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WIP Sentinel Events model #510

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merged 14 commits into from
Jan 20, 2025
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Merged

WIP Sentinel Events model #510

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0e741b4
WIP Sentinel Events model
Marymary-dev Oct 2, 2024
9523443
Removing the SDP CTE
Marymary-dev Oct 11, 2024
f54a2e8
Merge branch 'dev' of https://github.com/palladiumkenya/dwh-etl into …
Marymary-dev Dec 6, 2024
1da6667
Sentinel events for Sankey diagram
Marymary-dev Dec 18, 2024
ba6d680
Adding County and SubCounty to enable County level disagregations
Marymary-dev Jan 14, 2025
ffa4cc4
Refactoring the Model to read from FactViralLoads
Marymary-dev Jan 17, 2025
3fbaddc
Optimizing the model
Marymary-dev Jan 17, 2025
732408d
Adding latestViralload suppression column
Marymary-dev Jan 18, 2025
6d0bb9a
Reinstating the columns that were earlier ommited
Marymary-dev Jan 20, 2025
a5f0a57
Merge branch 'dev' of https://github.com/palladiumkenya/dwh-etl into …
Marymary-dev Jan 20, 2025
73f718f
Removing the commented line
Marymary-dev Jan 20, 2025
d2d2a28
Sending the latest script
Marymary-dev Jan 20, 2025
c32c9c6
Replacing the correct FactViralload
Marymary-dev Jan 20, 2025
3579ff0
Adjusting the viral loads to 200 copies/l
Marymary-dev Jan 20, 2025
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272 changes: 272 additions & 0 deletions Scripts/REPORTING/HIVCaseSurveillance/load_cs_sentinel_events.sql
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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.care.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].[Dim].[DimPatient] as ctpatients
left join NDWH.Fact.FACTART as art on ctpatients.patientkey=art.PatientKey
left join [NDWH].[Dim].[DimDate] as confirmed_date on confirmed_date.DateKey = ctpatients.DateConfirmedHIVPositiveKey
left join [NDWH].[Dim].[DimDate] as art_date on art_date.DateKey = art.StartARTDateKey
left join [NDWH].[Dim].[DimAgeGroup]as age on age.AgeGroupKey=art.AgeGroupKey



where DateConfirmedHIVPositiveKey is not null

) ,

BaselineCD4s As (
SELECT
PatientKey,
BaselineCD4,
BaselineCD4Date
from [NDWH].[Fact].[FactCD4]
where BaselineCD4 is not null
),
OtherCD4s As (
Select
Patientkey,
coalesce (secondCD4,LastCD4) as OtherCD4s,
coalesce (secondCD4Date,LastCD4Date)OtherCD4sDate,
LastCD4Percentage as OtherCD4Percent,
LastCD4Date as OtherCD4PercentDate
from [NDWH].[Fact].[FactCD4]

),
BaselineWHO As (
Select
Patientkey,
WHOStageATART,
AgeAtARTStart
from NDWH.Fact.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.Fact.FactOrderedViralLoads as viralloads
LEFT join NDWH.Dim.DimFacility fac on fac.FacilityKey = viralloads.FacilityKey
LEFT JOIN NDWH.Dim.DimAgency agency on agency.AgencyKey = viralloads.AgencyKey
LEFT JOIN [NDWH].[Dim].[DimPatient] pat on pat.PatientKey = viralloads.PatientKey
LEFT JOIN NDWH.Dim.DimPartner partner on partner.PartnerKey = viralloads.PartnerKey
left join [NDWH].[Dim].[DimDate] as ReportedbyDate on ReportedbyDate.DateKey = viralloads.ReportedbyDateKey
LEFT JOIN [NDWH].[Dim].[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)
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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
),
RegimenChanges as (
Select
Patientkey,
Facilitykey,
StartRegimen,
CurrentRegimen,
case when StartRegimen = CurrentRegimen Then 0 Else 1 End as RegimenChanged
from NDWH.Fact.FACTART
where StartRegimen is not null
),
OptimizedRegimen as (
Select
Patientkey,
Facilitykey,
StartRegimen,
CurrentRegimen,
case when CurrentRegimen like '3TC+DTG+TDF' THEN 1
Else 0 END AS OptimizedRegimen
from NDWH.Fact.FACTART
),

