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serofoi: Bayesian Estimation of the Force of Infection from Serological Data

Estimating the force of infection from time varying, age varying, or constant serocatalytic models from population based seroprevalence studies using a Bayesian framework, including data simulation functions enabling the generation of serological surveys based on this models. This tool also provides a flexible prior specification syntax for the force of infection and the seroreversion rate, as well as methods to assess model convergence and comparison criteria along with useful visualisation functions.

Version: 1.0.3
Depends: R (≥ 4.1.0)
Imports: bayesplot, checkmate, config, cowplot, dplyr, ggplot2, glue, graphics, loo, expm, methods, purrr, Rcpp (≥ 0.12.0), rstan (≥ 2.18.1), rstantools (≥ 2.3.1), stats, tibble, tidyr
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: knitr, rlang, rmarkdown, scales, spelling, testthat (≥ 3.0.0)
Published: 2025-03-31
DOI: 10.32614/CRAN.package.serofoi
Author: Zulma M. Cucunubá ORCID iD [aut, cre], Nicolás T. Domínguez ORCID iD [aut], Ben Lambert [aut], Pierre Nouvellet [aut], Geraldine Gómez ORCID iD [ctb], Jaime A. Pavlich-Mariscal ORCID iD [ctb], Hugo Gruson ORCID iD [ctb], David Santiago Quevedo ORCID iD [ctb], Miguel Gámez [ctb], Sumali Bajaj [ctb], Everlyn Kamau [ctb], Richard Creswell [ctb], International Development Research Center (IDRC) [fnd], Pontificia Universidad Javeriana [cph]
Maintainer: Zulma M. Cucunubá <zulma.cucunuba at javeriana.edu.co>
BugReports: https://github.com/epiverse-trace/serofoi/issues
License: MIT + file LICENSE
URL: https://github.com/epiverse-trace/serofoi, https://epiverse-trace.github.io/serofoi/
NeedsCompilation: yes
SystemRequirements: GNU make
Language: en-GB
Materials: README NEWS
CRAN checks: serofoi results

Documentation:

Reference manual: serofoi.pdf
Vignettes: An introduction to serofoi (source, R code)

Downloads:

Package source: serofoi_1.0.3.tar.gz
Windows binaries: r-devel: serofoi_1.0.3.zip, r-release: serofoi_1.0.3.zip, r-oldrel: serofoi_1.0.3.zip
macOS binaries: r-devel (arm64): serofoi_1.0.3.tgz, r-release (arm64): serofoi_1.0.3.tgz, r-oldrel (arm64): serofoi_1.0.3.tgz, r-devel (x86_64): serofoi_1.0.3.tgz, r-release (x86_64): serofoi_1.0.3.tgz, r-oldrel (x86_64): serofoi_1.0.3.tgz

Linking:

Please use the canonical form https://CRAN.R-project.org/package=serofoi to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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