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 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 , 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.