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. (2022) <doi:10.1371/journal.pcbi.1010618>. The negative binomial distribution is used to model the time series of incidence data. 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-adjusted Langevin algorithm for efficient sampling of the posterior distribution.
| Version: | 1.1.0 |
| Depends: | R (≥ 4.1.0) |
| Imports: | Rcpp (≥ 1.0.7), coda (≥ 0.19-4), EpiEstim (≥ 2.2-4), ggplot2 (≥ 3.3.5), gridExtra (≥ 2.3) |
| LinkingTo: | RcppArmadillo, Rcpp |
| Suggests: | rmarkdown, knitr |
| Published: | 2023-04-05 |
| Author: | Oswaldo Gressani 
[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_1.1.0.tar.gz |
| Windows binaries: | r-devel: EpiLPS_1.1.0.zip, r-release: EpiLPS_1.1.0.zip, r-oldrel: EpiLPS_1.1.0.zip |
| macOS binaries: | r-release (arm64): EpiLPS_1.1.0.tgz, r-oldrel (arm64): EpiLPS_1.1.0.tgz, r-release (x86_64): EpiLPS_1.1.0.tgz, r-oldrel (x86_64): EpiLPS_1.1.0.tgz |
| Old sources: | EpiLPS archive |
Linking:
Please use the canonical form https://CRAN.R-project.org/package=EpiLPS to link to this page.