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: | 1.0.0 |
| 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: | 2024-10-07 |
| 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 [issues need fixing before 2024-10-25] |
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_1.0.0.tar.gz |
| Windows binaries: | r-devel: serosv_1.0.0.zip, r-release: serosv_1.0.0.zip, r-oldrel: serosv_1.0.0.zip |
| macOS binaries: | r-release (arm64): serosv_1.0.0.tgz, r-oldrel (arm64): serosv_1.0.0.tgz, r-release (x86_64): serosv_1.0.0.tgz, r-oldrel (x86_64): serosv_1.0.0.tgz |
Linking:
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