SecondLatestHighVls as (
SELECT
PatientKey,
FacilityKey,
cast (LatestVLDate2Key as date) as LatestVLDate2Key,
LatestVL2
from NDWH.Fact.FactViralLoads as secondlatestvls
LEFT JOIN Ndwh.Dim.Dimdate AS SecondVLDate
ON SecondVLDate.Datekey = secondlatestvls.LatestVLDate2Key
where TRY_CAST(LatestVL2 as float) >=1000
AND DATEDIFF(month, LatestVLDate2Key , GETDATE()) <= 26
),
ConsecutiveHighVls as (
SELECT
latestvls.Patientkey,
latestvls.FacilityKey,
LatestVL1,
cast (LatestVLDate1Key as date ) as LatestVLDate
from NDWH.Fact.FactViralLoads as latestvls
inner join SecondLatestHighVls on SecondLatestHighVls.PatientKey=latestvls.PatientKey
LEFT JOIN Ndwh.Dim.Dimdate AS LatestVLDate
ON LatestVLDate.Datekey = latestvls.LatestVLDate1Key
where TRY_CAST(LatestVL1 as float) >=1000 and datediff(month, LatestVLDate1Key , eomonth(dateadd(mm,-1,getdate()))) <= 14

),
LatestSuppressedVL as (
Select
latestvls.Patientkey,
latestvls.FacilityKey,
LatestVL1 as LatestVLSuppressed,
cast (LatestVLDate1Key as date ) as LatestVLDate
from NDWH.Fact.FactViralLoads as latestvls
LEFT JOIN Ndwh.Dim.Dimdate AS LatestVLDate
ON latestvlDate.Datekey = latestvls.LatestVLDate1Key
where TRY_CAST(LatestVL2 as float) <1000
OR Latestvl1 IN ( 'undetectable', 'NOT DETECTED',
'0 copies/ml',
'LDL',
'Less than Low Detectable Level')
),
Retained as (
Select
Patientkey,
FacilityKey,
case when artoutcomekey= 6 then 1 Else 0 End as PatientRetained
from NDWH.Fact.FACTART
)
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))
AND whostageAtART IN (3, 4)
THEN 1
ELSE 0
END AS AHD,
case when whostageAtART is null then 1 else 0 End as NotStaged,
BaselineWHO.WHOStageATART,
BaselineWHO.AgeAtARTStart,
age.DATIMAgeGroup as ARTStartAgeGroup,
case when InitialViralLoads.patientkey is not null then 1 Else 0 End as WithInitialViralLoad,
case when InitialViralLoads.patientkey is null then 1 Else 0 End as WithoutInitialViralLoad,
coalesce(InitialViralLoads.IsSuppressedInitialViralload,0) As IsSuppressedInitialViralload,
case when IsSuppressedInitialViralload=0 Then 1 Else 0 End as IsNotSuppressedInitialViralload,
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,
coalesce (RegimenChanged,0) as RegimenChanged,
case when RegimenChanged=0 Then 1 else 0 End as RegimenNotChanged,
OptimizedRegimen,
case when LatestVL1 is not null then 1 Else 0 End as TreatmentFailure,
case when LatestVLSuppressed is not null then 1 Else 0 End as LatestVLSuppressed,
case when LatestVLSuppressed is null then 1 Else 0 End as LatestVLNotSuppressed,
coalesce (PatientRetained,0) as PatientRetained,
case when PatientRetained=0 then 1 Else 0 End as PatientNotRetained
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].[Dim].[DimAgeGroup]age on age.AgeGroupKey = confirmed_reported_cases_and_art.AgeGroupKey
left join NDWH.Dim.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.Dim.DimPartner as partner on partner.PartnerName = MFL_partner_agency_combination.SDP
left join NDWH.Dim.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
left join RegimenChanges on RegimenChanges.Patientkey=confirmed_reported_cases_and_art.PatientKey
left join OptimizedRegimen on OptimizedRegimen.Patientkey=confirmed_reported_cases_and_art.PatientKey
left join ConsecutiveHighVls on ConsecutiveHighVls.PatientKey=confirmed_reported_cases_and_art.PatientKey
left join LatestSuppressedVL on LatestSuppressedVL.PatientKey=confirmed_reported_cases_and_art.PatientKey
left join Retained on Retained.Patientkey=confirmed_reported_cases_and_art.PatientKey
end