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: 1.0.1
Depends: R (≥ 3.4.0)
Imports: deSolve, dplyr, ggplot2, locfit, magrittr, methods, mgcv, mixdist, patchwork, 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: 2024-10-18
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 ORCID iD [aut], Marc Choisy ORCID iD [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)
Modeling directly from antibody levels (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)

Downloads:

Package source: serosv_1.0.1.tar.gz
Windows binaries: r-devel: serosv_1.0.1.zip, r-release: serosv_1.0.1.zip, r-oldrel: serosv_1.0.1.zip
macOS binaries: r-release (arm64): serosv_1.0.1.tgz, r-oldrel (arm64): serosv_1.0.1.tgz, r-release (x86_64): serosv_1.0.1.tgz, r-oldrel (x86_64): serosv_1.0.1.tgz
Old sources: serosv archive

Linking:

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