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

Document Type

Article

Department

Paediatrics and Child Health

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 noise 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.

Comments

Volume, issue and pagination are not provided by the author/publisher.

Publication (Name of Journal)

medRxiv

DOI

10.1101/2025.06.04.25328941

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