{"doi":"10.1101/2025.06.04.25328941","title":"serocalculator, an R package for estimating seroincidence from cross-sectional serological data","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: 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: is freely available on CRAN, with development versions on GitHub.","journal":"medRxiv","year":2025,"id":558170,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9466,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1459068,"name":"Chris Orwa","orcid":null,"position":1,"is_corresponding":false},{"id":257483,"name":"Jessica C. Seidman","orcid":"0009-0005-1645-3789","position":2,"is_corresponding":false},{"id":860461,"name":"Denise O Garrett","orcid":"0000-0001-6411-3459","position":3,"is_corresponding":false},{"id":227070,"name":"Samir K. Saha","orcid":"0000-0003-3820-0748","position":4,"is_corresponding":false},{"id":509836,"name":"Dipesh Tamrakar","orcid":"0000-0002-0772-3653","position":5,"is_corresponding":false},{"id":752134,"name":"Farah Naz Qamar","orcid":"0000-0003-4173-680X","position":6,"is_corresponding":false},{"id":108258,"name":"Richelle C. Charles","orcid":"0000-0002-8881-1849","position":7,"is_corresponding":false},{"id":231886,"name":"Jason R. Andrews","orcid":"0000-0002-5967-251X","position":8,"is_corresponding":false},{"id":860460,"name":"Peter Teunis","orcid":"0000-0003-1904-6044","position":9,"is_corresponding":false},{"id":392039,"name":"Kristen Aiemjoy","orcid":"0000-0003-1886-2699","position":10,"is_corresponding":false},{"id":372090,"name":"Douglas E. Morrison","orcid":"0000-0002-7195-830X","position":11,"is_corresponding":false},{"id":409695,"name":"Kristina Lai","orcid":"0000-0002-5761-7437","position":0,"is_corresponding":true}],"reference_count":30,"raw_metadata":null,"created_at":"2026-07-19T02:55:25.969263Z","pmid":"40502584","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}