EpiLPS: A Bayesian Tool for Fast and Flexible Estimation of the Reproduction Number

Estimation of the instantaneous reproduction number with Laplacian-P-splines following the methodology of Gressani et al.(2021) <doi:10.1101/2021.12.02.21267189>. The negative Binomial distribution is used to model the time series of case counts. Two methods are available for inference : (1) a sampling-free approach based on a maximum a posteriori calibration of the hyperparameter vector and (2) a fully stochastic approach with a Metropolis-within-Gibbs algorithm and Langevin diffusions for efficient sampling of the posterior distribution.

Version: 1.0.6
Depends: R (≥ 4.1.0)
Imports: Rcpp (≥ 1.0.7), coda (≥ 0.19-4), progress (≥ 1.2.2), crayon (≥ 1.4.1), MASS (≥ 7.3-54), EpiEstim (≥ 2.2-4), ggplot2 (≥ 3.3.5), grDevices (≥ 4.1.0), gridExtra (≥ 2.3)
LinkingTo: RcppArmadillo, Rcpp
Suggests: rmarkdown, knitr
Published: 2022-08-08
Author: Oswaldo Gressani ORCID iD [aut, cre]
Maintainer: Oswaldo Gressani <oswaldo_gressani at hotmail.fr>
BugReports: https://github.com/oswaldogressani/EpiLPS/issues
License: GPL-3
Copyright: see file COPYRIGHTS
URL: <https://github.com/oswaldogressani/EpiLPS>
NeedsCompilation: yes
Citation: EpiLPS citation info
Materials: README NEWS
CRAN checks: EpiLPS results

Documentation:

Reference manual: EpiLPS.pdf
Vignettes: EpiLPS-vignette

Downloads:

Package source: EpiLPS_1.0.6.tar.gz
Windows binaries: r-devel: EpiLPS_1.0.6.zip, r-release: EpiLPS_1.0.6.zip, r-oldrel: EpiLPS_1.0.6.zip
macOS binaries: r-release (arm64): EpiLPS_1.0.5.tgz, r-oldrel (arm64): EpiLPS_1.0.5.tgz, r-release (x86_64): EpiLPS_1.0.6.tgz, r-oldrel (x86_64): EpiLPS_1.0.6.tgz
Old sources: EpiLPS archive

Linking:

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