOStageATART,
+    AgeAtARTStart,
+   age.DATIMAgeGroup as ARTStartAgeGroup,
+   case when InitialViralLoads.patientkey is not null then 1 Else 0 End as WithInitialViralLoad,
+   coalesce(InitialViralLoads.IsSuppressedInitialViralload,0) As IsSuppressedInitialViralload,
+   case when FirstFollowupViralloads.patientkey is not null then 1 Else 0 End As WithFirstFollowupViralload,
+   coalesce (FirstFollowupViralloads.IsSuppressedFirstFollowupViralloads,0) as IsSuppressedFirstFollowupViralloads,
+   case when SecondFollowupViralloads.patientkey is not null then 1 Else 0 End As WithSecondFollowupViralloads,
+   coalesce (SecondFollowupViralloads.IsSuppressedSecondFollowupViralloads,0) As IssuppressedSecondFollowupViralloads,
+   case when ThirdFollowupViralloads.patientkey is not null then 1 Else 0 End As WithThirdFollowupViralloads,
+   coalesce(ThirdFollowupViralloads.IsSuppressedThirdFollowupViralloads,0) As IsSuppressedThirdFollowupViralloads
+ into [HIVCaseSurveillance].[dbo].[CsSentinelEvents]
+ from confirmed_reported_cases_and_art
+ left join BaselineCD4s on BaselineCD4s.PatientKey=confirmed_reported_cases_and_art.PatientKey
+ left join BaselineWHO on BaselineWHO.patientkey=confirmed_reported_cases_and_art.PatientKey
+ left join NDWH.dbo.DimAgeGroup age on age.AgeGroupKey = confirmed_reported_cases_and_art.AgeGroupKey
+ left join NDWH.dbo.DimFacility as facility on facility.MFLCode = confirmed_reported_cases_and_art.SiteCode
+ left join MFL_partner_agency_combination on MFL_partner_agency_combination.MFL_Code = confirmed_reported_cases_and_art.SiteCode
+ left join NDWH.dbo.DimPartner as partner on partner.PartnerName = MFL_partner_agency_combination.SDP
+ left join NDWH.dbo.DimAgency as agency on agency.AgencyName = MFL_partner_agency_combination.Agency
+ left join OtherCD4s on OtherCD4s.Patientkey=confirmed_reported_cases_and_art.Patientkey
+ left join InitialViralLoads on InitialViralLoads.patientkey=confirmed_reported_cases_and_art.PatientKey
+ left join FirstFollowupViralloads on FirstFollowupViralloads.patientkey=confirmed_reported_cases_and_art.PatientKey
+ left join SecondFollowupViralloads on SecondFollowupViralloads.patientkey=confirmed_reported_cases_and_art.PatientKey
+ left join ThirdFollowupViralloads on ThirdFollowupViralloads.patientkey=confirmed_reported_cases_and_art.PatientKey
+ end
+