Incidence Inference using biomarkers for 'recent infection'

The tools available for download from this page, collectively called Assay-Based Incidence Estimation (ABIE) version 3, perform a number of analyses related to the estimation of incidence from cross-sectional surveys using tests for recent infection:

A detailed release note for this toolset can be obtained here. Please read the release note for guidance, background, further reading, and licensing. This document is also included, on a separate ‘worksheet’, in each of the spreadsheets (Microsoft Office 2010 Excel .xlsx format ‘Workbook’) which make up the toolkit, as is a spreadsheet-specific user guide.

There are five separate workbooks:

    • Incidence_Prevalence_Calculator - produces a prevalence and incidence estimate from a single cross-sectional survey
    • Incidence_Difference_Calculator - systematically compares incidence estimates from two cross-sectional surveys
    • Sample_Size_Calculator - calculates a minimal sample size to provide desired precision of incidence estimate (in a hypothetical context) or  “power” to detect a difference in incidence between two hypothetical contexts
    • Power_Calculator - calculates “power” to detect a hypothetical incidence difference/trend
    • Test_Performance_Calculator - summarises “performance” of a recent infection test (into a standard error of the incidence estimate), given estimated test properties and the prevalence/incidence in a hypothetical context

When using ABIE 3 to generate published data, please cite the following article which derives the underlying formulae (the incidence estimator and its uncertainty) used: Kassanjee R, McWalter TA, Bärnighausen T, Welte A. A new general biomarker-based incidence estimator.Epidemiology. 2012; 23(5): 721-728.

When using the Test Performance Calculator, the following article should also be referenced: Kassanjee R, McWalter TA, Welte A. Defining optimality of a test for recent infection for HIV incidence surveillance. AIDS Res Hum Retroviruses. 2013

 

Note on previous versions

The first major version of ABIE tools, namely ABIE v1, provided similar functionality, based on a less general analysis published previously: McWalter TA, Welte A. Relating recent infection prevalence to incidence with a sub-population of assay non-progressors. Journal of Mathematical Biology. 2009; 60(5):687-710. The use of this version of the tools is now not recommended. Version 2 marked the transition to the generalised analysis of Kassanjee et al, and version 3 adds functionality within that framework.