EpiLPS: a fast and flexible Bayesian tool for estimating epidemiological parameters

Oswaldo Gressani (oswaldo.gressani@uhasselt.be)

EpiLPS (Gressani et al. 2022) is an Epidemiological modeling tool using Laplacian-P-Splines. It can be used to estimate (key) epidemiological parameters such as the time-varying reproduction number (the average number of secondary cases generated by an infected individual) or the incubation period of an infectious disease. It can also be used for nowcasting. The website associated to the project https://epilps.com/ provides a detailed documentation (or vignette) on how to use the underlying routines.

Citation

Associated literature:

1. Gressani, O., Wallinga, J., Althaus, C. L., Hens, N. and Faes, C. (2022). EpiLPS: A fast and flexible Bayesian tool for estimation of the time-varying reproduction number. PLoS Comput Biol 18(10): e1010618. https://doi.org/10.1371/journal.pcbi.1010618.

2. Gressani, O., Torneri, A., Hens, N. and Faes, C. (2023). Flexible Bayesian estimation of incubation times. MedRxiv preprint. https://www.medrxiv.org/content/10.1101/2023.08.07.23293752v1.

3. Sumalinab, B., Gressani, O., Hens, N. and Faes, C. (2023). Bayesian nowcasting with Laplacian-P-splines. MedRxiv preprint. https://www.medrxiv.org/content/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. https://doi.org/10.1101/2023.10.30.23297251

To cite the EpiLPS package in publications starting from version 1.2.0 use:

Gressani, O. (2021). EpiLPS: A Fast and Flexible Bayesian Tool for 
Estimating Epidemiological Parameters. [Computer Software]. https://epilps.com/

For versions before 1.2.0 use:

Gressani, O. (2021). EpiLPS: A Fast and Flexible Bayesian Tool for 
Estimation of the Time-varying Reproduction Number. [Computer Software]. https://epilps.com/

Package version

This is version 1.3.0 (2024-03-07) - “Extension to nowcasting”.

Acknowledgments

This project is funded by the European Union’s Research and Innovation Action under the H2020 work programme, EpiPose (grant number 101003688). It is also supported by the ESCAPE project (101095619) and the VERDI project (101045989), funded by the European Union.

License

EpiLPS: a fast and flexible Bayesian tool for estimating epidemiological parameters. Copyright (C) 2021-2024 Oswaldo Gressani.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.