Estimation of incubation times
The EpiLPS package has been extended to deal with estimation of incubation times. A small vignette illustrates how to use the new routines. Read our preprint on MedRxiv for further details.
March 2024EpiLPS (an acronym for Epidemiological modeling with Laplacian-P-Splines) is a tool for fast and flexible Bayesian estimation of epidemiological parameters. It can be used (among others) to estimate the epidemic curve, the instantaneous reproduction number \(R_t\) and the incubation period of an infectious disease. Recent developments also permit nowcasting.
The core methodology behind the R package can be found in [1] Gressani et al. 2022. The aim of this website is to give a short overview of the functionalities of EpiLPS.
The in-development version of the package is available on this GitHub repository. The stable version is available on CRAN .
Version 1.3.0 of EpiLPS available on CRAN.
March 2024A new routine for nowcasting has been added to EpiLPS. Discover what you can do with it here.
March 2024[1] Gressani O, Wallinga J, Althaus CL, Hens N, Faes C (2022) EpiLPS: A fast and flexible Bayesian tool for estimation of the time-varying reproduction number. PLoS Comput Biol 18(10): e1010618. 10.1371/journal.pcbi.1010618
[2] Gressani, O., Torneri, A., Hens, N. and Faes, C. (2023). Flexible Bayesian estimation of incubation times. MedRxiv preprint. 10.1101/2023.08.07.23293752
[3] Sumalinab, B., Gressani, O., Hens, N. and Faes, C. (2023). Bayesian nowcasting with Laplacian-P-splines. MedRxiv preprint. 10.1101/2022.08.26.22279249v2
[4] Sumalinab, B., Gressani, O., Hens, N. and Faes, C. (2023). An efficient approach to nowcasting the time-varying reproduction number. MedRxiv preprint. 10.1101/2023.10.30.23297251