serocalculator, an R package for estimating seroincidence from cross-sectional serological data

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.

serocalculator is an open-source R package that uses a likelihood-based framework incorporating antibody decay models, biological variability, and measurement noise to estimate seroincidence rates from cross-sectional serological data.

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.

The package serocalculator is freely available on CRAN, with development versions on GitHub.