serocalculator, an R package for estimating seroincidence from cross-sectional serological data
Listed in
This article is not in any list yet, why not save it to one of your lists.Abstract
Motivation
Seroincidence—the rate of new infections in a population—is a key measure for understanding pathogen transmission dynamics and informing public health action. Estimating seroincidence from cross-sectional data is complicated by antibody waning, cross-reactivity, and individual heterogeneity in antibody responses.
Implementation
serocalculator is an open-source R package that uses a likelihood-based framework incorporating antibody decay models, biological variability, and measurement error to estimate seroincidence rates from cross-sectional serological data.
General features
The package supports overall and stratified seroincidence estimation using single or multiple biomarkers. It requires three inputs: (1) a pre-estimated seroresponse model characterizing post-infection antibody waning; (2) noise parameters capturing biological and assay-related variability; and (3) quantitative antibody responses from a cross-sectional survey. It is computationally efficient, well-documented, and includes a point-and-click R Shiny interface. These features promote usability across research and public health.
Availability
The package serocalculator is freely available on CRAN , with development versions on GitHub .
