Estimating the Undiagnosed Fraction: Jeanette Birnbaum 10/7/2014SPRC PHC1 presenting on behalf of...
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Transcript of Estimating the Undiagnosed Fraction: Jeanette Birnbaum 10/7/2014SPRC PHC1 presenting on behalf of...
SPRC PHC 1
Estimating the Undiagnosed Fraction:
Jeanette Birnbaum
10/7/2014
presenting on behalf ofMartina Morris, Ian Fellows and Matt Golden
Disseminating the “Testing History” Method
SPRC PHC 2
Overview
10/7/2014
• Summary and assumptions• KC & WA state analyses
The Method
• Prototype “Rshiny” web app
Dissemination
• Refining the method• Working with stakeholders
Your Feedback
SPRC PHC 4
Approach: Backcalculation
• New diagnoses today…• …are based on infections that occurred in the
past
10/7/2014
Time
10 diagnoses observed
2010 2011 2012 2013 2014
1 infection
1 infection
2 infections
3 infections
3 infections
SPRC PHC 5
Time
10 diagnoses observed
2010 2011 2012 2013 2014
1 infection
1 infection
2 infections
3 infections
3 infections
Time from Infection to Diagnosis (TID)
10/7/2014
TID = 4 yearsTID = 0 years
SPRC PHC 6
Backcalculation’s 3 Components
10/7/2014
Sum of ( *
)
Cases diagnosed at T
Incidence at X yrs ago
TID probability for X yrs ago
=OBSERVED
NEED AN ESTIMATE
BACKCALCULATE
SPRC PHC 7
TID from Testing History
“Have you ever had a
last negative test?”
Yes Use date provided
No Assign age 16 or age-18 years
Missing 2 data inclusion options
10/7/2014
Infection window = [Date of last negative test -> Date of diagnosis]
1) Get date of last negative test
2) Determine time of infection within the infection window
SPRC PHC 8
Impact of TID Assumptions on TID
10/7/2014
UNIFORM
# infections
Last neg test Diagnosis
AT LAST NEG TEST
# infections
Last neg test Diagnosis
OBSERVED ONLY
Density of last negative tests
18 years0 years
18 years
% undiagnosed“BASE CASE”
18 years
% undiagnosed“WORST CASE (OBS)”
SPRC PHC 910/7/2014
INCLUDING MISSINGDensity of last negative tests
18 years0 years
AT LAST NEG TEST
# infections
Last neg test Diagnosis 18 years
% undiagnosed
“WORST CASE (MISS)”
UNIFORM# infections
Last neg test Diagnosis
AT LAST NEG TEST# infections
Last neg test Diagnosis
OBSERVED ONLY
18 years
% undiagnosed
18 years
% undiagnosed
“BASE CASE”
“WORST CASE (OBS)”
Density of last negative tests
18 years0 years
Morris/Fellows/Golden SPRC PHC 11
KC MSM: Incidence ~ Constant
11/4/2013
15% missing testing history
SPRC PHC 17
Web Portal
• Goals:– Provide self-guided access to model for local use– Minimal learning curve– Minimal pre-processing of data– Outputs presented in most policy-relevant form
• Mechanism– “Rshiny” interface
10/7/2014
SPRC PHC 18
Protoype Rshiny App
https://hivbackcalc.shinyapps.io/HIVBackCalc_App/
10/7/2014
SPRC PHC 20
Issues
• Data privacy requirements– Local, protected upload, unprotected upload
• Detail in outputs– Race, mode, sex subgroup results?– Impact of missing data (suggestions for better
assumptions?)• Training for users
10/7/2014