Create a new linelist CsLinelistMortalityAssociatedRisks for mortalit…

[kevlanyo]

1. New line list to track HIV mortality associated risks

• Gets all HIV related deaths
• Then for each death, checks whether they had a late enrolment to treatment, interruption in treatment or failure in treatment
• These three indicators are tracked in columns hadDelayedEnrollment, hadInterruptedTreatment and hadTreatmentFailure

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Summary by Sourcery

New Features:

• Create a new line list CsLinelistMortalityAssociatedRisks to track HIV mortality associated risks.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request introduces a new line list, CsLinelistMortalityAssociatedRisks, to track HIV mortality associated risks. It identifies HIV-related deaths and then checks for late enrollment to treatment, interruption in treatment, or treatment failure for each death. These indicators are tracked in the hadDelayedEnrollment, hadInterruptedTreatment, and hadTreatmentFailure columns.

No diagrams generated as the changes look simple and do not need a visual representation.

File-Level Changes

Change	Details	Files
Create a new table CsLinelistMortalityAssociatedRisks to store data on HIV mortality associated risks.	Create the CsLinelistMortalityAssociatedRisks table if it does not exist, dropping it first if it does exist. Populate the table with data on HIV-related deaths and associated risk factors. Include facility, partner, and agency information, as well as patient demographics and cohort details. Calculate and include flags for delayed enrollment, interrupted treatment, and treatment failure.	Scripts/REPORTING/HIVCaseSurveillance/load_cs_linelist_mortality_associated_risks.sql
Implement logic to identify patients with delayed enrollment to treatment.	Join Exitdata with FactARTHistory to access ART enrollment information. Flag patients with a time to ART enrollment greater than 14 days as having delayed enrollment.	Scripts/REPORTING/HIVCaseSurveillance/load_cs_linelist_mortality_associated_risks.sql
Implement logic to identify patients with interruption in treatment (IIT).	Join Exitdata with FactARTHistory to access ART outcome information. Flag patients with an ART outcome of 'LOSS TO FOLLOW UP' or 'UNDOCUMENTED LOSS' within one year of their exit date as having interrupted treatment.	Scripts/REPORTING/HIVCaseSurveillance/load_cs_linelist_mortality_associated_risks.sql
Implement logic to identify patients with treatment failure.	Join Exitdata with FactViralLoads to access viral load data. Flag patients with two consecutive viral loads greater than 200 as having treatment failure.	Scripts/REPORTING/HIVCaseSurveillance/load_cs_linelist_mortality_associated_risks.sql

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[sourcery-ai]

Hey @kevlanyo - I've reviewed your changes - here's some feedback:

Overall Comments:

• Consider adding a comment explaining the logic behind the 14-day threshold in the DelayedEnrollment CTE.
• The date range filter in the IIT CTE might not be appropriate for all patients; consider the clinical implications of this one-year window.

Here's what I looked at during the review

• 🟢 General issues: all looks good
• 🟢 Security: all looks good
• 🟢 Testing: all looks good
• 🟢 Complexity: all looks good
• 🟢 Documentation: all looks good

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