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CRAN: Package serosv

serosv: Model Infectious Disease Parameters from Serosurveys

An easy-to-use and efficient tool to estimate infectious diseases parameters using serological data. Implemented models include SIR models (basic_sir_model(), static_sir_model(), mseir_model(), sir_subpops_model()), parametric models (polynomial_model(), fp_model()), nonparametric models (lp_model()), semiparametric models (penalized_splines_model()), hierarchical models (hierarchical_bayesian_model()). The package is based on the book "Modeling Infectious Disease Parameters Based on Serological and Social Contact Data: A Modern Statistical Perspective" (Hens, Niel & Shkedy, Ziv & Aerts, Marc & Faes, Christel & Damme, Pierre & Beutels, Philippe., 2013) <doi:10.1007/978-1-4614-4072-7>.

Version: 1.1.0 Depends: R (≥ 3.4.0) Imports: deSolve, dplyr, ggplot2, locfit, purrr, stringr, magrittr, methods, mgcv, mixdist, patchwork, assertthat, Rcpp (≥ 0.12.0), RcppParallel (≥ 5.0.1), rstan (≥ 2.18.1), rstantools (≥ 2.4.0), boot, stats4 LinkingTo: BH (≥ 1.66.0), Rcpp (≥ 0.12.0), RcppEigen (≥ 0.3.3.3.0), RcppParallel (≥ 5.0.1), rstan (≥ 2.18.1), StanHeaders (≥ 2.18.0) Suggests: covr, knitr, rmarkdown, bookdown, testthat (≥ 3.0.0) Published: 2025-04-09 DOI: 10.32614/CRAN.package.serosv Author: Anh Phan Truong Quynh [aut, cre], Nguyen Pham Nguyen The [aut], Long Bui Thanh [aut], Tuyen Huynh [aut], Thinh Ong [aut], Marc Choisy [aut] Maintainer: Anh Phan Truong Quynh <anhptq at oucru.org> BugReports: https://github.com/OUCRU-Modelling/serosv/issues License: MIT + file LICENSE URL: https://oucru-modelling.github.io/serosv/, https://github.com/OUCRU-Modelling/serosv NeedsCompilation: yes SystemRequirements: GNU make Materials: README NEWS CRAN checks: serosv results Documentation: Reference manual: serosv.pdf Vignettes: Data transformation (source, R code)
Hierarchical Bayesian models (source, R code)
Imperfect serological test (source, R code)
Input data (source, R code)
Modeling directly from antibody levels (source, R code)
Model selection (source, R code)
Nonparametric model (source, R code)
Parametric models (source, R code)
Semiparametric model (source, R code)
SIR model (source, R code)
Model visualization (source, R code)
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